@article{selwa_sampl6:_2018,
	title = {{SAMPL}6: calculation of macroscopic {pKa} values from ab initio quantum mechanical free energies},
	volume = {32},
	issn = {0920-654X, 1573-4951},
	shorttitle = {{SAMPL}6},
	url = {http://link.springer.com/article/10.1007/s10822-018-0138-6},
	doi = {10.1007/s10822-018-0138-6},
	abstract = {Macroscopic pKa values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pKa values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pKas with a maximum likelihood estimator and appropriately summed to yield macroscopic pKa values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pKas: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pKa. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pKa units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pKa values for novel compounds with reasonable accuracy.},
	language = {en},
	number = {10},
	urldate = {2018-08-16TZ},
	journal = {Journal of Computer-Aided Molecular Design},
	author = {Selwa, Edithe and Kenney, Ian M. and Beckstein, Oliver and Iorga, Bogdan I.},
	month = aug,
	year = {2018},
	pages = {1203--1216}
}

Macroscopic pKa values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pKa values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pKas with a maximum likelihood estimator and appropriately summed to yield macroscopic pKa values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pKas: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pKa. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pKa units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pKa values for novel compounds with reasonable accuracy.

@article{calabrese_topological_2017,
	title = {Topological {Dissection} of the {Membrane} {Transport} {Protein} {Mhp}1 {Derived} from {Cysteine} {Accessibility} and {Mass} {Spectrometry}},
	volume = {89},
	issn = {0003-2700},
	url = {http://dx.doi.org/10.1021/acs.analchem.7b01310},
	doi = {10.1021/acs.analchem.7b01310},
	abstract = {Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion–substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein’s conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.},
	number = {17},
	urldate = {2018-01-17TZ},
	journal = {Analytical Chemistry},
	author = {Calabrese, Antonio N. and Jackson, Scott M. and Jones, Lynsey N. and Beckstein, Oliver and Heinkel, Florian and Gsponer, Joerg and Sharples, David and Sans, Marta and Kokkinidou, Maria and Pearson, Arwen R. and Radford, Sheena E. and Ashcroft, Alison E. and Henderson, Peter J. F.},
	month = sep,
	year = {2017},
	pages = {8844--8852}
}

Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion–substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein’s conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.

@inproceedings{khoshlessan_parallel_2017,
	address = {Austin, TX},
	title = {Parallel {Analysis} in {MDAnalysis} using the {Dask} {Parallel} {Computing} {Library}},
	url = {http://conference.scipy.org/proceedings/scipy2017/mahzad_khoslessan.html},
	doi = {10.25080/shinma-7f4c6e7-00a},
	urldate = {2017-07-17TZ},
	booktitle = {Proceedings of the 16th {Python} in {Science} {Conference}},
	author = {Khoshlessan, Mahzad and Paraskevakos, Ioannis and Jha, Shantenu and Beckstein, Oliver},
	editor = {Huff, Katy and Lippa, David and Niederhut, Dillon and Pacer, M},
	year = {2017},
	pages = {64--72}
}

@article{domanski_ligandbook:_2017,
	title = {Ligandbook: an online repository for small and drug-like molecule force field parameters},
	volume = {33},
	issn = {1367-4803},
	shorttitle = {Ligandbook},
	url = {https://doi.org/10.1093/bioinformatics/btx037},
	doi = {10.1093/bioinformatics/btx037},
	number = {11},
	urldate = {2017-06-12TZ},
	journal = {Bioinformatics},
	author = {Domański, Jan and Beckstein, Oliver and Iorga, Bogdan I.},
	month = jun,
	year = {2017},
	pages = {1747--1749}
}

@article{coudray_structure_2017,
	title = {Structure of the {SLC}4 transporter {Bor}1p in an inward-facing conformation},
	volume = {26},
	doi = {10.1002/pro.3061},
	abstract = {Bor1p is a secondary transporter in yeast that is responsible for boron transport. Bor1p belongs to the SLC4 family which controls in bicarbonate exchange and pH regulation in animals as well as borate uptake in plants. The SLC4 family is more distantly related to members of the Amino acid-Polyamine-organoCation (APC) superfamily, which includes well studied transporters such as LeuT, Mhp1, AdiC, vSGLT, UraA, SLC26Dg. Their mechanism generally involve relative movements of two domains: a core domain that binds substrate and a gate domain that in many cases mediates dimerization. In order to shed light on conformational changes governing transport by the SLC4 family, we grew helical membrane crystals of Bor1p from Saccharomyces mikatae and determined a structure at {\textasciitilde}6 Å resolution using cryo-electron microscopy. In order to evaluate the conformation of Bor1p in these crystals, a homology model was built based on the related anion exchanger from red blood cells (AE1). This homology model was fitted to the cryo-EM density map using the Molecular Dynamics (MD) Flexible Fitting method and then relaxed by all-atom MD simulation in explicit solvent and membrane. Mapping of water accessibility indicates that the resulting structure represents an inward-facing conformation. Comparisons of the resulting Bor1p model with the X-ray structure of AE1 in an outward-facing conformation, together with MD simulations of inward-facing and outward-facing Bor1p models, suggest rigid body movements of the core domain relative to the gate domain. These movements are consistent with the rocking-bundle transport mechanism described for other members of the APC superfamily.},
	number = {1},
	journal = {Protein Science},
	author = {Coudray, Nicolas and Seyler, Sean L. and Lasala, Ralph and Zhang, Zhening and Clark, Kathy M. and Dumont, Mark E. and Rohou, Alexis and Beckstein, Oliver and Stokes, David L.},
	year = {2017},
	pages = {130--145}
}

Bor1p is a secondary transporter in yeast that is responsible for boron transport. Bor1p belongs to the SLC4 family which controls in bicarbonate exchange and pH regulation in animals as well as borate uptake in plants. The SLC4 family is more distantly related to members of the Amino acid-Polyamine-organoCation (APC) superfamily, which includes well studied transporters such as LeuT, Mhp1, AdiC, vSGLT, UraA, SLC26Dg. Their mechanism generally involve relative movements of two domains: a core domain that binds substrate and a gate domain that in many cases mediates dimerization. In order to shed light on conformational changes governing transport by the SLC4 family, we grew helical membrane crystals of Bor1p from Saccharomyces mikatae and determined a structure at \textasciitilde6 Å resolution using cryo-electron microscopy. In order to evaluate the conformation of Bor1p in these crystals, a homology model was built based on the related anion exchanger from red blood cells (AE1). This homology model was fitted to the cryo-EM density map using the Molecular Dynamics (MD) Flexible Fitting method and then relaxed by all-atom MD simulation in explicit solvent and membrane. Mapping of water accessibility indicates that the resulting structure represents an inward-facing conformation. Comparisons of the resulting Bor1p model with the X-ray structure of AE1 in an outward-facing conformation, together with MD simulations of inward-facing and outward-facing Bor1p models, suggest rigid body movements of the core domain relative to the gate domain. These movements are consistent with the rocking-bundle transport mechanism described for other members of the APC superfamily.

@inproceedings{gowers_mdanalysis:_2016,
	address = {Austin, TX},
	title = {{MDAnalysis}: {A} {Python} package for the rapid analysis of molecular dynamics simulations.},
	url = {http://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html},
	doi = {10.25080/Majora-629e541a-00e},
	abstract = {MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output trajectories in their own formats so that the development of new trajectory analysis algorithms is confined to specific user communities and widespread adoption and further development is delayed. MDAnalysis addresses this problem by abstracting access to the raw simulation data and presenting a uniform object-oriented Python interface to the user. It thus enables users to rapidly write code that is portable and immediately usable in virtually all biomolecular simulation communities. The user interface and modular design work equally well in complex scripted work flows, as foundations for other packages, and for interactive and rapid prototyping work in IPython / Jupyter notebooks, especially together with molecular visualization provided by nglview and time series analysis with pandas. MDAnalysis is written in Python and Cython and uses NumPy arrays for easy interoperability with the wider scientific Python ecosystem. It is widely used and forms the foundation for more specialized biomolecular simulation tools. MDAnalysis is available under the GNU General Public License v2.},
	booktitle = {Proceedings of the 15th {Python} in {Science} {Conference}},
	author = {Gowers, R. J and Linke, M. and Barnoud, J. and {T. J. E. Reddy} and Melo, M. N. and Seyler, S. L. and Dotson, D. L. and Domanski, J. and Buchoux, S. and Kenney, I. M. and Beckstein, O.},
	editor = {Benthall, Sebastian and Rostrup, Scott},
	year = {2016},
	pages = {102--109}
}

MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output trajectories in their own formats so that the development of new trajectory analysis algorithms is confined to specific user communities and widespread adoption and further development is delayed. MDAnalysis addresses this problem by abstracting access to the raw simulation data and presenting a uniform object-oriented Python interface to the user. It thus enables users to rapidly write code that is portable and immediately usable in virtually all biomolecular simulation communities. The user interface and modular design work equally well in complex scripted work flows, as foundations for other packages, and for interactive and rapid prototyping work in IPython / Jupyter notebooks, especially together with molecular visualization provided by nglview and time series analysis with pandas. MDAnalysis is written in Python and Cython and uses NumPy arrays for easy interoperability with the wider scientific Python ecosystem. It is widely used and forms the foundation for more specialized biomolecular simulation tools. MDAnalysis is available under the GNU General Public License v2.

@inproceedings{dotson_datreant:_2016,
	address = {Austin, TX},
	title = {datreant: persistent, {Pythonic} trees for heterogeneous data},
	url = {http://conference.scipy.org/proceedings/scipy2016/david_dotson.html},
	doi = {10.25080/Majora-629e541a-007},
	abstract = {n science the filesystem often serves as a de facto database, with directory trees being the zeroth-order scientific data structure. But it can be tedious and error prone to work directly with the filesystem to retrieve and store heterogeneous datasets. datreant makes working with directory structures and files Pythonic with Treants: specially marked directories with distinguishing characteristics that can be discovered, queried, and filtered. Treants can be manipulated individually and in aggregate, with mechanisms for granular access to the directories and files in their trees. Disparate datasets stored in any format (CSV, HDF5, NetCDF, Feather, etc.) scattered throughout a filesystem can thus be manipulated as meta-datasets of Treants. datreant is modular and extensible by design to allow specialized applications to be built on top of it, with MDSynthesis as an example for working with molecular dynamics simulation data. http://datreant.org/},
	booktitle = {Proceedings of the 15th {Python} in {Science} {Conference}},
	author = {Dotson, David L. and Seyler, Sean L and Linke, Max and Gowers, Richard J. and Beckstein, Oliver},
	editor = {Benthall, Sebastian and Rostrup, Scott},
	year = {2016},
	pages = {51 -- 56}
}

n science the filesystem often serves as a de facto database, with directory trees being the zeroth-order scientific data structure. But it can be tedious and error prone to work directly with the filesystem to retrieve and store heterogeneous datasets. datreant makes working with directory structures and files Pythonic with Treants: specially marked directories with distinguishing characteristics that can be discovered, queried, and filtered. Treants can be manipulated individually and in aggregate, with mechanisms for granular access to the directories and files in their trees. Disparate datasets stored in any format (CSV, HDF5, NetCDF, Feather, etc.) scattered throughout a filesystem can thus be manipulated as meta-datasets of Treants. datreant is modular and extensible by design to allow specialized applications to be built on top of it, with MDSynthesis as an example for working with molecular dynamics simulation data. http://datreant.org/

@article{coincon_crystal_2016,
	title = {Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters},
	volume = {23},
	copyright = {© 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1545-9993},
	url = {http://www.nature.com/nsmb/journal/v23/n3/full/nsmb.3164.html},
	doi = {10.1038/nsmb.3164},
	abstract = {To fully understand the transport mechanism of Na+/H+ exchangers, it is necessary to clearly establish the global rearrangements required to facilitate ion translocation. Currently, two different transport models have been proposed. Some reports have suggested that structural isomerization is achieved through large elevator-like rearrangements similar to those seen in the structurally unrelated sodium-coupled glutamate-transporter homolog GltPh. Others have proposed that only small domain movements are required for ion exchange, and a conventional rocking-bundle model has been proposed instead. Here, to resolve these differences, we report atomic-resolution structures of the same Na+/H+ antiporter (NapA from Thermus thermophilus) in both outward- and inward-facing conformations. These data combined with cross-linking, molecular dynamics simulations and isothermal calorimetry suggest that Na+/H+ antiporters provide alternating access to the ion-binding site by using elevator-like structural transitions.},
	language = {en},
	number = {3},
	urldate = {2016-04-04TZ},
	journal = {Nature Structural \& Molecular Biology},
	author = {Coincon, Mathieu and Uzdavinys, Povilas and Nji, Emmanuel and Dotson, David L. and Winkelmann, Iven and Abdul-Hussein, Saba and Cameron, Alexander D. and Beckstein, Oliver and Drew, David},
	month = mar,
	year = {2016},
	keywords = {Membrane proteins, X-ray crystallography},
	pages = {248--255}
}

To fully understand the transport mechanism of Na+/H+ exchangers, it is necessary to clearly establish the global rearrangements required to facilitate ion translocation. Currently, two different transport models have been proposed. Some reports have suggested that structural isomerization is achieved through large elevator-like rearrangements similar to those seen in the structurally unrelated sodium-coupled glutamate-transporter homolog GltPh. Others have proposed that only small domain movements are required for ion exchange, and a conventional rocking-bundle model has been proposed instead. Here, to resolve these differences, we report atomic-resolution structures of the same Na+/H+ antiporter (NapA from Thermus thermophilus) in both outward- and inward-facing conformations. These data combined with cross-linking, molecular dynamics simulations and isothermal calorimetry suggest that Na+/H+ antiporters provide alternating access to the ion-binding site by using elevator-like structural transitions.

@article{kenney_prediction_2016,
	title = {Prediction of cyclohexane-water distribution coefficients for the {SAMPL}5 data set using molecular dynamics simulations with the {OPLS}-{AA} force field},
	volume = {30},
	doi = {10.1007/s10822-016-9949-5},
	abstract = {All-atom molecular dynamics (MD) simulations were used to predict water-cyclohexane distribution coefficients Dcw of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the trans- ferable all-atom OPLS-AA force field, which required the derivation of new param- eters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy per- turbation with thermodynamic integration. This protocol resulted in an overall root mean square error (RMSE) in log Dcw of almost 4 log units and an overall signed er- ror of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error sug- gests a systematic error but the experimental Dcw data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.},
	number = {11},
	journal = {Journal of Computer-Aided Molecular Design},
	author = {Kenney, Ian M. and Beckstein, Oliver and Iorga, Bogdan I.},
	year = {2016},
	pages = {1045--1058}
}

All-atom molecular dynamics (MD) simulations were used to predict water-cyclohexane distribution coefficients Dcw of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the trans- ferable all-atom OPLS-AA force field, which required the derivation of new param- eters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy per- turbation with thermodynamic integration. This protocol resulted in an overall root mean square error (RMSE) in log Dcw of almost 4 log units and an overall signed er- ror of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error sug- gests a systematic error but the experimental Dcw data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.

@article{huang_mechanism_2016,
	title = {Mechanism of {pH}-dependent activation of the sodium-proton antiporter {NhaA}},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/doifinder/10.1038/ncomms12940},
	doi = {10.1038/ncomms12940},
	abstract = {Escherichia coli NhaA is a prototype sodium-proton antiporter, which has been extensively characterized by X-ray crystallography, biochemical and biophysical experiments. However, the identities of proton carriers and details of pH-regulated mechanism remain controversial. Here we report constant pH molecular dynamics data, which reveal that NhaA activation involves a net charge switch of a pH sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the funnel. The latter is triggered by charging of Asp164, the first proton carrier. The second proton carrier Lys300 forms a salt bridge with Asp163 in the inactive state, and releases a proton when a sodium ion binds Asp163. These data reconcile current models and illustrate the power of state-of-the-art molecular dynamics simulations in providing atomic details of proton-coupled transport across membrane which is challenging to elucidate by 
experimental techniques.},
	urldate = {2016-10-06TZ},
	journal = {Nature Communications},
	author = {Huang, Yandong and Chen, Wei and Dotson, David L. and Beckstein, Oliver and Shen, Jana},
	month = oct,
	year = {2016},
	pages = {12940}
}

Escherichia coli NhaA is a prototype sodium-proton antiporter, which has been extensively characterized by X-ray crystallography, biochemical and biophysical experiments. However, the identities of proton carriers and details of pH-regulated mechanism remain controversial. Here we report constant pH molecular dynamics data, which reveal that NhaA activation involves a net charge switch of a pH sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the funnel. The latter is triggered by charging of Asp164, the first proton carrier. The second proton carrier Lys300 forms a salt bridge with Asp163 in the inactive state, and releases a proton when a sodium ion binds Asp163. These data reconcile current models and illustrate the power of state-of-the-art molecular dynamics simulations in providing atomic details of proton-coupled transport across membrane which is challenging to elucidate by experimental techniques.

@article{geoffrey_charles_fox_datanet:_2016,
	title = {Datanet: {CIF}21 {DIBBs}: {Middleware} and {High} {Performance} {Analytics} {Libraries} for {Scalable} {Data} {Science} {NSF}14-43054 {Progress} {Report}},
	shorttitle = {Datanet},
	url = {https://doi.org/10.13140/RG.2.2.31163.21289},
	doi = {10.13140/RG.2.2.31163.21289},
	urldate = {2016-09-19TZ},
	author = {{Geoffrey Charles Fox} and {Judy Qiu} and {David Crandall} and {Gregor von Laszewski} and {Shantenu Jha} and {Fusheng Wang} and {Madhav Marathe} and {John Paden} and {Tom Cheatham} and {Oliver Beckstein}},
	year = {2016}
}

@article{ulmschneider_peptide_2015,
	title = {Peptide {Folding} in {Translocon}-{Like} {Pores}},
	volume = {248},
	issn = {0022-2631, 1432-1424},
	url = {http://link.springer.com/article/10.1007/s00232-015-9808-7},
	doi = {10.1007/s00232-015-9808-7},
	abstract = {The cellular translocon, present in all three domains of life, is one of the most versatile and important biological nanopores. This complex molecular apparatus is directly responsible for the secretion of globular proteins across membranes as well as the insertion of integral membrane proteins into lipid bilayers. Recently determined structures of the archaean SecY translocon reveal an hour-glass-shaped pore, which accommodates the nascent peptide chain during translocation. While these structures provide important insights into ribosome binding to the translocon, threading of the nascent chain into the channel, and lateral gate opening for releasing the folded helical peptide into the membrane bilayer, the exact folding pathway of the peptide inside the protein-conducting channel during translocation and prior to the lateral release into the bilayer remains elusive. In the present study, we use molecular dynamics simulations to investigate atomic resolution peptide folding in hour-glass-shaped pore models that are based on the SecY translocon channel structure. The theoretical setup allows systematic variation of key determinants of folding, in particular the degree of confinement of the peptide and the hydration level of the pore. A 27-residue hydrophobic peptide was studied that is preferentially inserted into membranes by the translocon. Our results show that both pore diameter as well as channel hydration are important determinants for folding efficiency and helical stability of the peptide, therefore providing important insights into translocon gating and lateral peptide partitioning.},
	language = {en},
	number = {3},
	urldate = {2015-07-01TZ},
	journal = {The Journal of Membrane Biology},
	author = {Ulmschneider, Martin B. and Leman, Julia Koehler and Fennell, Hayden and Beckstein, Oliver},
	month = may,
	year = {2015},
	keywords = {Biochemistry, general, Human Physiology, OPLS, Protein folding, SecY translocon, membrane protein, molecular dynamics},
	pages = {407--417}
}

The cellular translocon, present in all three domains of life, is one of the most versatile and important biological nanopores. This complex molecular apparatus is directly responsible for the secretion of globular proteins across membranes as well as the insertion of integral membrane proteins into lipid bilayers. Recently determined structures of the archaean SecY translocon reveal an hour-glass-shaped pore, which accommodates the nascent peptide chain during translocation. While these structures provide important insights into ribosome binding to the translocon, threading of the nascent chain into the channel, and lateral gate opening for releasing the folded helical peptide into the membrane bilayer, the exact folding pathway of the peptide inside the protein-conducting channel during translocation and prior to the lateral release into the bilayer remains elusive. In the present study, we use molecular dynamics simulations to investigate atomic resolution peptide folding in hour-glass-shaped pore models that are based on the SecY translocon channel structure. The theoretical setup allows systematic variation of key determinants of folding, in particular the degree of confinement of the peptide and the hydration level of the pore. A 27-residue hydrophobic peptide was studied that is preferentially inserted into membranes by the translocon. Our results show that both pore diameter as well as channel hydration are important determinants for folding efficiency and helical stability of the peptide, therefore providing important insights into translocon gating and lateral peptide partitioning.

@article{seyler_path_2015,
	title = {Path {Similarity} {Analysis}: {A} {Method} for {Quantifying} {Macromolecular} {Pathways}},
	volume = {11},
	shorttitle = {Path {Similarity} {Analysis}},
	url = {https://doi.org/10.1371/journal.pcbi.1004568},
	doi = {10.1371/journal.pcbi.1004568},
	abstract = {Author Summary Many proteins are nanomachines that perform mechanical or chemical work by changing their three-dimensional shape and cycle between multiple conformational states. Computer simulations of such conformational transitions provide mechanistic insights into protein function but such simulations have been challenging. In particular, it is not clear how to quantitatively compare current simulation methods or to assess their accuracy. To that end, we present a general and flexible computational framework for quantifying transition paths—by measuring mutual geometric similarity—that, compared with existing approaches, requires minimal a-priori assumptions and can take advantage of full atomic detail alongside heuristic information derived from intuition. Using our Path Similarity Analysis (PSA) framework in parallel with several existing quantitative approaches, we examine transitions generated for a toy model of a transition and two biological systems, the enzyme adenylate kinase and diphtheria toxin. Our results show that PSA enables the quantitative comparison of different path sampling methods and aids the identification of potentially important atomistic motions by exploiting geometric information in transition paths. The method has the potential to enhance our understanding of transition path sampling methods, validate them, and to provide a new approach to analyzing macromolecular conformational transitions.},
	number = {10},
	urldate = {2015-10-22TZ},
	journal = {PLoS Comput Biol},
	author = {Seyler, Sean L. and Kumar, Avishek and Thorpe, M. F. and Beckstein, Oliver},
	month = oct,
	year = {2015},
	pages = {e1004568}
}

Author Summary Many proteins are nanomachines that perform mechanical or chemical work by changing their three-dimensional shape and cycle between multiple conformational states. Computer simulations of such conformational transitions provide mechanistic insights into protein function but such simulations have been challenging. In particular, it is not clear how to quantitatively compare current simulation methods or to assess their accuracy. To that end, we present a general and flexible computational framework for quantifying transition paths—by measuring mutual geometric similarity—that, compared with existing approaches, requires minimal a-priori assumptions and can take advantage of full atomic detail alongside heuristic information derived from intuition. Using our Path Similarity Analysis (PSA) framework in parallel with several existing quantitative approaches, we examine transitions generated for a toy model of a transition and two biological systems, the enzyme adenylate kinase and diphtheria toxin. Our results show that PSA enables the quantitative comparison of different path sampling methods and aids the identification of potentially important atomistic motions by exploiting geometric information in transition paths. The method has the potential to enhance our understanding of transition path sampling methods, validate them, and to provide a new approach to analyzing macromolecular conformational transitions.

@article{hilton_understanding_2015,
	title = {Understanding {Thermosensitive} {Transient} {Receptor} {Potential} {Channels} as {Versatile} {Polymodal} {Cellular} {Sensors}},
	volume = {54},
	issn = {0006-2960},
	url = {http://dx.doi.org/10.1021/acs.biochem.5b00071},
	doi = {10.1021/acs.biochem.5b00071},
	abstract = {Transient receptor potential (TRP) ion channels are eukaryotic polymodal sensors that function as molecular cellular signal integrators. TRP family members sense and are modulated by a wide array of inputs, including temperature, pressure, pH, voltage, chemicals, lipids, and other proteins. These inputs induce signal transduction events mediated by nonselective cation passage through TRP channels. In this review, we focus on the thermosensitive TRP channels and highlight the emerging view that these channels play a variety of significant roles in physiology and pathophysiology in addition to sensory biology. We attempt to use this viewpoint as a framework to understand the complexity and controversy of TRP channel modulation and ultimately suggest that the complex functional behavior arises inherently because this class of protein is exquisitely sensitive to many diverse and distinct signal inputs. To illustrate this idea, we primarily focus on TRP channel thermosensing. We also offer a structural, biochemical, biophysical, and computational perspective that may help to bring more coherence and consensus in understanding the function of this important class of proteins.},
	number = {15},
	urldate = {2015-04-23TZ},
	journal = {Biochemistry},
	author = {Hilton, Jacob K. and Rath, Parthasarathi and Helsell, Cole V. M. and Beckstein, Oliver and Van Horn, Wade D.},
	month = apr,
	year = {2015},
	pages = {2401--2413}
}

Transient receptor potential (TRP) ion channels are eukaryotic polymodal sensors that function as molecular cellular signal integrators. TRP family members sense and are modulated by a wide array of inputs, including temperature, pressure, pH, voltage, chemicals, lipids, and other proteins. These inputs induce signal transduction events mediated by nonselective cation passage through TRP channels. In this review, we focus on the thermosensitive TRP channels and highlight the emerging view that these channels play a variety of significant roles in physiology and pathophysiology in addition to sensory biology. We attempt to use this viewpoint as a framework to understand the complexity and controversy of TRP channel modulation and ultimately suggest that the complex functional behavior arises inherently because this class of protein is exquisitely sensitive to many diverse and distinct signal inputs. To illustrate this idea, we primarily focus on TRP channel thermosensing. We also offer a structural, biochemical, biophysical, and computational perspective that may help to bring more coherence and consensus in understanding the function of this important class of proteins.

@article{simmons_molecular_2014,
	title = {Molecular mechanism of ligand recognition by a membrane transport protein, {Mhp}1},
	volume = {33},
	copyright = {© 2014 The Authors. Published under the terms of the CC BY 4.0 license. This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.},
	issn = {0261-4189, 1460-2075},
	url = {http://emboj.embopress.org/content/33/16/1831},
	doi = {10.15252/embj.201387557},
	abstract = {The hydantoin transporter Mhp1 is a sodium‐coupled secondary active transport protein of the nucleobase‐cation‐symport family and a member of the widespread 5‐helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site‐directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5‐substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5‐substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5‐(2‐naphthylmethyl)‐L‐hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1.
Synopsis



Structure‐function and molecular dynamics analysis of the hydantoin active transporter Mhp1 yields a novel intermediate state and delineates the basis for substrate specificity and membrane transport.

Hydantoin substrates like indolylmethylhydantoin (IMH) bind to the LeuT‐like Mhp1 transporter in an extended conformationSelectivity of Mhp1 for the substrate is conferred by hydrogen bonds to the hydantoin moiety and the fit of aromatic substituent into a hydrophobic pocketNaphthylmethylhydantoin (NMH) inhibits Mhp1 but is not transportedCrystal structure of Mhp1 with NMH shows TMH10 to adopt the position seen in the outward‐open rather than the occluded state.Mutation of Leu363Ala in TMH10 of Mhp1 converts NMH from an inhibitor to a substrate.},
	language = {en},
	urldate = {2014-06-25TZ},
	journal = {The EMBO Journal},
	author = {Simmons, Katie J. and Jackson, Scott M. and Brueckner, Florian and Patching, Simon G. and Beckstein, Oliver and Ivanova, Ekaterina and Geng, Tian and Weyand, Simone and Drew, David and Lanigan, Joseph and Sharples, David J. and Sansom, Mark SP and Iwata, So and Fishwick, Colin WG and Johnson, A. Peter and Cameron, Alexander D. and Henderson, Peter JF},
	month = jun,
	year = {2014},
	keywords = {Mhp1, five helix inverted repeat superfamily, hydantoin, membrane transport, molecular recognition, nucleobase‐cation‐symport, NCS1, family},
	pages = {1831--1844}
}

The hydantoin transporter Mhp1 is a sodium‐coupled secondary active transport protein of the nucleobase‐cation‐symport family and a member of the widespread 5‐helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site‐directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5‐substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5‐substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5‐(2‐naphthylmethyl)‐L‐hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1. Synopsis Structure‐function and molecular dynamics analysis of the hydantoin active transporter Mhp1 yields a novel intermediate state and delineates the basis for substrate specificity and membrane transport. Hydantoin substrates like indolylmethylhydantoin (IMH) bind to the LeuT‐like Mhp1 transporter in an extended conformationSelectivity of Mhp1 for the substrate is conferred by hydrogen bonds to the hydantoin moiety and the fit of aromatic substituent into a hydrophobic pocketNaphthylmethylhydantoin (NMH) inhibits Mhp1 but is not transportedCrystal structure of Mhp1 with NMH shows TMH10 to adopt the position seen in the outward‐open rather than the occluded state.Mutation of Leu363Ala in TMH10 of Mhp1 converts NMH from an inhibitor to a substrate.

@article{lee_crystal_2014,
	title = {Crystal structure of the sodium–proton antiporter {NhaA} dimer and new mechanistic insights},
	volume = {144},
	issn = {0022-1295, 1540-7748},
	url = {http://jgp.rupress.org/content/144/6/529},
	doi = {10.1085/jgp.201411219},
	abstract = {Back to TopAbstract
Sodium–proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport is not clear. Here, we report a crystal form of the prototypical sodium–proton antiporter NhaA from Escherichia coli in which the protein is seen as a dimer. In this new structure, we observe a salt bridge between an essential aspartic acid (Asp163) and a conserved lysine (Lys300). An equivalent salt bridge is present in the homologous transporter NapA, but not in the only other known crystal structure of NhaA, which provides the foundation of most existing structural models of electrogenic sodium–proton antiport. Molecular dynamics simulations show that the stability of the salt bridge is weakened by sodium ions binding to Asp164 and the neighboring Asp163. This suggests that the transport mechanism involves Asp163 switching between forming a salt bridge with Lys300 and interacting with the sodium ion. pKa calculations suggest that Asp163 is highly unlikely to be protonated when involved in the salt bridge. As it has been previously suggested that Asp163 is one of the two residues through which proton transport occurs, these results have clear implications to the current mechanistic models of sodium–proton antiport in NhaA.},
	language = {en},
	number = {6},
	urldate = {2014-11-30TZ},
	journal = {The Journal of General Physiology},
	author = {Lee, Chiara and Yashiro, Shoko and Dotson, David L. and Uzdavinys, Povilas and Iwata, So and Sansom, Mark S. P. and Ballmoos, Christoph von and Beckstein, Oliver and Drew, David and Cameron, Alexander D.},
	month = dec,
	year = {2014},
	pmid = {25422503},
	pages = {529--544}
}

Back to TopAbstract Sodium–proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport is not clear. Here, we report a crystal form of the prototypical sodium–proton antiporter NhaA from Escherichia coli in which the protein is seen as a dimer. In this new structure, we observe a salt bridge between an essential aspartic acid (Asp163) and a conserved lysine (Lys300). An equivalent salt bridge is present in the homologous transporter NapA, but not in the only other known crystal structure of NhaA, which provides the foundation of most existing structural models of electrogenic sodium–proton antiport. Molecular dynamics simulations show that the stability of the salt bridge is weakened by sodium ions binding to Asp164 and the neighboring Asp163. This suggests that the transport mechanism involves Asp163 switching between forming a salt bridge with Lys300 and interacting with the sodium ion. pKa calculations suggest that Asp163 is highly unlikely to be protonated when involved in the salt bridge. As it has been previously suggested that Asp163 is one of the two residues through which proton transport occurs, these results have clear implications to the current mechanistic models of sodium–proton antiport in NhaA.

@article{seyler_sampling_2014,
	title = {Sampling large conformational transitions: adenylate kinase as a testing ground},
	volume = {40},
	issn = {0892-7022},
	shorttitle = {Sampling large conformational transitions},
	url = {http://dx.doi.org/10.1080/08927022.2014.919497},
	doi = {10.1080/08927022.2014.919497},
	abstract = {A fundamental problem in computational biophysics is to deduce the function of a protein from the structure. Many biological macromolecules such as enzymes, molecular motors or membrane transport proteins perform their function by cycling between multiple conformational states. Understanding such conformational transitions, which typically occur on the millisecond to second time scale, is central to understanding protein function. Molecular dynamics (MD) computer simulations have become an important tool to connect molecular structure to function, but equilibrium MD simulations are rarely able to sample on time scales longer than a few microseconds – orders of magnitudes shorter than the time scales of interest. A range of different simulation methods have been proposed to overcome this time-scale limitation. These include calculations of the free energy landscape and path sampling methods to directly sample transitions between known conformations. All these methods solve the problem to sample infrequently occupied but important regions of configuration space. Many path-sampling algorithms have been applied to the closed open transition of the enzyme adenylate kinase (AdK), which undergoes a large, clamshell-like conformational transition between an open and a closed state. Here we review approaches to sample macromolecular transitions through the lens of AdK. We focus our main discussion on the current state of knowledge – both from simulations and experiments – about the transition pathways of ligand-free AdK, its energy landscape, transition rates and interactions with substrates. We conclude with a comparison of the discussed approaches with a view towards quantitative evaluation of path-sampling methods.},
	number = {10-11},
	urldate = {2014-08-12TZ},
	journal = {Molecular Simulation},
	author = {Seyler, Sean L. and Beckstein, Oliver},
	year = {2014},
	pages = {855--877}
}

A fundamental problem in computational biophysics is to deduce the function of a protein from the structure. Many biological macromolecules such as enzymes, molecular motors or membrane transport proteins perform their function by cycling between multiple conformational states. Understanding such conformational transitions, which typically occur on the millisecond to second time scale, is central to understanding protein function. Molecular dynamics (MD) computer simulations have become an important tool to connect molecular structure to function, but equilibrium MD simulations are rarely able to sample on time scales longer than a few microseconds – orders of magnitudes shorter than the time scales of interest. A range of different simulation methods have been proposed to overcome this time-scale limitation. These include calculations of the free energy landscape and path sampling methods to directly sample transitions between known conformations. All these methods solve the problem to sample infrequently occupied but important regions of configuration space. Many path-sampling algorithms have been applied to the closed open transition of the enzyme adenylate kinase (AdK), which undergoes a large, clamshell-like conformational transition between an open and a closed state. Here we review approaches to sample macromolecular transitions through the lens of AdK. We focus our main discussion on the current state of knowledge – both from simulations and experiments – about the transition pathways of ligand-free AdK, its energy landscape, transition rates and interactions with substrates. We conclude with a comparison of the discussed approaches with a view towards quantitative evaluation of path-sampling methods.

@article{beckstein_prediction_2014,
	title = {Prediction of hydration free energies for a diverse set of compounds using molecular dynamics simulations with the {OPLS}-{AA} force field},
	volume = {28},
	url = {http://doi.org/10.1007/s10822-014-9727-1},
	doi = {10.1007/s10822-014-9727-1},
	abstract = {All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of small molecules as part of the SAMPL4 challenge. Compounds were parametrized on the basis of the OPLS-AA force field using three different protocols for deriving partial charges: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms and derivation of new parameters for a number of distinct chemical groups (N-alkyl imidazole, nitrate) that were not present in the published force field; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian09 at the HF/6-31G* level), followed by two-stage RESP fitting. The absolute hydration free energy was computed by an established protocol including alchemical free energy perturbation with thermodynamic integration. The use of standard OPLS-AA charges (protocol 1) with a number of newly parametrized charges and the use of histidine derived parameters for imidazole yielded an overall root mean square deviation of the prediction from the experimental data of 1.75 kcal/mol. The precision of our results appears to be mainly limited by relatively poor reproducibility of the Lennard-Jones contribution towards the solvation free energy, for which we observed large variability that could be traced to a strong dependence on the initial system conditions.},
	number = {3},
	journal = {J Comput Aided Mol Des},
	author = {Beckstein, Oliver and Fourrier, Anaïs and Iorga, Bogdan I.},
	year = {2014},
	keywords = {FEP, HYDRATION FREE-ENERGIES, OPLS-AA, SAMPL4},
	pages = {265--276}
}

All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of small molecules as part of the SAMPL4 challenge. Compounds were parametrized on the basis of the OPLS-AA force field using three different protocols for deriving partial charges: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms and derivation of new parameters for a number of distinct chemical groups (N-alkyl imidazole, nitrate) that were not present in the published force field; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian09 at the HF/6-31G* level), followed by two-stage RESP fitting. The absolute hydration free energy was computed by an established protocol including alchemical free energy perturbation with thermodynamic integration. The use of standard OPLS-AA charges (protocol 1) with a number of newly parametrized charges and the use of histidine derived parameters for imidazole yielded an overall root mean square deviation of the prediction from the experimental data of 1.75 kcal/mol. The precision of our results appears to be mainly limited by relatively poor reproducibility of the Lennard-Jones contribution towards the solvation free energy, for which we observed large variability that could be traced to a strong dependence on the initial system conditions.

@article{stelzl_flexible_2014,
	title = {Flexible gates generate occluded intermediates in the transport cycle of {LacY}},
	volume = {426},
	url = {http://doi.org/10.1016/j.jmb.2013.10.024},
	doi = {10.1016/j.jmb.2013.10.024},
	abstract = {The Major Facilitator Superfamily (MFS) transporter lactose permease (LacY) alternates between cytoplasmic and periplasmic open conformations to co-transport a sugar molecule together with a proton across the plasma membrane. Indirect experimental evidence suggested the existence of an occluded transition intermediate of LacY, which would prevent leaking of the proton gradient. As no experimental structure is known, the conformational transition is not fully understood in atomic detail. We simulated transition events from a cytoplasmic open conformation to a periplasmic open conformation with the dynamic importance sampling (DIMS) molecular dynamics (MD) method and observed occluded intermediates. Analysis of water permeation pathways and the electrostatic free energy landscape of a solvated proton indicated that the occluded state contains a solvated central cavity inaccessible from either side of the membrane. We propose a pair of geometric order parameters that capture the state of the pathway through the MFS transporters as shown by a survey of available crystal structures and models. We present a model for the occluded state of apo-LacY, which is similar to the occluded crystal structures of the MFS transporters EmrD, PepTSo, NarU, PiPT and XylE. Our simulations are consistent with experimental double electron spin-spin distance measurements that have been interpreted to show occluded conformations. During the simulations a salt bridge formed that has been postulated to be involved in driving the conformational transition. Our results argue against a simple rigid body domain motion as implied by a strict "rocker-switch mechanism" and instead hint at an intricate coupling between two flexible gates.},
	journal = {J Mol Biol},
	author = {Stelzl, Lukas S and Fowler, Philip W and Sansom, Mark S P and Beckstein, Oliver},
	year = {2014},
	keywords = {DEER, DIMS, LacY, MD SIMULATION, POISSON-BOLTZMANN LacY, transporter},
	pages = {735--751}
}

The Major Facilitator Superfamily (MFS) transporter lactose permease (LacY) alternates between cytoplasmic and periplasmic open conformations to co-transport a sugar molecule together with a proton across the plasma membrane. Indirect experimental evidence suggested the existence of an occluded transition intermediate of LacY, which would prevent leaking of the proton gradient. As no experimental structure is known, the conformational transition is not fully understood in atomic detail. We simulated transition events from a cytoplasmic open conformation to a periplasmic open conformation with the dynamic importance sampling (DIMS) molecular dynamics (MD) method and observed occluded intermediates. Analysis of water permeation pathways and the electrostatic free energy landscape of a solvated proton indicated that the occluded state contains a solvated central cavity inaccessible from either side of the membrane. We propose a pair of geometric order parameters that capture the state of the pathway through the MFS transporters as shown by a survey of available crystal structures and models. We present a model for the occluded state of apo-LacY, which is similar to the occluded crystal structures of the MFS transporters EmrD, PepTSo, NarU, PiPT and XylE. Our simulations are consistent with experimental double electron spin-spin distance measurements that have been interpreted to show occluded conformations. During the simulations a salt bridge formed that has been postulated to be involved in driving the conformational transition. Our results argue against a simple rigid body domain motion as implied by a strict "rocker-switch mechanism" and instead hint at an intricate coupling between two flexible gates.

@incollection{cameron_5-helix_2013,
	address = {Berlin, Heidelberg},
	title = {The 5-helix inverted repeat superfamily of membrane transport proteins},
	isbn = {978-3-642-16711-9},
	url = {https://doi.org/10.1007/978-3-642-16712-6_772},
	booktitle = {Encylopedia of {Biophysics}},
	publisher = {Springer},
	author = {Cameron, Alexander D and Beckstein, Oliver and Henderson, Peter JF},
	editor = {Roberts, Gordon C. K.},
	year = {2013},
	pages = {1481--1485}
}

@incollection{jackson_mhp1_2013,
	address = {Berlin, Heidelberg},
	title = {Mhp1, the {Na}⁺-{Hydantoin} {Membrane} {Transport} {Protein}},
	isbn = {978-3-642-16711-9},
	url = {https://doi.org/10.1007/978-3-642-16712-6_670},
	abstract = {Mhp1 is a member of the Nucleobase-Cation-Symport-1 (NCS-1) family designated A.2.39.5 (Saier et al 2006, 2009; Ren and Paulsen, 2010), which carries out transport across membranes of hydantoins substituted with aromatic rings in the 5-position. The wild-type protein contains 489 amino acids (Suzuki and Henderson 2006), modestly modified in a genetic construct at the N-terminus and C-terminus, where a (His)6 tag is incorporated to facilitate amplified expression, purification and crystallisation (Suzuki and Henderson 2006; Shimamura et al, 2008). The transport reaction of Mhp1 is Hydantoin (out) + Na+ (out) –{\textgreater} Hydantoin (in) + Na+ (in) This reaction is of commercial interest, because of the potential for converting waste hydantoins to compounds of added value, for example L-amino acids (Suzuki et al 2005; Javier et al 2009).},
	booktitle = {Encylopedia of {Biophysics}},
	publisher = {Springer},
	author = {Jackson, Scott M and Ivanova, Ekaterina and Simmons, Katie and Patching, Simon G and Weyand, Simone and Shimamura, Tatsuro and Brückner, Florian and Iwata, So and Sharples, David J and Baldwin, Stephen A and Sansom, Mark PS and Beckstein, Oliver and Cameron, Alexander D and Henderson, Peter JF},
	editor = {Roberts, Gordon C. K.},
	year = {2013},
	pages = {1514--1521}
}

Mhp1 is a member of the Nucleobase-Cation-Symport-1 (NCS-1) family designated A.2.39.5 (Saier et al 2006, 2009; Ren and Paulsen, 2010), which carries out transport across membranes of hydantoins substituted with aromatic rings in the 5-position. The wild-type protein contains 489 amino acids (Suzuki and Henderson 2006), modestly modified in a genetic construct at the N-terminus and C-terminus, where a (His)6 tag is incorporated to facilitate amplified expression, purification and crystallisation (Suzuki and Henderson 2006; Shimamura et al, 2008). The transport reaction of Mhp1 is Hydantoin (out) + Na+ (out) –\textgreater Hydantoin (in) + Na+ (in) This reaction is of commercial interest, because of the potential for converting waste hydantoins to compounds of added value, for example L-amino acids (Suzuki et al 2005; Javier et al 2009).

@article{denning_influence_2013,
	title = {Influence of lipids on protein-mediated transmembrane transport},
	volume = {169},
	url = {http://doi.org/10.1016/j.chemphyslip.2013.02.007},
	doi = {10.1016/j.chemphyslip.2013.02.007},
	abstract = {Transmembrane proteins are responsible for transporting ions and small molecules across the hydrophobic region of the cell membrane. We are reviewing the evidence for regulation of these transport processes by interactions with the lipids of the membrane. We focus on ion channels, including potassium channels, mechanosensitive and pentameric ligand gated ion channels, and active transporters, including pumps, sodium or proton driven secondary transporters and ABC transporters. For ion channels it has been convincingly shown that specific lipid-protein interactions can directly affect their function. In some cases, a combined approach of molecular and structural biology together with computer simulations has revealed the molecular mechanisms. There are also many transporters whose activity depends on lipids but understanding of the molecular mechanisms is only beginning.},
	journal = {Chem Phys Lipids},
	author = {Denning, Elizabeth J. and Beckstein, Oliver},
	year = {2013},
	keywords = {Protein-lipid interactions, Transporters, ion channel, review},
	pages = {57--71}
}

Transmembrane proteins are responsible for transporting ions and small molecules across the hydrophobic region of the cell membrane. We are reviewing the evidence for regulation of these transport processes by interactions with the lipids of the membrane. We focus on ion channels, including potassium channels, mechanosensitive and pentameric ligand gated ion channels, and active transporters, including pumps, sodium or proton driven secondary transporters and ABC transporters. For ion channels it has been convincingly shown that specific lipid-protein interactions can directly affect their function. In some cases, a combined approach of molecular and structural biology together with computer simulations has revealed the molecular mechanisms. There are also many transporters whose activity depends on lipids but understanding of the molecular mechanisms is only beginning.

@article{fowler_detailed_2013,
	title = {A {Detailed} {Examination} of a {Single} {Conduction} {Event} in a {Potassium} {Channel}},
	volume = {4},
	url = {http://pubs.acs.org/doi/abs/10.1021/jz4014079},
	doi = {10.1021/jz4014079},
	abstract = {Although extensively studied, it has proved difficult to describe in detail how potassium ion channels conduct cations and water. We present a computational study that, by using strat- ified umbrella sampling, examines nearly an entire conduction event of the Kv1.2/2.1 paddle chimera and thereby identifies the expected stable configurations of ions and water in the se- lectivity filter of the channel. We describe in detail the motions of the ions and waters during a conduction event, focusing on how waters and ions enter the filter, the rotation of water molecules inside the filter and how potassium ions are coordinated as they move from a water to a protein environment. Finally we analyze the small conformational changes undergone by the protein, showing that the stable configurations are most similar to the experimental crystal structure.},
	journal = {J Phys Chem Lett},
	author = {Fowler, Philip William and Beckstein, Oliver and Abad, Enrique and Sansom, Mark S. P.},
	year = {2013},
	keywords = {KcsA, PMF, permeation},
	pages = {3104--3109}
}

Although extensively studied, it has proved difficult to describe in detail how potassium ion channels conduct cations and water. We present a computational study that, by using strat- ified umbrella sampling, examines nearly an entire conduction event of the Kv1.2/2.1 paddle chimera and thereby identifies the expected stable configurations of ions and water in the se- lectivity filter of the channel. We describe in detail the motions of the ions and waters during a conduction event, focusing on how waters and ions enter the filter, the rotation of water molecules inside the filter and how potassium ions are coordinated as they move from a water to a protein environment. Finally we analyze the small conformational changes undergone by the protein, showing that the stable configurations are most similar to the experimental crystal structure.

@article{lee_two-domain_2013,
	title = {A two-domain elevator mechanism for sodium/proton antiport},
	volume = {501},
	url = {http://dx.doi.org/10.1038/nature12484},
	doi = {10.1038/nature12484},
	abstract = {Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis. In humans, their dysfunction has been linked to diseases, such as hypertension, heart failure and epilepsy, and they are well-established drug targets. The best understood model system for Na+/H+ antiport is NhaA from Escherichia coli, for which both electron microscopy and crystal structures are available. NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein. Like many Na+/H+ antiporters, the activity of NhaA is regulated by pH, only becoming active above pH 6.5, at which point a conformational change is thought to occur. The only reported NhaA crystal structure so far is of the low pH inactivated form. Here we describe the active-state structure of a Na+/H+ antiporter, NapA from Thermus thermophilus, at 3 {\textbackslash}AA resolution, solved from crystals grown at pH 7.8. In the NapA structure, the core and dimerization domains are in different positions to those seen in NhaA, and a negatively charged cavity has now opened to the outside. The extracellular cavity allows access to a strictly conserved aspartate residue thought to coordinate ion binding directly, a role supported here by molecular dynamics simulations. To alternate access to this ion-binding site, however, requires a surprisingly large rotation of the core domain, some 20$^{\textrm{{\textbackslash}circ\$}}$ against the dimerization interface. We conclude that despite their fast transport rates of up to 1,500 ions per second, Na+/H+ antiporters operate by a two-domain rocking bundle model, revealing themes relevant to secondary-active transporters in general.},
	number = {7468},
	journal = {Nature},
	author = {Lee, Chiara and Kang, Hae Joo and von Ballmoos, Christoph and Newstead, Simon and Uzdavinys, Povilas and Dotson, David L. and Iwata, So and Beckstein, Oliver and Cameron, Alexander D. and Drew, David},
	year = {2013},
	keywords = {MD SIMULATION, Na+, NapA, NhaA, antiporter, transporter},
	pages = {573--577}
}

Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis. In humans, their dysfunction has been linked to diseases, such as hypertension, heart failure and epilepsy, and they are well-established drug targets. The best understood model system for Na+/H+ antiport is NhaA from Escherichia coli, for which both electron microscopy and crystal structures are available. NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein. Like many Na+/H+ antiporters, the activity of NhaA is regulated by pH, only becoming active above pH 6.5, at which point a conformational change is thought to occur. The only reported NhaA crystal structure so far is of the low pH inactivated form. Here we describe the active-state structure of a Na+/H+ antiporter, NapA from Thermus thermophilus, at 3 \textbackslashAA resolution, solved from crystals grown at pH 7.8. In the NapA structure, the core and dimerization domains are in different positions to those seen in NhaA, and a negatively charged cavity has now opened to the outside. The extracellular cavity allows access to a strictly conserved aspartate residue thought to coordinate ion binding directly, a role supported here by molecular dynamics simulations. To alternate access to this ion-binding site, however, requires a surprisingly large rotation of the core domain, some 20$^{\textrm{{\textbackslash}circ\$$ against the dimerization interface. We conclude that despite their fast transport rates of up to 1,500 ions per second, Na+/H+ antiporters operate by a two-domain rocking bundle model, revealing themes relevant to secondary-active transporters in general.

@article{fowler_energetics_2013,
	title = {Energetics of {Multi}-{Ion} {Conduction} {Pathways} in {Potassium} {Ion} {Channels}},
	volume = {9},
	url = {http://pubs.acs.org/doi/abs/10.1021/ct4005933},
	doi = {10.1021/ct4005933},
	abstract = {Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF). These can be used, in conjunction with the electro-diffusion theory, to predict the conductance of a specific ion channel. Here, we calculate seven independent PMFs, thereby studying the differences between two potassium ion channels, the effect of the CHARMM CMAP forcefield correction, and the sensitivity and reproducibility of the method. Thermodynamically stable ion–water configurations of the selectivity filter can be identified from all the free energy landscapes, but the heights of the kinetic barriers for potassium ions to move through the selectivity filter are, in nearly all cases, too high to predict conductances in line with experiment. This implies it is not currently feasible to predict the conductance of potassium ion channels, but other simpler channels may be more tractable.},
	number = {11},
	journal = {Journal of Chemical Theory and Computation},
	author = {Fowler, Philip W. and Abad, Enrique and Beckstein, Oliver and Sansom, Mark S. P.},
	year = {2013},
	keywords = {KcsA, PMF, ion permeation},
	pages = {5176--5189}
}

Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF). These can be used, in conjunction with the electro-diffusion theory, to predict the conductance of a specific ion channel. Here, we calculate seven independent PMFs, thereby studying the differences between two potassium ion channels, the effect of the CHARMM CMAP forcefield correction, and the sensitivity and reproducibility of the method. Thermodynamically stable ion–water configurations of the selectivity filter can be identified from all the free energy landscapes, but the heights of the kinetic barriers for potassium ions to move through the selectivity filter are, in nearly all cases, too high to predict conductances in line with experiment. This implies it is not currently feasible to predict the conductance of potassium ion channels, but other simpler channels may be more tractable.

@article{beckstein_prediction_2012,
	title = {Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the {OPLS}-{AA} force field},
	volume = {26},
	url = {http://doi.org/10.1007/s10822-011-9527-9},
	doi = {10.1007/s10822-011-9527-9},
	abstract = {All-atom molecular dynamics computer simula- tions were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermody- namic integration. Three different approaches to deriving partial charge parameters were pursued: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms; (2) calcula- tion of quantum mechanical charges via geometry optimiza- tion, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian03 at the HF/6- 31G* level), followed by two-stage RESP fitting. Protocol 3 generated the most accurate predictions with a root mean square (RMS) error of 1:2 kcal mol{\textasciicircum}-1 for the entire data set. It was found that the deficiency of the standard OPLS-AA parameters, protocol 1(RMS error 2.4 kcal mol{\textasciicircum}-1 overall), was mostly due to compounds with more than three chlo- rine substituents on an aromatic ring. For this latter subset, the RMS errors were 1:4 kcal mol{\textasciicircum}-1 (protocol 3) and 4:3 kcal mol{\textasciicircum}-1 (protocol 1), respectively. We propose new OPLS-AA atom types for aromatic carbon and chlorine atoms in rings with C4 Cl-substituents that perform better than the best QM-based approach, resulting in an RMS error of 1:2 kcal mol{\textasciicircum}-1 for these difficult compounds.},
	number = {5},
	journal = {J Comput Aided Mol Des},
	author = {Beckstein, Oliver and Iorga, Bogdan I.},
	year = {2012},
	keywords = {Chlorinated compounds, OPLS-AA, PBC, dioxane, hydration free energy},
	pages = {635--645}
}

All-atom molecular dynamics computer simula- tions were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermody- namic integration. Three different approaches to deriving partial charge parameters were pursued: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms; (2) calcula- tion of quantum mechanical charges via geometry optimiza- tion, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian03 at the HF/6- 31G* level), followed by two-stage RESP fitting. Protocol 3 generated the most accurate predictions with a root mean square (RMS) error of 1:2 kcal mol\textasciicircum-1 for the entire data set. It was found that the deficiency of the standard OPLS-AA parameters, protocol 1(RMS error 2.4 kcal mol\textasciicircum-1 overall), was mostly due to compounds with more than three chlo- rine substituents on an aromatic ring. For this latter subset, the RMS errors were 1:4 kcal mol\textasciicircum-1 (protocol 3) and 4:3 kcal mol\textasciicircum-1 (protocol 1), respectively. We propose new OPLS-AA atom types for aromatic carbon and chlorine atoms in rings with C4 Cl-substituents that perform better than the best QM-based approach, resulting in an RMS error of 1:2 kcal mol\textasciicircum-1 for these difficult compounds.

@article{lindau_coarse_2012,
	title = {Coarse grain simulations reveal movement of synaptobrevin {C} terminus in response to piconewton forces},
	volume = {103},
	url = {http://doi.org/10.1016/j.bpj.2012.08.007},
	doi = {10.1016/j.bpj.2012.08.007},
	abstract = {Fusion of neurosecretory vesicles with the plasma membrane is mediated by SNARE proteins, which transfer a force to the membranes. However, the mechanism by which this force transfer induces fusion pore formation is still unknown. The neuronal vesicular SNARE protein synaptobrevin 2 (syb2) is anchored in the vesicle membrane by a single C terminal transmembrane (TM) helix. In coarse grain molecular dynamics simulations self-assembly of the membrane occurred with the syb2 TM domain inserted as expected from experimental data. The free energy profile for the position of the syb2 membrane anchor in the membrane was determined using umbrella sampling. To predict the free energy landscapes for pulling syb2 towards the extravesicular side of the membrane, which is the direction of the force transfer from the SNARE complex, harmonic potentials were applied to the peptide in its unbiased position, pulling it towards new biased equilibrium positions. Applying a constant pulling force of 160 pN in the simulation detaches the synaptobrevin C terminus from the vesicle's inner leaflet lipid head groups within 100 ns and pulls the C terminus deeper into the membrane. This C terminal movement should occur on the physiological millisecond time scale at 120 pN force. It is facilitated and hindered by specific mutations in parallel with experimentally observed facilitation and inhibition of fusion. These results suggest a mechanism where fusion pore formation is induced by movement of the charged syb2 C terminus into the hydrophobic core of the membrane in response to the force generated by C terminal zippering of the SNARE complex. This displacement of the charged C terminus is expected to destabilize the membrane providing a plausible pathway to fusion pore formation.},
	journal = {Biophys J},
	author = {Lindau, Manfred and Hall, Benjamin A. and Chetwynd, Alan and Beckstein, Oliver and Sansom, Mark S. P.},
	year = {2012},
	keywords = {Exocytosis, Molecular simulation, PMF, SNARE, coarse grained, force, membrane, metastable states, synaptobrevin},
	pages = {959--969}
}

Fusion of neurosecretory vesicles with the plasma membrane is mediated by SNARE proteins, which transfer a force to the membranes. However, the mechanism by which this force transfer induces fusion pore formation is still unknown. The neuronal vesicular SNARE protein synaptobrevin 2 (syb2) is anchored in the vesicle membrane by a single C terminal transmembrane (TM) helix. In coarse grain molecular dynamics simulations self-assembly of the membrane occurred with the syb2 TM domain inserted as expected from experimental data. The free energy profile for the position of the syb2 membrane anchor in the membrane was determined using umbrella sampling. To predict the free energy landscapes for pulling syb2 towards the extravesicular side of the membrane, which is the direction of the force transfer from the SNARE complex, harmonic potentials were applied to the peptide in its unbiased position, pulling it towards new biased equilibrium positions. Applying a constant pulling force of 160 pN in the simulation detaches the synaptobrevin C terminus from the vesicle's inner leaflet lipid head groups within 100 ns and pulls the C terminus deeper into the membrane. This C terminal movement should occur on the physiological millisecond time scale at 120 pN force. It is facilitated and hindered by specific mutations in parallel with experimentally observed facilitation and inhibition of fusion. These results suggest a mechanism where fusion pore formation is induced by movement of the charged syb2 C terminus into the hydrophobic core of the membrane in response to the force generated by C terminal zippering of the SNARE complex. This displacement of the charged C terminus is expected to destabilize the membrane providing a plausible pathway to fusion pore formation.

@article{webster_novel_2012,
	title = {A novel congenital myasthenic syndrome due to decreased acetylcholine receptor ion channel conductance},
	volume = {135},
	url = {htpp://doi.org/10.1093/brain/aws016},
	doi = {10.1093/brain/aws016},
	abstract = {Muscle acetylcholine receptor ion channels mediate neurotransmission by depolarising the post-synaptic membrane at the neuromuscular junction. Inherited disorders of neuromuscular transmission, termed congenital myasthenic syndromes, are commonly caused by mutations in genes encoding the five subunits of the AChR that severely reduce endplate AChR numbers and/or cause kinetic abnormalities of AChR function. We tracked the cause of the myasthenic disorder in a woman with onset of first symptoms at birth, who displayed mildly progressive bulbar, respiratory and generalised limb weakness with ptosis and ophthalmoplegia. Direct DNA sequencing revealed heteroallelic mutations in exon 8 of the AChR epsilon subunit gene. On one allele there is the missense substitution p.εP282R, and on the second allele a deletion, c.798\_800delCTT, that results in the loss of a single amino acid, residue F266, within the M2 transmembrane domain. When AChR harbouring these mutations were expressed in HEK 293 cells, the p.εP282R mutation caused severely reduced expression on the cell surface whereas p.εΔF266 gave robust surface expression. Single channel analysis for p.εΔF266 AChR channels showed the longest burst duration population was not different from wild type AChR (4.39 \${\textbackslash}pm\$ 0.6 ms vs. 4.68 \${\textbackslash}pm\$ 0.7 ms, n= 5 each) but that the amplitude of channel openings was reduced. Channel amplitudes at different holding potentials showed that single channel conductance was significantly reduced in p.εΔF266 AChR channels (42.7 \${\textbackslash}pm\$ 1.4 pS, n= 8, compared with 70.9 \${\textbackslash}pm\$ 1.6 pS for wild type, n=6). Although a phenylalanine residue at this position within M2 is conserved through-out ligand gated excitatory cys-loop channel subunits, deletion of equivalent residues in the other subunits of muscle AChR did not have equivalent effects. Modelling the impact of p.εΔF266 revealed only a minor alteration to channel structure. In this study we uncover the novel mechanism of reduced AChR channel conductance as an underlying cause of congenital myasthenic syndrome, with the `low conductance' phenotype that results from the p.εΔF266 deletion mutation revealed by the coinheritance of the low expressor mutation p.εP282R.},
	number = {4},
	journal = {Brain},
	author = {Webster, Richard and Maxwell, Susan and Spearman, Hayley and Tai, Kaihsu and Beckstein, Oliver and Sansom, Mark and Beeson, David},
	year = {2012},
	keywords = {: AChR, GLIC, MODELLER, congenital myasthenic syndrome, deletion mutation, ion-channel conductance, mutant, nAChR},
	pages = {1070--1080}
}

Muscle acetylcholine receptor ion channels mediate neurotransmission by depolarising the post-synaptic membrane at the neuromuscular junction. Inherited disorders of neuromuscular transmission, termed congenital myasthenic syndromes, are commonly caused by mutations in genes encoding the five subunits of the AChR that severely reduce endplate AChR numbers and/or cause kinetic abnormalities of AChR function. We tracked the cause of the myasthenic disorder in a woman with onset of first symptoms at birth, who displayed mildly progressive bulbar, respiratory and generalised limb weakness with ptosis and ophthalmoplegia. Direct DNA sequencing revealed heteroallelic mutations in exon 8 of the AChR epsilon subunit gene. On one allele there is the missense substitution p.εP282R, and on the second allele a deletion, c.798_800delCTT, that results in the loss of a single amino acid, residue F266, within the M2 transmembrane domain. When AChR harbouring these mutations were expressed in HEK 293 cells, the p.εP282R mutation caused severely reduced expression on the cell surface whereas p.εΔF266 gave robust surface expression. Single channel analysis for p.εΔF266 AChR channels showed the longest burst duration population was not different from wild type AChR (4.39 \${\textbackslash}pm\$ 0.6 ms vs. 4.68 \${\textbackslash}pm\$ 0.7 ms, n= 5 each) but that the amplitude of channel openings was reduced. Channel amplitudes at different holding potentials showed that single channel conductance was significantly reduced in p.εΔF266 AChR channels (42.7 \${\textbackslash}pm\$ 1.4 pS, n= 8, compared with 70.9 \${\textbackslash}pm\$ 1.6 pS for wild type, n=6). Although a phenylalanine residue at this position within M2 is conserved through-out ligand gated excitatory cys-loop channel subunits, deletion of equivalent residues in the other subunits of muscle AChR did not have equivalent effects. Modelling the impact of p.εΔF266 revealed only a minor alteration to channel structure. In this study we uncover the novel mechanism of reduced AChR channel conductance as an underlying cause of congenital myasthenic syndrome, with the `low conductance' phenotype that results from the p.εΔF266 deletion mutation revealed by the coinheritance of the low expressor mutation p.εP282R.

@article{pongprayoon_biomimetic_2012,
	title = {Biomimetic {Design} of a {Brush}-{Like} {Nanopore}: {Simulation} {Studies}},
	volume = {116},
	url = {http://pubs.acs.org/doi/abs/10.1021/jp206754w},
	doi = {10.1021/jp206754w},
	abstract = {Combining a high degree of selectivity and nanoscale dimensions, biological pores are attractive potential components for nanotechnology devices and applications. Biomimetic design will facilitate production of stable synthetic nanopores with defined functionality. Bacterial porins offer a good source of possible templates for such nanopores as they form stable, selective pores in lipid bilayers. Molecular dynamics simulations have been used to design simple model nanopores with permeation free energy profiles that can be made to mimic a template protein, the OprP porin, which forms pores selective for anions. In particular we explored the effects of varying the nature of pore-lining groups on free energy profiles for phosphate and chloride ions along the pore axis and the total charge of the permeation pathway of the pore. Cationic “sidechains” lining the model nanopore are required to model the local detail the OprP permeation landscape whereas the total charge contributes to its magnitude. These studies indicate that a locally accurate biomimetic design has captured the essentials of the structure/function relationship of the parent protein.},
	number = {1},
	journal = {J Phys Chem B},
	author = {Pongprayoon, Prapasiri and Beckstein, Oliver and Sansom, Mark S. P.},
	year = {2012},
	keywords = {Kd, OprP, PMF, anion, nano pores, phosphate},
	pages = {462--468}
}

Combining a high degree of selectivity and nanoscale dimensions, biological pores are attractive potential components for nanotechnology devices and applications. Biomimetic design will facilitate production of stable synthetic nanopores with defined functionality. Bacterial porins offer a good source of possible templates for such nanopores as they form stable, selective pores in lipid bilayers. Molecular dynamics simulations have been used to design simple model nanopores with permeation free energy profiles that can be made to mimic a template protein, the OprP porin, which forms pores selective for anions. In particular we explored the effects of varying the nature of pore-lining groups on free energy profiles for phosphate and chloride ions along the pore axis and the total charge of the permeation pathway of the pore. Cationic “sidechains” lining the model nanopore are required to model the local detail the OprP permeation landscape whereas the total charge contributes to its magnitude. These studies indicate that a locally accurate biomimetic design has captured the essentials of the structure/function relationship of the parent protein.

@incollection{weyand_nucleobase-cation-symport-1_2011,
	series = {Encyclopedia of {Inorganic} and {Bioinorganic} {Chemistry}},
	title = {The {Nucleobase}-{Cation}-{Symport}-1 {Family} of {Membrane} {Transport} {Proteins}},
	url = {https://doi.org/10.1002/9781119951438.eibc0685},
	abstract = {The evolutionary relationships of membrane transport proteins of the nucleobase-cation-symport (NCS-1) family from bacteria, fungi, and plants are described. The reported substrates of the NCS-1 family include nucleobases, hydantoins, and vitamins. Secondary active transport of substrate accompanied by a sodium ion, or possibly a proton, is the usual mechanism of energization. A strategy for the amplified expression, purification, and activity assays of bacterial members of the NCS-1 family is described. Conditions are given for the production of diffracting crystals of one member, the Na+-coupled transporter for aromatic hydantoins, `Mhp1', from Microbacterium liquefaciens. The 3D structures of three forms of the Mhp1 protein are discussed in terms of one open-outward, one substrate-occluded, and one inward-open conformation contributing to a molecular dynamics simulation of the alternating-access model of membrane transport. The unexpected similarity of the protein fold of Mhp1 to those of transport proteins, hitherto thought to be from different evolutionary families, is discussed.},
	booktitle = {Handbook of {Metalloproteins}},
	publisher = {Wiley},
	author = {Weyand, Simone and Ma, Pikyee and Saidijam, Massoud and Baldwin, Jocelyn and Beckstein, Oliver and Jackson, Scott and Suzuki, Shun'ichi and Patching, Simon G and Shimamura, Tatsuro and Sansom, Mark S. P. and Iwata, So and Cameron, Alexander D and Baldwin, Stephen A and Henderson, Peter J. F.},
	editor = {Messerschmidt, Albrecht},
	year = {2011},
	keywords = {CodB, HMET 268, MD SIMULATION, Membrane Transport, Mhp1, Na+, PacI, hydantoin, membrane transport protein, nucleobase, review, sodium, transporter structure}
}

The evolutionary relationships of membrane transport proteins of the nucleobase-cation-symport (NCS-1) family from bacteria, fungi, and plants are described. The reported substrates of the NCS-1 family include nucleobases, hydantoins, and vitamins. Secondary active transport of substrate accompanied by a sodium ion, or possibly a proton, is the usual mechanism of energization. A strategy for the amplified expression, purification, and activity assays of bacterial members of the NCS-1 family is described. Conditions are given for the production of diffracting crystals of one member, the Na+-coupled transporter for aromatic hydantoins, `Mhp1', from Microbacterium liquefaciens. The 3D structures of three forms of the Mhp1 protein are discussed in terms of one open-outward, one substrate-occluded, and one inward-open conformation contributing to a molecular dynamics simulation of the alternating-access model of membrane transport. The unexpected similarity of the protein fold of Mhp1 to those of transport proteins, hitherto thought to be from different evolutionary families, is discussed.

@article{michaud-agrawal_mdanalysis:_2011,
	title = {{MDAnalysis}: {A} {Toolkit} for the {Analysis} of {Molecular} {Dynamics} {Simulations}},
	volume = {32},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144279/},
	doi = {10.1002/jcc.21787},
	abstract = {MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU Public License from http://mdanalysis.googlecode.com.},
	journal = {J Comp Chem},
	author = {Michaud-Agrawal, Naveen and Denning, Elizabeth Jane and Woolf, Thomas B. and Beckstein, Oliver},
	year = {2011},
	keywords = {MDAnalysis, Python, molecular dynamics (MD) simulation},
	pages = {2319--2327}
}

MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU Public License from http://mdanalysis.googlecode.com.

@article{perilla_computing_2011,
	title = {Computing ensembles of transitions from stable states: {Dynamic} {Importance} {Sampling}},
	volume = {32},
	url = {http://doi.org/10.1002/jcc.21564},
	doi = {10.1002/jcc.21564},
	abstract = {There is an increasing dataset of solved biomolecular structures in more than one conformation and increasing evidence that large-scale conformational change is critical for biomolecular function. In this article, we present our implementation of a dynamic importance sampling (DIMS) algorithm that is directed toward improving our understanding of important intermediate states between experimentally defined starting and ending points. This complements traditional molecular dynamics methods where most of the sampling time is spent in the stable free energy wells defined by these initial and final points. As such, the algorithm creates a candidate set of transitions that provide insights for the much slower and probably most important, functionally relevant degrees of freedom. The method is implemented in the program CHARMM and is tested on six systems of growing size and complexity. These systems, the folding of Protein A and of Protein G, the conformational changes in the calcium sensor S100A6, the glucose-galactose-binding protein, maltodextrin, and lactoferrin, are also compared against other approaches that have been suggested in the literature. The results suggest good sampling on a diverse set of intermediates for all six systems with an ability to control the bias and thus to sample distributions of trajectories for the analysis of intermediate states.},
	number = {2},
	journal = {J Comp Chem},
	author = {Perilla, J. R. and Beckstein, O. and Denning, E. J. and Woolf, T.B.},
	year = {2011},
	keywords = {3-HELIX BUNDLE, CONFORMATIONAL CHANGE, DIMS, MBP, S1006A, cooperative motion, dynamic importance sampling, enhanced sampling, glucose/galactose binding protein, kinetics, lactoferrin, maltose binding protein, molecular dynamics, protein dynamics},
	pages = {186--209}
}

There is an increasing dataset of solved biomolecular structures in more than one conformation and increasing evidence that large-scale conformational change is critical for biomolecular function. In this article, we present our implementation of a dynamic importance sampling (DIMS) algorithm that is directed toward improving our understanding of important intermediate states between experimentally defined starting and ending points. This complements traditional molecular dynamics methods where most of the sampling time is spent in the stable free energy wells defined by these initial and final points. As such, the algorithm creates a candidate set of transitions that provide insights for the much slower and probably most important, functionally relevant degrees of freedom. The method is implemented in the program CHARMM and is tested on six systems of growing size and complexity. These systems, the folding of Protein A and of Protein G, the conformational changes in the calcium sensor S100A6, the glucose-galactose-binding protein, maltodextrin, and lactoferrin, are also compared against other approaches that have been suggested in the literature. The results suggest good sampling on a diverse set of intermediates for all six systems with an ability to control the bias and thus to sample distributions of trajectories for the analysis of intermediate states.

@article{weyand_alternating_2011,
	title = {The alternating access mechanism of transport as observed in the sodium-hydantoin transporter {Mhp}1},
	volume = {18},
	url = {http://doi.org/10.1107/S0909049510032449},
	doi = {10.1107/S0909049510032449},
	abstract = {Secondary active transporters move molecules across cell membranes by coupling this process to the energetically favourable downhill movement of ions or protons along an electrochemical gradient. They function by the alternating access model of transport in which, through conformational changes, the substrate binding site alternately faces either side of the membrane. Owing to the difficulties in obtaining the crystal structure of a single transporter in different conformational states, relatively little structural information is known to explain how this process occurs. Here, the structure of the sodium-benzylhydantoin transporter, Mhp1, from Microbacterium liquefaciens, has been determined in three conformational states; from this a mechanism is proposed for switching from the outward-facing open conformation through an occluded structure to the inward-facing open state.},
	number = {1},
	journal = {J. Synchrotron Rad.},
	author = {Weyand, Simone and Shimamura, Tatsuro and Beckstein, Oliver and Sansom, Mark S. P. and Iwata, So and Henderson, Peter J. F. and Cameron, Alexander D.},
	year = {2011},
	keywords = {Membrane Transport, Mhp1, alternating access, hydantoins, transport protein},
	pages = {20--23}
}

Secondary active transporters move molecules across cell membranes by coupling this process to the energetically favourable downhill movement of ions or protons along an electrochemical gradient. They function by the alternating access model of transport in which, through conformational changes, the substrate binding site alternately faces either side of the membrane. Owing to the difficulties in obtaining the crystal structure of a single transporter in different conformational states, relatively little structural information is known to explain how this process occurs. Here, the structure of the sodium-benzylhydantoin transporter, Mhp1, from Microbacterium liquefaciens, has been determined in three conformational states; from this a mechanism is proposed for switching from the outward-facing open conformation through an occluded structure to the inward-facing open state.

@article{shimamura_molecular_2010,
	title = {Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter {Mhp}1},
	volume = {328},
	url = {http://doi.org/10.1126/science.1186303},
	doi = {10.1126/science.1186303},
	abstract = {The structure of the sodium-benzylhydantoin transport protein Mhp1 from Microbacterium liquefaciens comprises a five-helix inverted repeat, which is widespread among secondary transporters. Here, we report the crystal structure of an inward-facing conformation of Mhp1 at 3.8 angstroms resolution, complementing its previously described structures in outward-facing and occluded states. From analyses of the three structures and molecular dynamics simulations, we propose a mechanism for the transport cycle in Mhp1. Switching from the outward- to the inward-facing state, to effect the inward release of sodium and benzylhydantoin, is primarily achieved by a rigid body movement of transmembrane helices 3, 4, 8, and 9 relative to the rest of the protein. This forms the basis of an alternating access mechanism applicable to many transporters of this emerging superfamily.},
	number = {5977},
	journal = {Science},
	author = {Shimamura, Tatsuro and Weyand, Simone and Beckstein, Oliver and Rutherford, Nicholas G and Hadden, Jonathan M and Sharples, David and Sansom, Mark S P and Iwata, So and Henderson, Peter J F and Cameron, Alexander D},
	year = {2010},
	keywords = {DIMS, LeuT, MD SIMULATION, Mhp1},
	pages = {470--473}
}

The structure of the sodium-benzylhydantoin transport protein Mhp1 from Microbacterium liquefaciens comprises a five-helix inverted repeat, which is widespread among secondary transporters. Here, we report the crystal structure of an inward-facing conformation of Mhp1 at 3.8 angstroms resolution, complementing its previously described structures in outward-facing and occluded states. From analyses of the three structures and molecular dynamics simulations, we propose a mechanism for the transport cycle in Mhp1. Switching from the outward- to the inward-facing state, to effect the inward release of sodium and benzylhydantoin, is primarily achieved by a rigid body movement of transmembrane helices 3, 4, 8, and 9 relative to the rest of the protein. This forms the basis of an alternating access mechanism applicable to many transporters of this emerging superfamily.

@article{domanski_lipidbook:_2010,
	title = {Lipidbook: {A} {Public} {Repository} for {Force}-{Field} {Parameters} {Used} in {Membrane} {Simulations}},
	volume = {236},
	url = {http://dx.doi.org/10.1007/s00232-010-9296-8},
	doi = {10.1007/s00232-010-9296-8},
	number = {3},
	journal = {J Membr Biol},
	author = {Domański, Jan and Stansfeld, Phillip and Sansom, Mark and Beckstein, Oliver},
	year = {2010},
	keywords = {Biomedical and Life Sciences, Lipidbook, WebCite, database, force field parameters, lipids, web server},
	pages = {255--258}
}

@article{beckstein_new_2009,
	title = {New and {Notable}: {Teaching} old coefficients new tricks: new insight into the meaning of the osmotic and diffusive permeation coefficients.},
	volume = {96},
	issn = {1542-0086 (Electronic)},
	url = {http://doi.org/10.1016/j.bpj.2008.10.048},
	doi = {10.1016/j.bpj.2008.10.048},
	language = {eng},
	number = {3},
	journal = {Biophys J},
	author = {Beckstein, Oliver},
	month = feb,
	year = {2009},
	keywords = {liquid vapor oscillations, model pores, news \& views},
	pages = {763--764}
}

@article{beckstein_zipping_2009,
	title = {Zipping and {Unzipping} of {Adenylate} {Kinase}: {Atomistic} {Insights} into the {Ensemble} of {Open} ↔ {Closed} {Transitions}},
	volume = {394},
	url = {http://doi.org/10.1016/j.jmb.2009.09.009},
	doi = {10.1016/j.jmb.2009.09.009},
	abstract = {Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free-energy calculations and with our new dynamic importance sampling (DIMS) molecular dynamics method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular, four ionic bonds that open in a sequential, zipper-like fashion and, thus, dominate the free-energy landscape of the transition are identified. Transitions between the closed and open conformations only have to overcome moderate free-energy barriers. Unexpectedly, the closed state and the open state encompass broad free-energy basins that contain conformations differing in domain hinge motions by up to 40$^{\textrm{{\textbackslash}circ\$}}$. The significance of these extended states is discussed in relation to recent experimental Förster resonance energy transfer measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS molecular dynamics computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK.},
	number = {1},
	journal = {J Mol Biol},
	author = {Beckstein, Oliver and Denning, Elizabeth J. and Perilla, Juan R. and Woolf, Thomas B.},
	year = {2009},
	keywords = {AdK, DIMS, Free energy, PMF, adenylate kinase, importance sampling, molecular dynamics, transitions},
	pages = {160--176}
}

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free-energy calculations and with our new dynamic importance sampling (DIMS) molecular dynamics method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular, four ionic bonds that open in a sequential, zipper-like fashion and, thus, dominate the free-energy landscape of the transition are identified. Transitions between the closed and open conformations only have to overcome moderate free-energy barriers. Unexpectedly, the closed state and the open state encompass broad free-energy basins that contain conformations differing in domain hinge motions by up to 40$^{\textrm{{\textbackslash}circ\$$. The significance of these extended states is discussed in relation to recent experimental Förster resonance energy transfer measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS molecular dynamics computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK.

@article{furini_permeation_2009,
	title = {Permeation of water through the {KcsA} {K}⁺ channel.},
	volume = {74},
	issn = {1097-0134 (Electronic)},
	url = {http://doi.org/10.1002/prot.22163},
	doi = {10.1002/prot.22163},
	abstract = {Previous studies have reported that the KcsA potassium channel has an osmotic permeability coefficient of 4.8 x 10(-12) cm3/s, giving it a significantly higher osmotic permeability coefficient than that of some membrane channels specialized in water transport. This high osmotic permeability is proposed to occur when the channel is depleted of potassium ions, the presence of which slow down the water permeation process. The atomic structure of the potassium-depleted KcsA channel and the mechanisms of water permeation have not been well characterized so far. Here, all-atom molecular dynamics simulations, in conjunction with an umbrella sampling strategy and a nonequilibrium approach to simulate pressure gradients are employed to illustrate the permeation of water in the absence of ions through the KcsA K+ channel. Equilibrium molecular dynamics simulations (95 ns combined total length) identified a possible structure of the potassium-depleted KcsA channel, and umbrella sampling calculations (160 ns combined total length) revealed that this structure is not permeable by water molecules moving along the channel axis. The simulation of a pressure gradient across the channel (30 ns combined total length) identified an alternative permeation pathway with a computed osmotic permeability of approximately (2.7 +/- 0.9) x 10(-13) cm3/s. Water fluxes along this pathway did not proceed through collective water motions or transitions to vapor state. All of the major results of this study were robust against variations in a wide set of simulation parameters (force field, water model, membrane model, and channel conformation).},
	language = {eng},
	number = {2},
	journal = {Proteins},
	author = {Furini, Simone and Beckstein, Oliver and Domene, Carmen},
	year = {2009},
	keywords = {liquid vapor oscillations, molecular dynamics, osmotic permeability, potassium channels, pressure-induced water transport},
	pages = {437--448}
}

Previous studies have reported that the KcsA potassium channel has an osmotic permeability coefficient of 4.8 x 10(-12) cm3/s, giving it a significantly higher osmotic permeability coefficient than that of some membrane channels specialized in water transport. This high osmotic permeability is proposed to occur when the channel is depleted of potassium ions, the presence of which slow down the water permeation process. The atomic structure of the potassium-depleted KcsA channel and the mechanisms of water permeation have not been well characterized so far. Here, all-atom molecular dynamics simulations, in conjunction with an umbrella sampling strategy and a nonequilibrium approach to simulate pressure gradients are employed to illustrate the permeation of water in the absence of ions through the KcsA K+ channel. Equilibrium molecular dynamics simulations (95 ns combined total length) identified a possible structure of the potassium-depleted KcsA channel, and umbrella sampling calculations (160 ns combined total length) revealed that this structure is not permeable by water molecules moving along the channel axis. The simulation of a pressure gradient across the channel (30 ns combined total length) identified an alternative permeation pathway with a computed osmotic permeability of approximately (2.7 +/- 0.9) x 10(-13) cm3/s. Water fluxes along this pathway did not proceed through collective water motions or transitions to vapor state. All of the major results of this study were robust against variations in a wide set of simulation parameters (force field, water model, membrane model, and channel conformation).

@article{pongprayoon_simulations_2009,
	title = {Simulations of anion transport through {OprP} reveal the molecular basis for high affinity and selectivity for phosphate},
	volume = {106},
	url = {http://doi.org/10.1073/pnas.0907315106},
	doi = {10.1073/pnas.0907315106},
	abstract = {The outer membrane protein OprP from Pseudomonas aeruginosa forms a phosphate selective pore. To understand the mechanism of phosphate permeation and selectivity, we used three simulation techniques [equilibrium molecular dynamics simulations, steered molecular dynamics, and calculation of a potential of mean force (PMF)]. The PMF for phosphate reveals a deep free energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of ≈8 kT, are identified close to the L3 loop in the most constricted region of the pore. A dissociation constant for phosphate of 6 μM is computed from the PMF, within the range of reported experimental values. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a “charged brush” to facilitate phosphate passage between the two subsites. OprP also binds chloride, but less strongly than phosphate, as calculated from a Cl− PMF. The difference in affinity and hence selectivity is due to the “Lys-cluster” motif, the positive charges of which interact strongly with a partially dehydrated phosphate ion but are shielded from a Cl− by the hydration shell of the smaller ion. Our simulations suggest that OprP does not conform to the conventional picture of a channel with relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.},
	number = {51},
	journal = {Proc Natl Acad Sci U S A},
	author = {Pongprayoon, Prapasiri and Beckstein, Oliver and Wee, Chze-Ling and Sansom, Mark S. P.},
	year = {2009},
	keywords = {MD SIMULATION, Molecular dynamics simulation, OprP, anion selectivity, free energy profile, hydration, phosphate chloride, potential of mean force},
	pages = {21614--21618}
}

The outer membrane protein OprP from Pseudomonas aeruginosa forms a phosphate selective pore. To understand the mechanism of phosphate permeation and selectivity, we used three simulation techniques [equilibrium molecular dynamics simulations, steered molecular dynamics, and calculation of a potential of mean force (PMF)]. The PMF for phosphate reveals a deep free energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of ≈8 kT, are identified close to the L3 loop in the most constricted region of the pore. A dissociation constant for phosphate of 6 μM is computed from the PMF, within the range of reported experimental values. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a “charged brush” to facilitate phosphate passage between the two subsites. OprP also binds chloride, but less strongly than phosphate, as calculated from a Cl− PMF. The difference in affinity and hence selectivity is due to the “Lys-cluster” motif, the positive charges of which interact strongly with a partially dehydrated phosphate ion but are shielded from a Cl− by the hydration shell of the smaller ion. Our simulations suggest that OprP does not conform to the conventional picture of a channel with relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.

@article{millar_brownian_2008,
	title = {Brownian {Simulation} of {Charge} {Transport} in α-{Haemolysin}},
	volume = {7},
	url = {http://doi.org/10.1007/s10825-008-0230-6},
	doi = {10.1007/s10825-008-0230-6},
	abstract = {In this paper we present the results of self-consistent Brownian Dynamics simulations of the ion Channel alpha-Haemolysin. We show that with simple scaling, excellent agreement with experimental measurement of the current voltage characteristics of this molecule.},
	number = {1},
	journal = {Journal of Computational Electronics},
	author = {Millar, C. and Madathil, R. and Beckstein, O. and Sansom, M. S. P. and Roy, S. and Asenov, A.},
	month = mar,
	year = {2008},
	keywords = {BROWNIAN DYNAMICS, Current-Voltage, Simulation, alpha-Haemolysin, drift diffusion, experiment},
	pages = {28--33}
}

In this paper we present the results of self-consistent Brownian Dynamics simulations of the ion Channel alpha-Haemolysin. We show that with simple scaling, excellent agreement with experimental measurement of the current voltage characteristics of this molecule.

@unpublished{rogers_opening_2008,
	title = {Opening a hydrophobic gate: the nicotinic acetylcholine receptor as an example},
	url = {http://arxiv.org/abs/0902.1417},
	author = {Rogers, Sarah E. and Tai, Kaihsu and Beckstein, Oliver and Sansom, Mark S. P.},
	year = {2008},
	note = {arXiv:0902.1417v1},
	keywords = {NICOTINIC ACETYLCHOLINE RECEPTOR, Poisson-Boltzmann, electrostatics, gating, ion channel, molecular dynamics, nAChR, transmembrane domain}
}

@article{millar_continuum_2007,
	title = {Continuum vs. particle simulations of model nano-pores},
	volume = {6},
	url = {http://dx.doi.org/10.1007/s10825-006-0131-5},
	doi = {10.1007/s10825-006-0131-5},
	abstract = {The class of biological macromolecules known as ion channels are becoming of great interest to physical scientists and engineers, as well as biophysicists and pharmacologists. The long term stability and wide range of properties displayed by this large group of proteins makes them one of the most popular contenders to bridge the gap between solid state electronics and biological systems. However, many of the most basic mechanisms by which these molecules conduct ions are still poorly understood. We present a comparison between the behaviour of continuum and discrete particle methods in simulations of sub-nanometre diameter model pores. Using Drift Diffusion and Self Consistent Brownian dynamics simulations we demonstrate that, without serious modification, continuum methods are insufficient to model even simple pores of these dimensions.},
	number = {1},
	journal = {Journal of Computational Electronics},
	author = {Millar, C. and Roy, S. and Beckstein, O. and Sansom, M. and Asenov, A.},
	year = {2007},
	keywords = {BROWNIAN DYNAMICS, CONTINUUM ELECTROSTATICS, pores},
	pages = {367--371}
}

The class of biological macromolecules known as ion channels are becoming of great interest to physical scientists and engineers, as well as biophysicists and pharmacologists. The long term stability and wide range of properties displayed by this large group of proteins makes them one of the most popular contenders to bridge the gap between solid state electronics and biological systems. However, many of the most basic mechanisms by which these molecules conduct ions are still poorly understood. We present a comparison between the behaviour of continuum and discrete particle methods in simulations of sub-nanometre diameter model pores. Using Drift Diffusion and Self Consistent Brownian dynamics simulations we demonstrate that, without serious modification, continuum methods are insufficient to model even simple pores of these dimensions.

@article{beckstein_hydrophobic_2006,
	title = {A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor},
	volume = {3},
	url = {http://stacks.iop.org/1478-3975/3/147},
	doi = {10.1088/1478-3975/3/2/007},
	abstract = {The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the 'Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine, gamma-aminobutyric acid and serotonin. Cryo-electron microscopy has yielded a three-dimensional structure of the nAChR in its closed state. However, the exact nature and location of the channel gate remains uncertain. Although the transmembrane pore is constricted close to its center, it is not completely occluded. Rather, the pore has a central hydrophobic zone of radius about 3 angstrom. Model calculations suggest that such a constriction may form a hydrophobic gate, preventing movement of ions through a channel. We present a detailed and quantitative simulation study of the hydrophobic gating model of the nicotinic receptor, in order to fully evaluate this hypothesis. We demonstrate that the hydrophobic constriction of the nAChR pore indeed forms a closed gate. Potential of mean force (PMF) calculations reveal that the constriction presents a barrier of height about 10 kT to the permeation of sodium ions, placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 angstrom radius hydrophobic pore can form a functional barrier to the permeation of a 1 angstrom radius Na+ ion. Using a united-atom force field for the protein instead of an all-atom one retains the qualitative features but results in differing conductances, showing that the PMF is sensitive to the detailed molecular interactions.},
	number = {2},
	journal = {Physical Biology},
	author = {Beckstein, Oliver and Sansom, Mark S. P.},
	year = {2006},
	keywords = {5-HT3A RECEPTOR, BROWNIAN DYNAMICS, CRYSTAL-STRUCTURE, DESENSITIZED STATES, FORCE-FIELDS, GATING MECHANISM, MECHANOSENSITIVE CHANNEL, MOLECULAR-DYNAMICS, POISSON-BOLTZMANN EQUATION, SMALL-CONDUCTANCE},
	pages = {147--159}
}

The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the 'Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine, gamma-aminobutyric acid and serotonin. Cryo-electron microscopy has yielded a three-dimensional structure of the nAChR in its closed state. However, the exact nature and location of the channel gate remains uncertain. Although the transmembrane pore is constricted close to its center, it is not completely occluded. Rather, the pore has a central hydrophobic zone of radius about 3 angstrom. Model calculations suggest that such a constriction may form a hydrophobic gate, preventing movement of ions through a channel. We present a detailed and quantitative simulation study of the hydrophobic gating model of the nicotinic receptor, in order to fully evaluate this hypothesis. We demonstrate that the hydrophobic constriction of the nAChR pore indeed forms a closed gate. Potential of mean force (PMF) calculations reveal that the constriction presents a barrier of height about 10 kT to the permeation of sodium ions, placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 angstrom radius hydrophobic pore can form a functional barrier to the permeation of a 1 angstrom radius Na+ ion. Using a united-atom force field for the protein instead of an all-atom one retains the qualitative features but results in differing conductances, showing that the PMF is sensitive to the detailed molecular interactions.

@phdthesis{beckstein_principles_2005,
	address = {Oxford, UK},
	type = {{DPhil} {Thesis}},
	title = {Principles of {Gating} {Mechanisms} of {Ion} {Channels}},
	url = {http://doi.org/10.6084/m9.figshare.1166494},
	abstract = {Ion channels such as the nicotinic acetylcholine receptor (nAChR) fulfil essential roles in fast nerve transmission and cell signalling by converting an external signal into an ionic current, which in turn triggers further down-stream signalling events in the cell. Increasing structural evidence suggests that the actual mechanisms by which channels gate i.e. switch their ion permeability) are fairly universal: Conduction pathways are either physically occluded by localised sidechains or the pore is narrowed by large-scale protein motions so that a constriction lined by hydrophobic sidechains is formed. In this work the latter mechanism, termed hydrophobic gating, is investigated by atomistic computer simulations.
Simple hydrophobic model pores were constructed with dimensions estimated for the putative gate region of nAChR (length 0.8 nm, radius varied between 0.15 nm and 1.0 nm). In long classical molecular dynamics (MD) simulations, water confined in the pore was found to oscillate between a liquid and a vapour phase on a nano second time scale. Water would rarely permeate a pore less wide than three water molecules. A simple thermodynamic model based on surface energies was developed, which explains the observed liquid-vapour oscillations and their dependence on pore radius and surface hydrophobicity. Similarly, sodium ion flux is only appreciable for pore radii greater than 0.6 nm. Calculation of the free energy profile of translocating ions showed barriers to permeation of greater 10 kT for pore radii less than 0.4 nm. Comparison to continuum-electrostatic Poisson-Boltzmann calculations indicates that the behaviour of the solvent, i.e. water, is crucial for a correct description of ions in apolar pores. Together, these results indicate that a hydrophobic constriction site can act as a hydrophobic gate.
An ongoing debate concerns the nature and position of the gate in nAChR. Based on the recent cryo-electron microscopy structure of the transmembrane domain at 4 Å resolution, and using techniques established for the model pores, equilibrium densities and free energy profiles were calculated for Na+, Cl-, and water. It was found that ions would have to overcome a sizable free energy barrier of about 10 kT at a hydrophobic girdle between residues L9' and V13', previously implicated in gating. This suggests strongly that nAChR contains a hydrophobic gate. Furthermore, charged rings at both ends of the pore act as concentrators of ions up to about six times the bulk concentration; an effect which would increase the ion current in the open state. The robustness of the results is discussed with respect to different parameter sets (force fields) and the applied modelling procedure.},
	language = {English},
	urldate = {2014-11-06TZ},
	school = {University of Oxford},
	author = {Beckstein, Oliver},
	year = {2005},
	keywords = {Gibbs free energy, Ion Channels, gating, hydrophobic gating, hydrophobicity, ion permeation, molecular dynamics, potential of mean force, water}
}

Ion channels such as the nicotinic acetylcholine receptor (nAChR) fulfil essential roles in fast nerve transmission and cell signalling by converting an external signal into an ionic current, which in turn triggers further down-stream signalling events in the cell. Increasing structural evidence suggests that the actual mechanisms by which channels gate i.e. switch their ion permeability) are fairly universal: Conduction pathways are either physically occluded by localised sidechains or the pore is narrowed by large-scale protein motions so that a constriction lined by hydrophobic sidechains is formed. In this work the latter mechanism, termed hydrophobic gating, is investigated by atomistic computer simulations. Simple hydrophobic model pores were constructed with dimensions estimated for the putative gate region of nAChR (length 0.8 nm, radius varied between 0.15 nm and 1.0 nm). In long classical molecular dynamics (MD) simulations, water confined in the pore was found to oscillate between a liquid and a vapour phase on a nano second time scale. Water would rarely permeate a pore less wide than three water molecules. A simple thermodynamic model based on surface energies was developed, which explains the observed liquid-vapour oscillations and their dependence on pore radius and surface hydrophobicity. Similarly, sodium ion flux is only appreciable for pore radii greater than 0.6 nm. Calculation of the free energy profile of translocating ions showed barriers to permeation of greater 10 kT for pore radii less than 0.4 nm. Comparison to continuum-electrostatic Poisson-Boltzmann calculations indicates that the behaviour of the solvent, i.e. water, is crucial for a correct description of ions in apolar pores. Together, these results indicate that a hydrophobic constriction site can act as a hydrophobic gate. An ongoing debate concerns the nature and position of the gate in nAChR. Based on the recent cryo-electron microscopy structure of the transmembrane domain at 4 Å resolution, and using techniques established for the model pores, equilibrium densities and free energy profiles were calculated for Na+, Cl-, and water. It was found that ions would have to overcome a sizable free energy barrier of about 10 kT at a hydrophobic girdle between residues L9' and V13', previously implicated in gating. This suggests strongly that nAChR contains a hydrophobic gate. Furthermore, charged rings at both ends of the pore act as concentrators of ions up to about six times the bulk concentration; an effect which would increase the ion current in the open state. The robustness of the results is discussed with respect to different parameter sets (force fields) and the applied modelling procedure.

@article{amiri_alpha7_2005,
	title = {The alpha7 nicotinic acetylcholine receptor: {Molecular} modelling, electrostatics and energetics of permeation},
	volume = {22},
	url = {http://dx.doi.org/10.1080/09687860500063340},
	doi = {10.1080/09687860500063340},
	abstract = {The structure of a homopentameric agr7 nicotinic acetylcholine receptor is modelled by combining structural information from two sources: the X-ray structure of a water soluble acetylcholine binding protein from Lymnea stagnalis, and the electron microscopy derived structure of the transmembrane domain of the Torpedo nicotinic receptor. The agr7 nicotinic receptor model is generated by simultaneously optimising: (i) chain connectivity, (ii) avoidance of stereochemically unfavourable contacts, and (iii) contact between the b.beta1-b.beta2 and M2-M3 loops that have been suggested to be involved in transmission of conformational change between the extracellular and transmembrane domains. A Gaussian network model was used to predict patterns of residue mobility in the agr7 model. The results of these calculations suggested a flexibility gradient along the transmembrane domain, with the extracellular end of the domain more flexible that the intracellular end. Poisson-Boltzmann (PB) energy calculations and atomistic (molecular dynamics) simulations were used to estimate the free energy profile of a Na+ ion as a function of position along the axis of the pore-lining M2 helix bundle of the transmembrane domain. Both types of calculation suggested a significant energy barrier to exist in the centre of the (closed) pore, consistent with a 'hydrophobic gating' model. Estimations of the PB energy profile as a function of ionic strength suggest a role of the extracellular domain in determining the cation selectivity of the agr7 nicotinic receptor. These studies illustrate how molecular models of members of the nicotinic receptor superfamily of channels may be used to study structure-function relationships.},
	journal = {Mol Mem Biol},
	author = {Amiri, Shiva and Tai, Kaihsu and Beckstein, Oliver and Biggin, Philip C. and Sansom, Mark S. P.},
	year = {2005},
	keywords = {Gaussian network model, MOLECULAR DYNAMICS CALCULATION, Nicotinic receptor, alpha 7 receptor, electrostatics, molecular modelling, nAChR},
	pages = {151--162}
}

The structure of a homopentameric agr7 nicotinic acetylcholine receptor is modelled by combining structural information from two sources: the X-ray structure of a water soluble acetylcholine binding protein from Lymnea stagnalis, and the electron microscopy derived structure of the transmembrane domain of the Torpedo nicotinic receptor. The agr7 nicotinic receptor model is generated by simultaneously optimising: (i) chain connectivity, (ii) avoidance of stereochemically unfavourable contacts, and (iii) contact between the b.beta1-b.beta2 and M2-M3 loops that have been suggested to be involved in transmission of conformational change between the extracellular and transmembrane domains. A Gaussian network model was used to predict patterns of residue mobility in the agr7 model. The results of these calculations suggested a flexibility gradient along the transmembrane domain, with the extracellular end of the domain more flexible that the intracellular end. Poisson-Boltzmann (PB) energy calculations and atomistic (molecular dynamics) simulations were used to estimate the free energy profile of a Na+ ion as a function of position along the axis of the pore-lining M2 helix bundle of the transmembrane domain. Both types of calculation suggested a significant energy barrier to exist in the centre of the (closed) pore, consistent with a 'hydrophobic gating' model. Estimations of the PB energy profile as a function of ionic strength suggest a role of the extracellular domain in determining the cation selectivity of the agr7 nicotinic receptor. These studies illustrate how molecular models of members of the nicotinic receptor superfamily of channels may be used to study structure-function relationships.

@article{beckstein_influence_2004,
	title = {The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores},
	volume = {1},
	url = {http://stacks.iop.org/1478-3975/1/42},
	doi = {10.1088/1478-3967/1/1/005},
	abstract = {A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of ion channels, e.g. the nicotinic receptor, bacterial mechanosensitive channels (MscL and MscS) and perhaps in some potassium channels (e.g. KcsA, MthK and KvAP). Simplified pore models allow one to investigate the primary characteristics of a conduction pathway, namely its geometry (shape, pore length, and radius), the chemical character of the pore wall surface, and its local flexibility and surface roughness. Our extended (about 0.1 μs) molecular dynamic simulations show that a short hydrophobic pore is closed to water for radii smaller than 0.45 nm. By increasing the polarity of the pore wall (and thus reducing its hydrophobicity) the transition radius can be decreased until for hydrophilic pores liquid water is stable down to a radius comparable to a water molecule's radius. Ions behave similarly but the transition from conducting to non-conducting pores is even steeper and occurs at a radius of 0.65 nm for hydrophobic pores. The presence of water vapour in a constriction zone indicates a barrier for ion permeation. A thermodynamic model can explain the behaviour of water in nanopores in terms of the surface tensions, which leads to a simple measure of \‘hydrophobicity\’ in this context. Furthermore, increased local flexibility decreases the permeability of polar species. An increase in temperature has the same effect, and we hypothesize that both effects can be explained by a decrease in the effective solvent\–surface attraction which in turn leads to an increase in the solvent\–wall surface free energy.},
	number = {1},
	journal = {Physical Biology},
	author = {Beckstein, Oliver and Sansom, Mark S. P.},
	year = {2004},
	pages = {42--52}
}

A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of ion channels, e.g. the nicotinic receptor, bacterial mechanosensitive channels (MscL and MscS) and perhaps in some potassium channels (e.g. KcsA, MthK and KvAP). Simplified pore models allow one to investigate the primary characteristics of a conduction pathway, namely its geometry (shape, pore length, and radius), the chemical character of the pore wall surface, and its local flexibility and surface roughness. Our extended (about 0.1 μs) molecular dynamic simulations show that a short hydrophobic pore is closed to water for radii smaller than 0.45 nm. By increasing the polarity of the pore wall (and thus reducing its hydrophobicity) the transition radius can be decreased until for hydrophilic pores liquid water is stable down to a radius comparable to a water molecule's radius. Ions behave similarly but the transition from conducting to non-conducting pores is even steeper and occurs at a radius of 0.65 nm for hydrophobic pores. The presence of water vapour in a constriction zone indicates a barrier for ion permeation. A thermodynamic model can explain the behaviour of water in nanopores in terms of the surface tensions, which leads to a simple measure of ‘hydrophobicity’ in this context. Furthermore, increased local flexibility decreases the permeability of polar species. An increase in temperature has the same effect, and we hypothesize that both effects can be explained by a decrease in the effective solvent–surface attraction which in turn leads to an increase in the solvent–wall surface free energy.

@article{beckstein_not_2004,
	title = {Not ions alone: {Barriers} to {Ion} {Permeation} in {Nanopores} and {Channels}},
	volume = {126},
	url = {http://dx.doi.org/10.1021/ja045271e},
	doi = {10.1021/ja045271e},
	abstract = {A hydrophobic pore of subnanometer dimensions can appear impermeable to an ion even though its radius is still much wider than that of the ion. Pores of molecular dimensions can be found, for instance, in carbon nanotubes, zeolites, or ion channel proteins. We quantify this barrier to ion permeation by calculating the potential of mean force from umbrella-sampled molecular dynamics simulations and compare them to continuum-electrostatic Poisson-Boltzmann calculations. The latter fail to describe the ion barrier because they do not account for the properties of water in the pore. The barrier originates from the energetic cost to desolvate the ion. Even in wide pores, which could accommodate an ion and its hydration shell, a barrier of several kT remains because the liquid water phase is not stable in the hydrophobic pore. Thus, the properties of the solvent play a crucial role in determining permeation properties of ions in confinement at the molecular scale.},
	number = {45},
	journal = {J Am Chem Soc},
	author = {Beckstein, Oliver and Tai, Kaihsu and Sansom, Mark S. P.},
	year = {2004},
	pages = {14694--14695}
}

A hydrophobic pore of subnanometer dimensions can appear impermeable to an ion even though its radius is still much wider than that of the ion. Pores of molecular dimensions can be found, for instance, in carbon nanotubes, zeolites, or ion channel proteins. We quantify this barrier to ion permeation by calculating the potential of mean force from umbrella-sampled molecular dynamics simulations and compare them to continuum-electrostatic Poisson-Boltzmann calculations. The latter fail to describe the ion barrier because they do not account for the properties of water in the pore. The barrier originates from the energetic cost to desolvate the ion. Even in wide pores, which could accommodate an ion and its hydration shell, a barrier of several kT remains because the liquid water phase is not stable in the hydrophobic pore. Thus, the properties of the solvent play a crucial role in determining permeation properties of ions in confinement at the molecular scale.

@article{beckstein_liquid-vapor_2003,
	title = {Liquid-vapor oscillations of water in hydrophobic nanopores},
	volume = {100},
	url = {http://www.pnas.org/cgi/content/abstract/100/12/7063},
	doi = {10.1073/pnas.1136844100},
	abstract = {Water plays a key role in biological membrane transport. In ion channels and water-conducting pores (aquaporins), one-dimensional confinement in conjunction with strong surface effects changes the physical behavior of water. In molecular dynamics simulations of water in short (0.8 nm) hydrophobic pores the water density in the pore fluctuates on a nanosecond time scale. In long simulations (460 ns in total) at pore radii ranging from 0.35 to 1.0 nm we quantify the kinetics of oscillations between a liquid-filled and a vapor-filled pore. This behavior can be explained as capillary evaporation alternating with capillary condensation, driven by pressure fluctuations in the water outside the pore. The free-energy difference between the two states depends linearly on the radius. The free-energy landscape shows how a metastable liquid state gradually develops with increasing radius. For radii {\textgreater}=0.55 nm it becomes the globally stable state and the vapor state vanishes. One-dimensional confinement affects the dynamic behavior of the water molecules and increases the self diffusion by a factor of 2–3 compared with bulk water. Permeabilities for the narrow pores are of the same order of magnitude as for biological water pores. Water flow is not continuous but occurs in bursts. Our results suggest that simulations aimed at collective phenomena such as hydrophobic effects may require simulation times {\textgreater}50 ns. For water in confined geometries, it is not possible to extrapolate from bulk or short time behavior to longer time scales.},
	journal = {Proc Natl Acad Sci U S A},
	author = {Beckstein, Oliver and Sansom, Mark S. P.},
	year = {2003},
	pages = {7063--7068}
}

Water plays a key role in biological membrane transport. In ion channels and water-conducting pores (aquaporins), one-dimensional confinement in conjunction with strong surface effects changes the physical behavior of water. In molecular dynamics simulations of water in short (0.8 nm) hydrophobic pores the water density in the pore fluctuates on a nanosecond time scale. In long simulations (460 ns in total) at pore radii ranging from 0.35 to 1.0 nm we quantify the kinetics of oscillations between a liquid-filled and a vapor-filled pore. This behavior can be explained as capillary evaporation alternating with capillary condensation, driven by pressure fluctuations in the water outside the pore. The free-energy difference between the two states depends linearly on the radius. The free-energy landscape shows how a metastable liquid state gradually develops with increasing radius. For radii \textgreater=0.55 nm it becomes the globally stable state and the vapor state vanishes. One-dimensional confinement affects the dynamic behavior of the water molecules and increases the self diffusion by a factor of 2–3 compared with bulk water. Permeabilities for the narrow pores are of the same order of magnitude as for biological water pores. Water flow is not continuous but occurs in bursts. Our results suggest that simulations aimed at collective phenomena such as hydrophobic effects may require simulation times \textgreater50 ns. For water in confined geometries, it is not possible to extrapolate from bulk or short time behavior to longer time scales.

@article{beckstein_ion_2003,
	title = {Ion channel gating: insights via molecular simulations},
	volume = {555},
	url = {http://dx.doi.org/10.1016/S0014-5793(03)01151-7},
	journal = {FEBS Lett},
	author = {Beckstein, O. and Biggin, P. C. and Bond, P. and Bright, J. N. and Domene, C. and Grottesi, A. and Holyoake, J. and Sansom, M. S. P.},
	year = {2003},
	pages = {85--90}
}

@inproceedings{sansom_water_2002,
	series = {Novartis {Foundation} {Symposia}},
	title = {Water in ion channels and pores—simulation studies},
	volume = {245},
	url = {http://doi.wiley.com/10.1002/0470868759.ch6},
	doi = {10.1002/0470868759.ch6},
	booktitle = {Ion channels: from atomic resolution physiology to functional genomics},
	publisher = {John Wiley \& Sons, Chicester},
	author = {Sansom, Mark S. P. and Bond, Peter and Beckstein, Oliver and Biggin, Philip C. and Faraldo-Goméz, José and Law, Richard J. and Patargias, George and Tieleman, D. Peter},
	editor = {Bock, Gregory and Goode, Jamie A.},
	year = {2002},
	keywords = {GlpF, OmpA, hydrophobic gate, review, water},
	pages = {66--78}
}

@techreport{beckstein_elastic_2001,
	address = {Erlangen},
	title = {Elastic {Constants} {How}-{To}},
	url = {http://doi.org/10.6084/m9.figshare.1164130},
	abstract = {This report describes how to calculate elastic constants with a DFT code for cubic, tatragonal bodycentered, and simple orthorhombic crystals. It uses as examples Pt, Si, and the platinum silicides PtSi and Pt2Si. The DFT code is the linear muffin tin orbital (LMTO) code nfp but the theory and explicit formulas for the deformations are independent of the specific code used.},
	language = {English},
	urldate = {2014-11-06TZ},
	institution = {Universität Erlangen-Nürnberg},
	author = {Beckstein, Oliver},
	year = {2001},
	keywords = {LMTO, deformation, dft, elastic properties, equation of state, platinum, silicide, silicon}
}

This report describes how to calculate elastic constants with a DFT code for cubic, tatragonal bodycentered, and simple orthorhombic crystals. It uses as examples Pt, Si, and the platinum silicides PtSi and Pt2Si. The DFT code is the linear muffin tin orbital (LMTO) code nfp but the theory and explicit formulas for the deformations are independent of the specific code used.

@article{klepeis_chemical_2001,
	title = {Chemical bonding, elasticity, and valence force field models: {A} case study for α-{Pt}₂{Si} and {PtSi}},
	volume = {64},
	issn = {0163-1829},
	url = {http://publish.aps.org/abstract/PRB/v64/e155110},
	doi = {10.1103/PhysRevB.64.155110},
	number = {15},
	journal = {Phys Rev B},
	author = {Klepeis, J. E. and Beckstein, O. and Pankratov, O. and Hart, G. L. W.},
	year = {2001},
	keywords = {DFT, Elasticity, LMTO-band-structure-calculations, Pt, PtSi, Si},
	pages = {155110}
}

@article{beckstein_first-principles_2001,
	title = {First-principles elastic constants and electronic structure of α-{Pt}₂{Si} and {PtSi}},
	volume = {63},
	issn = {0163-1829},
	url = {http://publish.aps.org/abstract/PRB/v63/e134112},
	doi = {10.1103/PhysRevB.63.134112},
	number = {13},
	journal = {Phys Rev B},
	author = {Beckstein, O. and Klepeis, J. E. and Hart, G. L. W. and Pankratov, O.},
	year = {2001},
	keywords = {DFT, Elasticity, LMTO-band-structure-calculations, Pt, PtSi, Si},
	pages = {134112}
}

@article{beckstein_hydrophobic_2001,
	title = {A {Hydrophobic} {Gating} {Mechanism} for {Nanopores}},
	volume = {105},
	url = {http://dx.doi.org/10.1021/jp012233y},
	doi = {10.1021/jp012233y S1089-5647(01)02233-7},
	abstract = {Water-filled pores of nanometer dimensions play important roles in chemistry and biology, e.g., as channels through biological membranes. Biological nanopores are frequently gated, i.e., they switch between an open and a closed state. In several ion channel structures the gate is formed by a ring of hydrophobic side chains that do not physically occlude the pore. Here we investigate whether a hydrophobic pore can act as a gate via molecular dynamics simulations of the passage of water through atomistic models of nanopores embedded within a membrane mimetic. Both the geometry of a nanopore and the hydrophilicity vs hydrophobicity of its lining determine whether water enters the channel. For purely hydrophobic pores there is an abrupt transition from a closed state (no water in the pore cavity) to an open state (cavity water at approximately bulk density) once a critical pore radius is exceeded. This critical radius depends on the length of the pore and the radius of the mouth region. Furthermore, a closed hydrophobic nanopore can be opened by adding dipoles to its lining.},
	number = {51},
	journal = {J Phys Chem B},
	author = {Beckstein, Oliver and Biggin, Philip C. and Sansom, Mark S. P.},
	month = dec,
	year = {2001},
	keywords = {hydrophobic gate, model pores, water},
	pages = {12902--12905}
}

Water-filled pores of nanometer dimensions play important roles in chemistry and biology, e.g., as channels through biological membranes. Biological nanopores are frequently gated, i.e., they switch between an open and a closed state. In several ion channel structures the gate is formed by a ring of hydrophobic side chains that do not physically occlude the pore. Here we investigate whether a hydrophobic pore can act as a gate via molecular dynamics simulations of the passage of water through atomistic models of nanopores embedded within a membrane mimetic. Both the geometry of a nanopore and the hydrophilicity vs hydrophobicity of its lining determine whether water enters the channel. For purely hydrophobic pores there is an abrupt transition from a closed state (no water in the pore cavity) to an open state (cavity water at approximately bulk density) once a critical pore radius is exceeded. This critical radius depends on the length of the pore and the radius of the mouth region. Furthermore, a closed hydrophobic nanopore can be opened by adding dipoles to its lining.

@phdthesis{beckstein_strukturelle_1999,
	address = {Erlangen, Germany},
	type = {Diplom ({Physik})},
	title = {Strukturelle und elektronische {Eigenschaften} der {Platinsilizide} aus ab initio {Rechnungen}},
	url = {http://doi.org/10.6084/m9.figshare.1166496},
	abstract = {Diplomarbeit (in German) carried out under the supervision of Dr Oleg Pankratov at the Universität Erlangen-Nürnberg, Germany.
The elastic constants for Pt, Si, Pt2Si and PtSi are calculated via density functional theory (DFT) within the LDA approximation. In addition, Kohn-Sham band structures and the electron density are predicted.
Most of the results were published in two papers in Phys Rev B:
First-principles elastic constants and electronic structure of α-Pt₂Si and PtSi Beckstein, O.; Klepeis, J. E.; Hart, G. L.W.; and Pankratov, O. Phys Rev B, 63(13):134112. 2001.
Chemical bonding, elasticity, and valence force field models: A case study for α-Pt₂Si and PtSi Klepeis, J. E.; Beckstein, O.; Pankratov, O.; and Hart, G. L.W. Phys Rev B, 64(15):155110. 2001.},
	language = {German},
	urldate = {2014-11-06TZ},
	school = {Universität Erlangen-Nürnberg},
	author = {Beckstein, Oliver},
	year = {1999},
	keywords = {LMTO, band structure, density functional theory, dft, elastic constants, elastic properties, lattice, platinum, silicide, silicon}
}

Diplomarbeit (in German) carried out under the supervision of Dr Oleg Pankratov at the Universität Erlangen-Nürnberg, Germany. The elastic constants for Pt, Si, Pt2Si and PtSi are calculated via density functional theory (DFT) within the LDA approximation. In addition, Kohn-Sham band structures and the electron density are predicted. Most of the results were published in two papers in Phys Rev B: First-principles elastic constants and electronic structure of α-Pt₂Si and PtSi Beckstein, O.; Klepeis, J. E.; Hart, G. L.W.; and Pankratov, O. Phys Rev B, 63(13):134112. 2001. Chemical bonding, elasticity, and valence force field models: A case study for α-Pt₂Si and PtSi Klepeis, J. E.; Beckstein, O.; Pankratov, O.; and Hart, G. L.W. Phys Rev B, 64(15):155110. 2001.