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Tag Archives: membrane
Molecular basis of ion translocation in sodium/proton antiporters

Molecular basis of ion translocation in sodium/proton antiporters

We studied the process of sodium/proton antiport in the NapA transporter. Through a combination of X-ray crystallography, biochemistry and computer simulations we could show that the antiporter undergoes a large conformational transition that resembles a *elevator*-like movement whereby a single domain moves up- and down through the membrane and carries a sodium ion with it.

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Research Experience for Undergraduates (Summer 2015)

Research Experience for Undergraduates (Summer 2015)

The Beckstein Lab offers a fully funded ten-week research program in computational biophysics for a highly motivated undergraduate student. This is a NSF-sponsored Research Experience for Undergraduates. Deadline for applications is May 31, 2015.

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Influence of lipids on transmembrane transport proteins

Influence of lipids on transmembrane transport proteins

We are reviewing the evidence for direct effects of lipids on the transport properties of ion channels and active transporters. For ion channels it has been convincingly shown that specific lipid-protein interactions can directly affect their function. For transporters, the evidence is more ambiguous. In all areas, however, the use of computer simulations extends the way in which we understand protein-membrane interactions.

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X-ray crystallography and Simulations

X-ray crystallography and Simulations

Structures of membrane proteins can be obtained by the experimental technique of X-ray crystallography. However, proteins are typically not crystallized in their native environment, the lipid membrane. Molecular dynamics simulations of the protein in the membrane provide a realistic model of the interactions between transporter and lipid bilayer.

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David Dotson

David Dotson

David worked as a research software engineer in the lab. He left in June 2017 for industry.

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Lipidbook

Lipidbook

Lipidbook is a public repository and database for force field parameters with a special emphasis on lipids, detergents, and similar molecules that are of interest when simulating biological membranes.

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Atomically detailed molecular dynamics simulations

Atomically detailed molecular dynamics simulations

Using molecular dynamics (MD) computer simulations we can study membrane proteins in atomic detail, down to the movements of individual water molecules. For example, the Mhp1 transporter protein shown here switches between three different functional states: A: outward facing; B: occluded; C: inward facing — as predicted byt the alternating access model.

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Transporters

Transporters

Transporter proteins are used by cells to “pump” molecules or ions into or out of the cell. They are present in all cells (digestive system, nervous system, blood, …) with important roles in metabolism. Secondary active transporters move their substrates against a electrochemical potential gradient and therefore couple uptake/excretion to an energetically favourable flow of sodium ions or protons into the cell.

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