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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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Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights

Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights

A new crystal structure of the Escherichia coli NhaA dimer reveals a previously unidentified salt bridge between two highly conserved residues at the putative binding site. The combination of structural data with molecular dynamics simulations yields new insights into the transport mechanism.

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Summer Book Club 2014: Molecular Simulations and Theory

Summer Book Club 2014: Molecular Simulations and Theory

This summer’s Lab Book Club is designed to provide a thorough review of fundamental concepts for understanding biomolecular simulation and, in particular,molecular dynamics simulations (MD). The material is primarily based on chapters from Statistical Mechanics: Theory and Molecular Simulation by Mark Tuckerman.

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Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

We show that one of the best-studied secondary active transporters, the lactose permease LacY, goes through an occluded conformation during its transport cycle. We propose an atomically detailed model of the apo-occluded state. The simulations predict the formation of a transient salt bridge that has been hypothesized in the canonical model for transport of LacY. The simulations are validated by comparison to experimental EPR DEER data, using a new approach to simulate spin-label distance distributions through post-processing of molecular dynamics trajectories. We also define a set of order parameters that consistently classify all known MFS transporter structures as outward-open, occluded, or inward-open conformations.

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Molecular Dynamics Simulation of a Carbon Nanotube Gigahertz Oscillator

Molecular Dynamics Simulation of a Carbon Nanotube Gigahertz Oscillator

As part of his final project for the course Simulation Approaches to Bio- and Nanophysics (ASU PHY494/PHY598), C. Michael Gilbert performed classical molecular dynamics simulations of a smaller carbon nanotube in a larger one.

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