Tag 1 | Beckstein Lab

Kurtis Ottman is an undergraduate student studying chemical engineering at Arizona State University. He participated in the 2021 REU working on conformational transitions of membrane proteins.

Cryo-electron microscopy has become a powerful new structural technique to obtain atomic resolution structures of membrane proteins. By combining the experimental structures with molecular dynamics simulations of the protein in a realistic environment including a membrane and solvent (water and ions), new insights regarding the protein function can be obtained that are not available from a single technique alone.

NHE9 is a sodium/proton exchanger in mammals, part of a large family of secondary active transporters. Our collaborators (David Drew at the University of Stockholm) solved the structure of NHE9 (SLC9A9) from horse with cryo electron-microscopy to 3.2 Å resolution in an inward facing conformation, the first structure of a mammalian sodium/proton antiporter. Functional measurements, structural bioinformatics, and MD simulations all indicate that many components of the transport mechanism are similar between prokaryotic and mammalian 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.

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.

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.

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.

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.