Research 5 | Beckstein Lab

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Molecular dynamics simulations

Molecular dynamics simulations

Molecular dynamics (MD) is a computational method to compute the trajectories of a large number of particles that interact with each other. Classical MD approximates interactions between atoms by classical forces but fully quantum mechanical MD has also been carried out. Experimental observables are calculated from trajectories using statistical mechanics.

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The alternating access mechanism in Mhp1

The alternating access mechanism in Mhp1

Secondary transporters couple the free energy stored in an ionic gradient to the movement of solutes across the cell membrane. The coupling enables these transmembrane proteins to transport small molecules against their own concentration gradients. The transporters function by cycling between different conformational states in which access to the central binding site is switched from the extracellular solution to the intracellular compartment. Using experimental and computational approaches we could visualize for the first time how this process occurs for a secondary transporter.

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Simulations of membrane proteins

Simulations of membrane proteins

Many proteins in the living cell can be understood as molecular machines that use a source of energy to produce mechanical or chemical work. My lab’s primary interest is in those proteins located in the cell membrane that move nutrients, signalling molecules, or waste products into and out of the cell. We study their molecular mechanisms of action by detailed molecular dynamics simulations, which provide a “movie” of full atomic detail of a working protein.

Current areas of interest focus on the mechanisms of secondary active transport; methods to accurately simulate macromolecular transitions that are crucial in understanding ligand binding, gating in ion channels, or the translocation of substrates through the cell membrane; and the role of water in confined geometries, for instance in ion channel gating mechanisms, ligand discrimination, or drug binding.