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. 2023:2646:27-34.
doi: 10.1007/978-1-0716-3060-0_3.

Molecular Simulation to Investigate Open-Close Motion of a Flagellar Export Apparatus Protein FlhAC

Akio Kitao  1
Affiliations

Molecular Simulation to Investigate Open-Close Motion of a Flagellar Export Apparatus Protein FlhAC

Akio Kitao. Methods Mol Biol. 2023.

Abstract

Molecular dynamics (MD) simulation and parallel cascade selection molecular dynamics (PaCS-MD) are widely used to investigate large-amplitude motions of proteins. PaCS-MD is an enhanced conformational sampling method consisting of cycles of parallel unbiased MD simulations combined with a selection of MD snapshots as the initial structures for the next cycle. In addition, free energy calculation can be achieved by the combination of PaCS-MD and the Markov state model (MSM). In this chapter, the protocols to investigate the open-close motion of a flagellar export apparatus protein, FlhAC, by MD and the combination of PaCS-MD and MSM are described.

Keywords: Free energy profile; Markov state model; Molecular dynamics simulation; Open–close motion; Parallel cascade selection molecular dynamics.

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