Functional protein dynamics in a crystal

Eugene Klyshko, Justin Sung-Ho Kim, Lauren McGough, Victoria Valeeva, Ethan Lee, Rama Ranganathan and Sarah Rauscher ()
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Eugene Klyshko: University of Toronto
Justin Sung-Ho Kim: University of Toronto
Lauren McGough: University of Chicago
Victoria Valeeva: University of Toronto Mississauga
Ethan Lee: University of Toronto Mississauga
Rama Ranganathan: University of Chicago
Sarah Rauscher: University of Toronto

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning. Here, we establish robust and accurate methods for simulating dynamics in protein crystals, a nontrivial process requiring careful attention to equilibration, environmental composition, and choice of force fields. With more than seven milliseconds of sampling of a single chain, we identify critical factors controlling agreement between simulation and experiments and show that simulated motions recapitulate ligand-induced conformational changes. This work enables a virtuous cycle between simulation and experiments for visualizing and understanding the basic functional motions of proteins.

Date: 2024
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DOI: 10.1038/s41467-024-47473-4

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