SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies

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• 作者：Andrey Alekseenko ; Olga Kononova ; Yaroslav Kholodov ; Kenneth A. Marx and Valeri Barsegov
• 刊名：Journal of Computational Chemistry
• 出版年：2016
• 出版时间：June 30, 2016
• 年：2016
• 卷：37
• 期：17
• 页码：1537-1551
• 全文大小：1156K
• ISSN：1096-987X

文摘

Hydrodynamic interactions (HI) are incorporated into Langevin dynamics of the C_α-based protein model using the Truncated Expansion approximation (TEA) to the Rotne–Prager–Yamakawa diffusion tensor. Computational performance of the obtained GPU realization demonstrates the model's capability for describing protein systems of varying complexity (10²–10⁵ residues), including biological particles (filaments, virus shells). Comparison of numerical accuracy of the TEA versus exact description of HI reveals similar results for the kinetics and thermodynamics of protein unfolding. The HI speed up and couple biomolecular transitions through cross-communication among protein domains, which result in more collective displacements of structure elements governed by more deterministic (less variable) dynamics. The force-extension/deformation spectra from nanomanipulations in silico exhibit sharper force signals that match well the experimental profiles. Hence, biomolecular simulations without HI overestimate the role of tension/stress fluctuations. Our findings establish the importance of incorporating implicit water-mediated many-body effects into theoretical modeling of dynamic processes involving biomolecules.