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Optimized OPEP Force Field for Simulation of Crowded Protein Solutions
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SYSNO ASEP 0571064 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Optimized OPEP Force Field for Simulation of Crowded Protein Solutions Author(s) Timr, Štěpán (UFCH-W)
Melchionna, S. (IT)
Derreumaux, P. (FR)
Sterpone, F. (FR)Source Title Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 127, č. 16 (2023), s. 3616-3623Number of pages 8 s. Language eng - English Country US - United States Keywords Optimized Potential for Efficient Protein ; diffusion ; molecular mechanics Subject RIV CF - Physical ; Theoretical Chemistry OECD category Physical chemistry Method of publishing Open access Institutional support UFCH-W - RVO:61388955 UT WOS 000975438500001 EID SCOPUS 85153989015 DOI 10.1021/acs.jpcb.3c00253 Annotation Macromolecular crowding has profound effects on the mobility of proteins, with strong implications on the rates of intracellular processes. To describe the dynamics of crowded environments, detailed molecular models are needed, capturing the structures and interactions arising in the crowded system. In this work, we present OPEPv7, which is a coarse-grained force field at amino-acid resolution, suited for rigid-body simulations of the structure and dynamics of crowded solutions formed by globular proteins. Using the OPEP protein model as a starting point, we have refined the intermolecular interactions to match the experimentally observed dynamical slowdown caused by crowding. The resulting force field successfully reproduces the diffusion slowdown in homogeneous and heterogeneous protein solutions at different crowding conditions. Coupled with the lattice Boltzmann technique, it allows the study of dynamical phenomena in protein assemblies and opens the way for the in silico rheology of protein solutions. Workplace J. Heyrovsky Institute of Physical Chemistry Contact Michaela Knapová, michaela.knapova@jh-inst.cas.cz, Tel.: 266 053 196 Year of Publishing 2024 Electronic address https://hdl.handle.net/11104/0342374
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