Optimized OPEP Force Field for Simulation of Crowded Protein Solutions

0571064 - ÚFCH JH 2024 RIV US eng J - Journal Article
Timr, Štěpán - Melchionna, S. - Derreumaux, P. - Sterpone, F.
Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.
Journal of Physical Chemistry B. Roč. 127, č. 16 (2023), s. 3616-3623. ISSN 1520-6106. E-ISSN 1520-5207
EU Projects: European Commission(XE) 840395
Institutional support: RVO:61388955
Keywords : Optimized Potential for Efficient Protein * diffusion * molecular mechanics
OECD category: Physical chemistry
Impact factor: 3.3, year: 2022
Method of publishing: Open access

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.
Permanent Link: https://hdl.handle.net/11104/0342374