Optimized OPEP Force Field for Simulation of Crowded Protein Solutions
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388955%3A_____%2F23%3A00571064" target="_blank" >RIV/61388955:_____/23:00571064 - isvavai.cz</a>
Result on the web
<a href="https://hdl.handle.net/11104/0342374" target="_blank" >https://hdl.handle.net/11104/0342374</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jpcb.3c00253" target="_blank" >10.1021/acs.jpcb.3c00253</a>
Alternative languages
Result language
angličtina
Original language name
Optimized OPEP Force Field for Simulation of Crowded Protein Solutions
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Physical Chemistry B
ISSN
1520-6106
e-ISSN
1520-5207
Volume of the periodical
127
Issue of the periodical within the volume
16
Country of publishing house
US - UNITED STATES
Number of pages
8
Pages from-to
3616-3623
UT code for WoS article
000975438500001
EID of the result in the Scopus database
2-s2.0-85153989015