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Improved Parameterization of Protein-DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA
Authors
Hong-Guen Lee
Jejoong Yoo
Kimoon Kim
Seonju You
Publication date
1 July 2020
Publisher
'American Chemical Society (ACS)'
Doi
Cite
Abstract
© 2020 American Chemical Society, As the field of molecular dynamics simulation utilizing the force fields is moving toward more complex systems, the accuracy of intermolecular interactions has become a central issue of the field. Here, we quantitatively evaluate the accuracy of the protein-DNA interactions in AMBER and CHARMM force fields by comparing experimental and simulated diffusion coefficients of proliferating cell nuclear antigen. We find that both force fields underestimate diffusion coefficients by at least an order of magnitude because the interactions between basic amino acids and DNA phosphate groups are too attractive. Then, we propose Lennard-Jones parameters optimized using the experimental osmotic pressure data of model chemicals, by using which one can reproduce the experimental diffusion coefficients. Newly optimized parameters will have a broad impact on general protein-DNA interactions11Nsciescopu
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포항공과대학교
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oai:oasis.postech.ac.kr:2014.o...
Last time updated on 24/06/2021
IBS Publications Repository
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oai:pr.ibs.re.kr:8788114/7758
Last time updated on 01/03/2021