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Improved Parameterization of Protein-DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA

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Title
Improved Parameterization of Protein-DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA
Author(s)
Seonju You; Hong-Guen Lee; Kimoon Kim; Jejoong Yoo
Publication Date
2020-07
Journal
Journal of Chemical Theory and Computation, v.16, no.7, pp.4006 - 4013
Publisher
AMER CHEMICAL SOC
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 interactions
URI
https://pr.ibs.re.kr/handle/8788114/7758
DOI
10.1021/acs.jctc.0c00241
ISSN
1549-9618
Appears in Collections:
Center for Self-assembly and Complexity(복잡계 자기조립 연구단) > 1. Journal Papers (저널논문)
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