Improved Parameterization of Protein–DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA
| Autor: | Jejoong Yoo, Hong-Guen Lee, Seonju You, Kimoon Kim |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Field (physics)
Static Electricity Protein dna Complex system Molecular Dynamics Simulation 01 natural sciences Diffusion chemistry.chemical_compound Molecular dynamics Protein structure Proliferating Cell Nuclear Antigen 0103 physical sciences Static electricity Osmotic pressure Amino Acid Sequence Physical and Theoretical Chemistry Diffusion (business) Protein Structure Quaternary Physics Quantitative Biology::Biomolecules biology 010304 chemical physics Intermolecular force DNA Phosphate Proliferating cell nuclear antigen Computer Science Applications chemistry Biophysics biology.protein Biological system Order of magnitude Protein Binding |
| Zdroj: | Journal of Chemical Theory and Computation. 16:4006-4013 |
| ISSN: | 1549-9626 1549-9618 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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