Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations

doi:10.1088/1674-1056/ac1e0e

中国物理B ›› 2021, Vol. 30 ›› Issue (10): 108703-108703.doi: 10.1088/1674-1056/ac1e0e

Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations

Weiwei Zhang(张伟伟) and Jian Zhang(张建)^†

National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China

收稿日期:2021-04-11 修回日期:2021-07-07 接受日期:2021-08-17 出版日期:2021-09-17 发布日期:2021-10-08
通讯作者: Jian Zhang E-mail:jzhang@nju.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11974173 and 11774158) and the HPC center of Nanjing University.

Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations

Weiwei Zhang(张伟伟) and Jian Zhang(张建)^†

National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China

Received:2021-04-11 Revised:2021-07-07 Accepted:2021-08-17 Online:2021-09-17 Published:2021-10-08
Contact: Jian Zhang E-mail:jzhang@nju.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11974173 and 11774158) and the HPC center of Nanjing University.

摘要/Abstract

摘要： Protein XPA plays critical roles in nucleotide excision repair pathway. Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site. Here, we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations. The results demonstrated strong salt concentration dependence of the diffusion mechanisms. At low salt concentrations, the one-dimensional diffusion with rotational coupling is the dominant mechanism. At high salt concentrations, the diffusion by three-dimensional mechanism becomes more probable. At wide range of salt concentrations, the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature. This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions. In addition, we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA, which increases the exposure extent of the sites for the binding of other repair proteins.

关键词: nucleotide excision repair, XPA, one-dimensional diffusion along DNA, molecular simulation

Abstract: Protein XPA plays critical roles in nucleotide excision repair pathway. Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site. Here, we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations. The results demonstrated strong salt concentration dependence of the diffusion mechanisms. At low salt concentrations, the one-dimensional diffusion with rotational coupling is the dominant mechanism. At high salt concentrations, the diffusion by three-dimensional mechanism becomes more probable. At wide range of salt concentrations, the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature. This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions. In addition, we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA, which increases the exposure extent of the sites for the binding of other repair proteins.

Key words: nucleotide excision repair, XPA, one-dimensional diffusion along DNA, molecular simulation

中图分类号: (Proteins)

87.14.E-

87.14.gk (DNA) 87.15.kj (Protein-polynucleotide interactions) 87.10.Tf (Molecular dynamics simulation)

Weiwei Zhang(张伟伟) and Jian Zhang(张建). Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations[J]. 中国物理B, 2021, 30(10): 108703-108703.

Weiwei Zhang(张伟伟) and Jian Zhang(张建). Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations[J]. Chin. Phys. B, 2021, 30(10): 108703-108703.

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Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations

Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations

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