Development of Accurate Forces for Mg2+ and Triphosphate Interactions in ATP<middle dot>Mg2+ and GTP<middle dot>Mg2+ Complexes

被引:0
|
作者
Hu, Fangchen [1 ]
Zhang, Yuwei [2 ]
Li, Pengfei [3 ]
Wu, Ruibo [4 ]
Xia, Fei [1 ]
机构
[1] East China Normal Univ, NYU ECNU Ctr Computat Chem, Sch Chem & Mol Engn, NYU Shanghai, Shanghai 200062, Peoples R China
[2] Nanjing Normal Univ, Jiangsu Collaborat Innovat Ctr Biomed Funct Mat, Sch Chem & Mat Sci, Jiangsu Key Lab New Power Batteries, Nanjing 210023, Peoples R China
[3] Loyola Univ Chicago, Dept Chem & Biochem, Chicago, IL 60660 USA
[4] Sun Yat Sen Univ, Sch Pharmaceut Sci, Guangzhou 510006, Peoples R China
基金
中国国家自然科学基金;
关键词
MOLECULAR-DYNAMICS; NUCLEIC-ACIDS; RAS PROTEIN; FIELD; ENERGY; PARAMETERS; GTP; SIMULATION; MECHANICS; BACKBONE;
D O I
10.1021/acs.jctc.4c01142
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
In cells, adenosine triphosphate (ATP) and guanosine triphosphate (GTP) molecules typically form tricoordinated or bicoordinated ATP<middle dot>Mg2+ or GTP<middle dot>Mg2+ complexes with Mg2+ ions and bind to proteins, participating in and regulating many important cellular functions. The accuracy of their force field parameters plays a crucial role in studying the function-related conformations of ATP<middle dot>Mg2+ or GTP<middle dot>Mg2+ using molecular dynamics (MD) simulations. The parameters developed based on the methyl triphosphate model in existing AMBER force fields cannot accurately describe the conformational distribution of tricoordinated or bicoordinated ATP<middle dot>Mg2+ or GTP<middle dot>Mg2+ complexes in solution. In this study, we develop force field parameters for the triphosphate group based on the new ribosyl triphosphate model, considering the dihedral coupling effect, accurate van der Waals (vdW) interactions, and the influence of strongly polarized charges on conformational balance. The new force fields can accurately describe the conformational balance of tricoordinated and bicoordinated ATP<middle dot>Mg2+ or GTP<middle dot>Mg2+ conformations in solution and can be applied to simulate biological systems containing ATP<middle dot>Mg2+ or GTP<middle dot>Mg2+ complexes.
引用
收藏
页数:11
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