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The Stabilization Effect of Dielectric Constant and Acidic Amino Acids on Arginine-Arginine (Arg-Arg) Pairings: Database Survey and Computational Studies

文献类型：期刊论文

作者Zhang, Zhengyan1,2; Xu, Zhijian1; Yang, Zhuo1; Liu, Yingtao1; Wang, Jin'an1; Shao, Qiang1; Li, Shujin2; Lu, Yunxiang3; Zhu, Weiliang1
刊名JOURNAL OF PHYSICAL CHEMISTRY B
出版日期2013-05-02
卷号117期号:17页码:4827-4835
ISSN号1520-6106
DOI10.1021/jp4001658
文献子类Article
英文摘要Database survey in this study revealed that about one-third of the protein. structures deposited in the Protein Data Bank (PDB) Contain arginine arginine (Arg-Arg) pairing with a carbon center dot center dot center dot carbon (CZ center dot center dot center dot CZ). interaction distance less than 5 A. All the Arg-Arg pairings were found to bury in a polar environment: composed of acidic residues, water molecules, and strong polarizable or negatively charged moieties from binding site or bound ligand. Most of the Arg-Arg pairings are solvent exposed and 68.3% Arg-Arg pairings are Stabilized by acidic residues, forming Arg-Arg-Asp/Glu clusters. Density functional theory (DFT) was: then employed to study the effect of environment on the poring structures It Was revealed that Arg-Arg pairings become thermodynamically stable (about -1 kcal/mol) as the dielectric constant increases to 46.8 (DMSO), in good agreement with the results of the PDB survey. DFT calculations also demonstrated that perpendicular Arg-Arg pairing structures are favorable in low dielectric constant environment, while in high dielectric constant environment parallel Structures are favorable: Additionally, the acidic residues can stabilize the Arg-Arg pairing structures to a large degree:, Energy decomposition analysis of Arg-Arg pairings and Arg-Arg-Asp/Glu clusters showed that both solvation and electrostatic energies contribute significantly to their stability. The results, reported herein should be very helpful for understanding Arg-Arg pairing and its application in drug design.
WOS关键词ENERGY DECOMPOSITION ANALYSIS ; MOLECULAR-DYNAMICS ; GUANIDINIUM ION ; WATER ; FORCE ; DFT ; PI
资助项目Ministry of Science and Technology[2012AA01A305] ; National Major Project[2012ZX09301001-004] ; National Natural Science Foundation[81273435] ; National Natural Science Foundation[20977064] ; National Natural Science Foundation[21103047] ; National Natural Science Foundation[91013008] ; National Natural Science Foundation[21021063] ; Priority Academic Program Development of Jiangsu Higher Education Institutions[00000000]
WOS研究方向Chemistry
语种英语
WOS记录号WOS:000318536700011
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.183/handle/2S10ELR8/277626]  
专题药物发现与设计中心
通讯作者Li, Shujin
作者单位1.Chinese Acad Sci, Shanghai Inst Mat Med, CAS Key Lab Receptor Res, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China;
2.Soochow Univ, Coll Chem Chem Engn & Mat Sci, Suzhou 215123, Jiangsu, Peoples R China;
3.E China Univ Sci & Technol, Dept Chem, Shanghai 200237, Peoples R China
推荐引用方式
GB/T 7714		 Zhang, Zhengyan,Xu, Zhijian,Yang, Zhuo,et al. The Stabilization Effect of Dielectric Constant and Acidic Amino Acids on Arginine-Arginine (Arg-Arg) Pairings: Database Survey and Computational Studies[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2013,117(17):4827-4835.
APA Zhang, Zhengyan.,Xu, Zhijian.,Yang, Zhuo.,Liu, Yingtao.,Wang, Jin'an.,...&Zhu, Weiliang.(2013).The Stabilization Effect of Dielectric Constant and Acidic Amino Acids on Arginine-Arginine (Arg-Arg) Pairings: Database Survey and Computational Studies.JOURNAL OF PHYSICAL CHEMISTRY B,117(17),4827-4835.
MLA Zhang, Zhengyan,et al."The Stabilization Effect of Dielectric Constant and Acidic Amino Acids on Arginine-Arginine (Arg-Arg) Pairings: Database Survey and Computational Studies".JOURNAL OF PHYSICAL CHEMISTRY B 117.17(2013):4827-4835.

入库方式： OAI收割

来源：上海药物研究所

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