Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems

被引：11
|
作者：
Nakamura, Taiji [1 ]
Yokaichiya, Tomoko [1 ,2 ]
Fedorov, Dmitri G. [1 ]
机构：
[1] Natl Inst Adv Ind Sci & Technol, Res Ctr Computat Design Adv Funct Mat CD FMat, Tsukuba, Ibaraki 3058568, Japan
[2] Univ Tokyo, Grad Sch Engn, Dept Chem Syst Engn, Hongo 7-3-1, Tokyo 1138656, Japan
来源：
JOURNAL OF PHYSICAL CHEMISTRY LETTERS | 2021年 / 12卷 / 36期
关键词：
FUNCTIONAL TIGHT-BINDING; MOLECULAR-ORBITAL METHOD;
D O I：
10.1021/acs.jpclett.1c02510
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：
A fast quantum-mechanical approach, density-functional tight-binding combined with the fragment molecular orbital method and periodic boundary conditions, is used to optimize atomic coordinates and cell parameters for a set of protein crystals: 1ETL, SOQZ, 3Q8J, 1CBN, and 2VB1. Good agreement between experimental and calculated structures is obtained for both atomic coordinates and cell parameters. Sterical clashes present in the experimental structures are corrected by simulations. The partition analysis is extended to treat periodic boundary conditions and applied to analyze protein-solvent interactions in crystals.
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页码：8757 / 8762
页数：6
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