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

Taiji Nakamura; Tomoko Yokaichiya; Dmitri G. Fedorov

doi:10.1021/acs.jpclett.1c02510

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

Taiji Nakamura, Tomoko Yokaichiya, Dmitri G. Fedorov

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Abstract

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, 5OQZ, 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.

Original language	English
Pages (from-to)	8757-8762
Number of pages	6
Journal	Journal of Physical Chemistry Letters
DOIs	https://doi.org/10.1021/acs.jpclett.1c02510
Publication status	Accepted/In press - 2021
Externally published	Yes

All Science Journal Classification (ASJC) codes

Materials Science(all)
Physical and Theoretical Chemistry

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10.1021/acs.jpclett.1c02510

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title = "Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems",

abstract = "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, 5OQZ, 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.",

author = "Taiji Nakamura and Tomoko Yokaichiya and Fedorov, {Dmitri G.}",

note = "Funding Information: The financial support by JSPS KAKENHI (grant number 19H02682) is gratefully acknowledged. Publisher Copyright: {\textcopyright} 2021 American Chemical Society.",

year = "2021",

doi = "10.1021/acs.jpclett.1c02510",

language = "English",

pages = "8757--8762",

journal = "Journal of Physical Chemistry Letters",

issn = "1948-7185",

publisher = "American Chemical Society",

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T1 - Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems

AU - Nakamura, Taiji

AU - Yokaichiya, Tomoko

AU - Fedorov, Dmitri G.

PY - 2021

Y1 - 2021

N2 - 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, 5OQZ, 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.

AB - 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, 5OQZ, 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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AN - SCOPUS:85115128777

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SP - 8757

EP - 8762

JO - Journal of Physical Chemistry Letters

JF - Journal of Physical Chemistry Letters

ER -

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

Abstract

All Science Journal Classification (ASJC) codes

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