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 journalArticlepeer-review

11 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 languageEnglish
Pages (from-to)8757-8762
Number of pages6
JournalJournal of Physical Chemistry Letters
Volume12
Issue number36
DOIs
Publication statusPublished - Sept 16 2021
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Materials Science
  • Physical and Theoretical Chemistry

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