TY - JOUR
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.
N1 - Funding Information:
The financial support by JSPS KAKENHI (grant number 19H02682) is gratefully acknowledged.
Publisher Copyright:
© 2021 American Chemical Society.
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.
UR - http://www.scopus.com/inward/record.url?scp=85115128777&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85115128777&partnerID=8YFLogxK
U2 - 10.1021/acs.jpclett.1c02510
DO - 10.1021/acs.jpclett.1c02510
M3 - Article
C2 - 34478310
AN - SCOPUS:85115128777
SN - 1948-7185
SP - 8757
EP - 8762
JO - Journal of Physical Chemistry Letters
JF - Journal of Physical Chemistry Letters
ER -