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Clarification of the role of protein in carbonmonoxy myoglobin by investigating electronic states
Author(s) -
Chiba Kouji,
Hirano Toshiyuki,
Sato Fumitoshi,
Okamoto Masahiro
Publication year - 2013
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.24459
Subject(s) - myoglobin , chemistry , protonation , histidine , tautomer , qm/mm , proton , electronic structure , heme , hemeprotein , computational chemistry , molecular dynamics , chemical physics , stereochemistry , physics , quantum mechanics , amino acid , organic chemistry , ion , biochemistry , enzyme
This article reports the proton tautomerization effects of distal histidine residues in carbonmonoxy myoglobin according to the density functional calculations of the whole protein. The electron eigenstates and electrostatic potential (ESP) distributed around heme and its pocket vary significantly depending on the protonation positions of the distal histidine residues. To investigate the range over which the electronic structures are affected by the proton tautomerization, the quantum mechanics/molecular mechanics (QM/MM) method is applied to probe the QM size to reproduce the atomic partial charges and ESP around the active center. Consequently, we show that these properties converged for the 300 pm QM/MM system in this study. During the analysis, we also find that amino residues such as Phe43, Val68, and Phe138 interact strongly with heme through orbital mixing, indicating that the protein is a medium not only interacting with the reaction center, but also buffering on electrons. © 2013 Wiley Periodicals, Inc.