Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin

Xian Wei Wang, John Z.H. Zhang, Xiao He

Research output: Contribution to journalArticle

Abstract

Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named as B1 and B2 states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B1 and B2 states correspond to Fe»CO (with carbon atom closer to iron center of heme) and Fe»OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B1 and B2 is 13.1 cm-1, which is in good agreement with experimental value of 11.5 cm-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107, and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.

Original languageEnglish (US)
Pages (from-to)705-716
Number of pages12
JournalChinese Journal of Chemical Physics
Volume30
Issue number6
DOIs
StatePublished - Dec 27 2017

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Keywords

  • Electric field
  • Electrostatic polarization effect
  • QM/MM simulation
  • Stark shift

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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