Ligand migration in myoglobin: a combined study of computer simulation and x-ray crystallography

The Journal of Chemical Physics
Takayuki TsudukiTakahisa Yamato

Abstract

A ligand-migration mechanism of myoglobin was studied by a multidisciplinary approach that used x-ray crystallography and molecular dynamics simulation. The former revealed the structural changes of the protein along with the ligand migration, and the latter provided the statistical ensemble of protein conformations around the thermal average. We developed a novel computational method, homogeneous ensemble displacement, and generated the conformational ensemble of ligand-detached species from that of ligand-bound species. The thermally averaged ligand-protein interaction was illustrated in terms of the potential of mean force. Although the structural changes were small, the presence of the ligand molecule in the protein matrix significantly affected the 3D scalar field of the potential of mean force, in accordance with the self-opening model proposed in the previous x-ray study.

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Citations

Apr 9, 2014·Scientific Reports·Masayoshi TakayanagiMasataka Nagaoka
Nov 8, 2013·The Journal of Physical Chemistry. B·Shuji Kaieda, Bertil Halle
Apr 26, 2013·The Journal of Physical Chemistry. B·Masayoshi TakayanagiMasataka Nagaoka
Jan 5, 2019·The Journal of Physical Chemistry. B·Kunitaka Ota, Takahisa Yamato

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Methods Mentioned

BETA
x-ray crystallography
X-ray

Software Mentioned

GROMOS
REFMAC
GROMOS96
GROMACS
CCP4

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