title: Ligand migration in myoglobin: a combined study of computer simulation and x-ray crystallography.
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.
authors.affiliation: Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Tsuduki
authors.forename: Ayana
authors.initials: A
authors.lastname: Tomita
authors.forename: Shin-ya
authors.initials: SY
authors.lastname: Koshihara
authors.forename: Shin-ichi
authors.initials: S
authors.lastname: Adachi
authors.forename: Takahisa
authors.initials: T
authors.lastname: Yamato
mesh_terms: D018360:Crystallography, X-Ray; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*
chemical_list: D008024:Ligands; D009211:Myoglobin