title: Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation.
abstract: The conformational change taking place in myoglobin concomitantly with the observed geometrical change at the heme-His(F8) linkage upon oxygenation is studied by normal mode analysis, which is based on the quadratic approximation of the conformational energy function. The heme-globin interaction energy increases for this change by 8.114 kcal/mol when both the heme group and the globin molecule are held rigid. When they are permitted flexibility, the interaction energy relaxes by 7.038 kcal/mol, and the difference (1.076 kcal/mol) is distributed as strain energy within the molecule. This increase is the work necessary for the heme group to move against the force exerted by the globin. If the force is assumed to be invariable during this move, the work is small, 0.276 kcal/mol, meaning that the force is strongly variable. Furthermore, this means that the heme group is located near the equilibrium point of the potential energy of the heme-globin interaction. The change in the localized strain energy stored in the force field at the linkage between the heme and the imidazole of HisF8 is estimated to be of the same order of magnitude as the distributed energy. The largest atomic displacements are observed at the region from the F helix to the beginning of the G helix, and secondary large displacements occur at several regions, i.e, the A helix, from the C helix to the CD corner, the E helix, and the C-terminal side of the H helix. All of these regions have strong dynamic interactions with the heme group, either directly or indirectly. Their secondary structures show complex deformations. In other parts, relatively rigid segments undergo rotational and/or bending changes in a way consistent with the large changes described above and close atomic packing within the molecule. The calculated conformational change is decomposed to vibrational normal modes of deoxymyoglobin. The magnitude of the conformational change, measured by the mass-weighted mean-square atomic displacement, is accounted for up to 92.0% by the 151 normal modes with frequencies lower than 40 cm-1. In descending order of contribution, the first six modes, each of which has a frequency lower than 12 cm-1, account for up to 57.4%. This means that the functionally important conformational change can well be expressed in terms of a relatively small number of collective low frequency normal modes.
authors.affiliation: Department of Physics, Faculty of Science, Nagoya University, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Seno
authors.forename: N
authors.initials: N
authors.lastname: Go
mesh_terms: D002151:Calorimetry; D006454:Hemoglobins / Q000378:metabolism; D008433:Mathematics; D008962:Models, Theoretical; D009211:Myoglobin / Q000031:analogs & derivatives* / Q000378:metabolism*; D011487:Protein Conformation; D014732:Vibration
chemical_list: D006454:Hemoglobins; D009211:Myoglobin; C055547:deoxymyoglobin; C017595:oxymyoglobin