title: Heme distortions in sperm-whale carbonmonoxy myoglobin: correlations between rotational strengths and heme distortions in MD-generated structures.
abstract: We have investigated the effects of heme rotational isomerism in sperm-whale carbonmonoxymyoglobin using computational techniques. Several molecular dynamics simulations have been performed for the two rotational isomers A and B, which are related by a 180 degrees rotation around the alpha-gamma axis of the heme, of sperm-whale carbonmonoxy myoglobin in water. Both neutron diffraction and NMR structures were used as starting structures. In the absence of an experimental structure, the structure of isomer B was generated by rotating the heme in the structure of isomer A. Distortions of the heme from planarity were characterized by normal coordinate structural decomposition and by the angle of twist of the pyrrole rings from the heme plane. The heme distortions of the neutron diffraction structure were conserved in the MD trajectories, but in the NMR-based trajectories, where the heme distortions are less well defined, they differ from the original heme deformations. The protein matrix induced similar distortions on the hemes in orientations A and B. Our results suggest that the binding site prefers a particular macrocycle conformation, and a 180 degrees rotation of the heme does not significantly alter the protein's preference for this conformation. The intrinsic rotational strengths of the two Soret transitions, separated according to their polarization in the heme plane, show strong correlations with the ruffling deformation and the average twist angle of the pyrrole rings. The total rotational strength, which includes contributions from the chromophores in the protein, shows a weaker correlation with heme distortions.
authors.affiliation: Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
authors.forename: Christoph
authors.initials: C
authors.lastname: Kiefl
authors.forename: Narasimha
authors.initials: N
authors.lastname: Sreerama
authors.forename: Raid
authors.initials: R
authors.lastname: Haddad
authors.forename: Lisong
authors.initials: L
authors.lastname: Sun
authors.forename: Walter
authors.initials: W
authors.lastname: Jentzen
authors.forename: Yi
authors.initials: Y
authors.lastname: Lu
authors.forename: Yan
authors.initials: Y
authors.lastname: Qiu
authors.forename: John A
authors.initials: JA
authors.lastname: Shelnutt
authors.forename: Robert W
authors.initials: RW
authors.lastname: Woody
mesh_terms: D000818:Animals; D003198:Computer Simulation; D006418:Heme / Q000737:chemistry*; D009211:Myoglobin / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D020033:Protein Isoforms; D014907:Whales
chemical_list: D009211:Myoglobin; D020033:Protein Isoforms; C018013:carboxymyoglobin; D006418:Heme