Heme Distortions in Sperm-Whale Carbonmonoxy Myoglobin: Correlations between Rotational Strengths and Heme Distortions in MD-Generated Structures

• Main Authors: KIEFL,CHRISTOPH, SCREERAMA,NARASIMHA, LU,YI, QIU,YAN, SHELNUTT,JOHN A., WOODY,ROBERT W.
• Language: unknown
• Published: 2009
• Subjects: 59 BASIC BIOLOGICAL SCIENCES; HEME; ISOMERS; MYOGLOBIN; PROTEINS; ROTATION; MOLECULAR DYNAMICS METHOD; CETACEANS; PROTEIN STRUCTURE; DEFORMATION; Sperm whale
• Online Access: http://www.osti.gov/servlets/purl/759889; https://www.osti.gov/biblio/759889

The authors have investigated the effects of heme rotational isomerism in sperm-whale carbonmonoxy myoglobin using computational techniques. Several molecular dynamics simulations have been performed for the two rotational isomers A and B, which are related by a 180{degree} 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 heroes in orientations A and B. The results suggest that the binding site prefers a particular macrocycle conformation, and a 180{degree} 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 ruf-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.