MOLECULAR-DYNAMICS SIMULATIONS OF HUMAN DEOXYMYOGLOBIN WITH A MODIFIED PROXIMAL SIDE OF THE HEME GROUP

Myoglobins (Mbs) are heme proteins which serve as oxygen storage in li ving organisms. In order to understand the mechanism of binding of oxy gen and other small molecules both experimental and theoretical studie s of Mbs with carefully designed point mutations in a protein backbone are performed. In this paper a series of H93G mutants of human deoxym yoglobin was studied using constant temperature (T = 300 K) 50-ps mole cular dynamics simulations. In these mutant proteins the proximal hist idine F8 was replaced by ligands having an increasing volume: imidazol e (Im), 2-methylimidazole (2-Melm), 4-methylimidazole (4-MeIm), 2,4-di methylimidazole (2,4-diMeIm), 1-methylimidazole (1-MeIm), 2-ethylimida zole (2-EtIm), 4-hydroxomethylimidazole (4-MeOHIm) and pyridine (Pyr). The impact of bulky ligands on the protein structure and dynamics was analysed with an emphasis on changes in the heme proximal side geomet ry. It was found that all modifications lead to stable structures, alt hough in certain cases (i.e. pyridine) large rearrangements of the hem e position are observed. In general, ligands which are not covalently bound to the backbone exhibit greater ''flexibility'' than the WT hist idine ligand. Two groups of ligands are indicated: (a) those with a la rge-amplitude torsional oscillation around the Fe-N-epsilon bond (sigm a(phi) = 18-20 degrees) (Im, 4-MeIm and 4-MeOHIm), and (b) those with limited flexibility (sigma(phi) = 3-8 degrees) (all the others). Our d ata indicate that making a direct correlation between structural param eters extracted from X-ray crystallography and NMR spectra or small li gand rebinding kinetics may be misleading. (C) 1997 Elsevier Science B .V.