Role of proximal His93 in nitric oxide binding to metmyoglobin. Application of continuum solvation in Monte Carlo protein simulations.
Monte Carlo protein simulations with continuum solvation were used to explore the conformational mobility of NO within the active site of metmyoglobin. To the best of our knowledge this is the first application of a continuum solvation model for exploring protein binding sites. The usefulness of the Monte Carlo conformational analysis was demonstrated in comparative molecular dynamics simulations. Analysis of conformer populations revealed that Monte Carlo conformational analysis is more effective in mapping the relevant region of the potential surface. Distribution of low-energy conformers obtained for the metmyoglobin-NO complex was found to depend on the orientation of proximal His93. Different charge distributions corresponding to the two experimentally verified possible torsions of this proximal residue result in strong binding of NO or its release to a nearby hydrophobic trap. Conformer populations obtained by Monte Carlo conformational analysis were grouped into three main families: one, with the NO directly bound to the iron, appears when the CA-CB-CG-CD2 torsion of His93 is at its ligand binding value (-113 degrees); and two conformers exist where NO is trapped in a nearby hydrophobic pocket, the same cavity that was determined to be the geminate trap of CO in ferrous Mb as a result of the torsional flip of His93 to its ligand releasing state (-125 degrees). Based on this analysis, we suggest that the electrostatic rearrangement coupled to the conformational fluctuation of the proximal His leads to the geminate trapping of the ligand. Conformational rearrangement of the proximal side would provide the possibility of rebinding of the ligand to Fe.
Keserü
G M
GM
Department of Chemical Information Technology, Technical University of Budapest, Hungary.
Menyhárd
D K
DK
D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D006639:Histidine / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008786:Metmyoglobin / Q000737:chemistry* / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D009010:Monte Carlo Method; D009569:Nitric Oxide / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D012996:Solutions; D012997:Solvents; D055672:Static Electricity
D008024:Ligands; D012996:Solutions; D012997:Solvents; D008786:Metmyoglobin; D009569:Nitric Oxide; D006639:Histidine