A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c--solvation and dynamic properties of the two oxidation states.
Molecular dynamics calculations have been performed over long trajectories with the inclusion of explicit solvent molecules on the reduced and the oxidized states of yeast iso-1-cytochrome c. The resulting structures have been analyzed and compared both in terms of structural properties and dynamical behavior. The structure of the buried water molecules around the heme has been also analyzed for the two oxidation states and compared with the experimental observations on the X-ray and the solution NMR structures. From the overall analysis we learn that, as also observed experimentally through NMR, no significant differences are present between the structures of the two oxidation states beside the arrangement of a few side chains. Also the internal mobility is similar for the two oxidation states, even if interesting differences are observed for some residues, as for Tyr67, a residue present at the heme site. The location and the mobility of the ordered water molecules, observed in solution by NMR, are completely reproduced in the molecular dynamics simulations, which have been able to predict the different displacements of the catalytically relevant water molecule WAT166, similar to those observed in solution for the two oxidation states, at variance with that observed in the starting crystallographic structures. The relevance of these findings with respect to the prediction of structural and dynamical properties is discussed.
Banci
L
L
Department of Chemistry, University of Florence, Italy. lucia@risc1.lrm.fi.cnr.it
Gori-Savellini
G
G
Turano
P
P
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003574:Cytochrome c Group / Q000737:chemistry*; D045304:Cytochromes c; D005656:Fungal Proteins / Q000737:chemistry*; D006418:Heme / Q000737:chemistry; D006860:Hydrogen Bonding; D007501:Iron / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins; D012984:Software; D012995:Solubility; D014867:Water / Q000737:chemistry
C014059:CYC1 protein, S cerevisiae; D003574:Cytochrome c Group; D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; D014867:Water; D006418:Heme; D045304:Cytochromes c; D007501:Iron