Molecular statistics of cytochrome c: structural plasticity and molecular environment.
Nuclear magnetic resonance experiments performed on yeast mitochondrial cytochrome c (Cytc), a paradigmatic electron transfer protein, reveal that the two oxidation states have similar structures, but different mobility: despite the few structural differences compared with the reduced form, the oxidized form displays a larger unfolding propensity. Molecular dynamics simulations performed on both NMR reduced and NMR oxidized forms show that the reduced form has a larger solvent-accessible surface area (SASA). Starting from this observation, a molecular statistical approach was then applied in order to correlate the molecular surface to molecular mobility. Simulations started from biased initial conditions corresponding to different molecular sizes were combined with the maximal constrained entropy method. The NMR structure of oxidized Cytc is more suited to expose a smaller SASA than the NMR structure of the reduced form, but the accessible conformational landscape at 300 K around the NMR oxidized structure is flatter than for the NMR reduced structure. Protein configurations of smaller SASA and size display larger plasticity when they resemble the NMR oxidized structure, whereas they are more rigid when they resemble the NMR reduced structure. Implications of the results for the protein properties during its functional process are discussed.
La Penna
Giovanni
G
Institute for Macromolecular Studies, National Research Council, Via De Marini 6, 16149, Genoa, Italy. lapenna@ge.ismac.cnr.it
Furlan
Sara
S
Banci
Lucia
L
D003198:Computer Simulation / Q000706:statistics & numerical data*; D045304:Cytochromes c / Q000737:chemistry*; D004579:Electron Transport; D008958:Models, Molecular; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D010084:Oxidation-Reduction; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions / Q000737:chemistry*
D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions; D045304:Cytochromes c