title: Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c.
abstract: A series of multi-nanosecond molecular dynamics (MD) simulations of wild-type cytochrome c and its spin-labeled variants with the methanethiosulfonate moiety attached at position C102 were performed (1) to elucidate the effect of the spin probe presence on the protein structure and (2) to describe the structure and dynamics of the spin-label moiety. Comparisons with the reference crystal structure of cytochrome c (PDB entry: 1YCC) indicate that the protein secondary structure is well preserved during simulations of the wild-type cytochrome c but slightly changed in simulations of the cytochrome c labeled at position C102. At the time scale covered in our simulations, the spin label exhibits highly dynamical behavior. The number of observed distinct conformations of the spin label moiety is between 3 and 13. The spin probe was found to form short-lived hydrogen bonds with the protein. Temporary hydrophobic interactions between the probe and the protein were also detected. The MD simulations directly show that the disulfide bond in the tether linking a spin probe with a protein strongly influence the behavior of the nitroxide group. The conformational flexibility and interaction with the protein are different for each of the two low energy conformations of the disulfide bond.
authors.affiliation: Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, Krakow, Poland. murzyn@mol.uj.edu.pl
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Murzyn
authors.forename: Tomasz
authors.initials: T
authors.lastname: Róg
authors.forename: Wojciech
authors.initials: W
authors.lastname: Blicharski
authors.forename: Małgorzata
authors.initials: M
authors.lastname: Dutka
authors.forename: Janusz
authors.initials: J
authors.lastname: Pyka
authors.forename: Sebastian
authors.initials: S
authors.lastname: Szytula
authors.forename: Wojciech
authors.initials: W
authors.lastname: Froncisz
mesh_terms: D003198:Computer Simulation; D045304:Cytochromes c / Q000737:chemistry* / Q000378:metabolism*; D004220:Disulfides / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry; D013113:Spin Labels
chemical_list: D004220:Disulfides; D011994:Recombinant Proteins; D013113:Spin Labels; D045304:Cytochromes c