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Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c
Author(s) -
Murzyn Krzysztof,
Róg Tomasz,
Blicharski Wojciech,
Dutka Małgorzata,
Pyka Janusz,
Szytula Sebastian,
Froncisz Wojciech
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20838
Subject(s) - moiety , chemistry , molecular dynamics , spin label , crystallography , cytochrome , hydrogen bond , cytochrome c , myoglobin , stereochemistry , hemeprotein , protein data bank (rcsb pdb) , heme , protein structure , computational chemistry , molecule , enzyme , biochemistry , organic chemistry , membrane , mitochondrion
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. Proteins 2006. © 2006 Wiley‐Liss, Inc.