Conformational flexibility decreased due to Y67F and F82H mutations in cytochrome c: Molecular dynamics simulation studies

Cytochrome c (cyt c), a mitochondrial protein, has dual functions in controlling both cellular energetic metabolism and apoptosis (programmed cell death). During apoptosis, cyt c (Fe3+) released into the cytosol initiates caspase activation leading to apoptosis. Since, X-ray crystallography gives only the static structure, we report here the dynamic behavior of holo and apo wild type (WT), Y67F and F82H mutant cyt c's (Fe3+) in their apoptotic states. Four nanosecond MD simulations were run for holo WT, Y67F and F82H cyt c's with and without Fe center dot center dot center dot S (Met-80) bond and also for apo WT and mutated cyt c's (Y67F and F82H) in water using GROMOS96 force field. Mutations of Y67F and F82H resulted in the decrease of backbone and Cot RMSDs, and radii of gyration (backbone and protein) in both the holo and apo forms. MD and ED results revealed that the flexibility of mutated holo cyt c's decreased perhaps affecting their ability to take part in mitochondrial electron/proton transfer process. Without Fe center dot center dot center dot S bond, the backbone and C alpha RMSD increased in holo cyt c's perhaps resulting in enhanced peroxidase activity. ED revealed that four to six eigenvectors involved in over all motions of holo cyt c's without Fe center dot center dot center dot S bond, and six to eight eigenvectors in apo cyt c's in comparison to three to four eigenvectors for holo cyt c's with Fe center dot center dot center dot S bond. (C) 2009 Elsevier Inc. All rights reserved.