Sergey Shityakov and Thomas Dandekar
Scientific Tracks Abstracts: JAA
Molecular dynamics trajectories are Cartesian coordinates produced by recording of dynamical changes over time representing the positions of each atom along a series of small time step. Here, we implemented atomistic molecular dynamics simulations of prototype foamy virus (PFV) protease monomer to investigate the conformational changes of the fl ap region, N- and C-termini in aqueous solution. Th e PFV protease monomer undergoes some changes of secondary structure but remains stable during 10 ns simulation time. In particular, the fl ap region and the N- and C-termini turned out to be highly fl exible. Nevertheless, retroviral protease dimerization process occurs through the anti-parallel �²-sheet, which is absent in the PFV protease. Although the overall folds of �²-sheets and �±-helices are remained quite similar and stable, the PFV protease dimerization mechanism reveals signifi cant diff erences in the dimerization interface relative to other retroviral proteases, such as HIV protease. Th erefore, PFV protease dimerization event might be mediated through the additional viral or cellular cofactors. Finally, the results provide a model for the fl ap region, N- and C-termini overall dynamics that is considered to be important for regulation of the enzyme function.
Dr. Sergey Shityakov M.D Ph.D is a virologist from the Institute for Virology and Immunobiology (VIM) University of W?rzburg in Germany. He has a wide experience in applied experimental and theoretical research ranging from basic virology to computational biochemistry. He is recognized for conducting research on retroviruses such as human immunodefi ciency viruses (HIV) and prototype foamy viruses (PFV) to elucidate the mechanism of their nuclear import. His several papers regarding to retroviral pathogenesis and functional morphology have been published in various international peer-reviewed scientifi c journals. He is currently working at the University of W?rzburg in the department of bioinformatics. He holds a membership of the Euroscience Association.
