Bioinformatics Open Source Conference (BOSC 2011) Call for Abstracts | O|B|F News.
Molecular dynamics of prototype foamy virus protease flap region, N- and C-termini in aqueous solution
Sergey Shityakov and Thomas Dandekar
Department of Bioinformatics
University of Würzburg
97074 Würzburg, Germany
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 flap region, N- and C-termini in aqueous solution. The PFV protease monomer undergoes some changes of secondary structure but remains stable during 10 ns simulation time. In particular, the flap region and the N- and C-termini turned out to be highly flexible. Nevertheless, retroviral protease dimerization process occurs through the anti-parallel β-sheet, which is absent in the PFV protease. Although the overall folds of β-sheets and α-helices are remained quite similar and stable, the PFV protease dimerization mechanism reveals significant differences in the dimerization interface relative to other retroviral proteases, such as HIV protease. Therefore, PFV protease dimerization event might be mediated through the additional viral or cellular cofactors. Finally, the results provide a model for the flap region, N- and C-termini overall dynamics that is considered to be important for regulation of the enzyme function.
Keywords: molecular dynamics, foamy virus protease, flap region, termini
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