Dresden 2011 – scientific programme

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BP: Fachverband Biologische Physik

BP 8: Posters: Protein Structure \& Dynamics

BP 8.5: Poster

Monday, March 14, 2011, 17:15–20:00, P3

Rigidity analysis of HIV-1 protease — Jack Heal, Stephen Wells, Emilio Jimenez-Roldan, and •Rudolf Roemer — Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom

We show the effect of different inhibitors on the rigidity profile of HIV-1 protease as it unfolds. A rigidity analysis of 40 protein crystal structures from the protein data bank is made using the software FIRST. The results are compared with and without inhibitors present. This study builds on a recent comparative study of protein structures using FIRST. In a simulated rigidity dilution, the unfolding pattern of the protein can be observed. The presence of an inhibitor slows the rigidity loss, in particular around the active site of the enzyme. FIRST is not computationally demanding and its results can be calculated on a timescale of CPU-minutes. We study protein mobility along low-frequency normal modes of motion using the FRODA software and the elastic network model. The presence of an inhibitor changes the extent to which the protein is able to move in these directions.