Rigidity analysis of HIV-1 protease

J W Heal, S A Wells, E Jimenez-roldan, R F Freedman, R A Römer

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Abstract

We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes significantly in the presence of an inhibitor. Our study shows that the action of the inhibitors is to restrict the flexibility of the β-hairpin flaps which allow access to the active site. The results are discussed in the context of full molecular dynamics simulations as well as data from NMR experiments.
Original languageEnglish
Article number012006
JournalJournal of Physics: Conference Series
Volume286
Issue number1
DOIs
Publication statusPublished - 1 Mar 2011

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    Heal, J. W., Wells, S. A., Jimenez-roldan, E., Freedman, R. F., & Römer, R. A. (2011). Rigidity analysis of HIV-1 protease. Journal of Physics: Conference Series, 286(1), [012006]. https://doi.org/10.1088/1742-6596/286/1/012006