Temperature dependence of fluctuations in HIV1-protease
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Revealing the structure and the intrinsic dynamics of a protein is paramount to understand its function and other properties of evolutionary importance. Several schemes to obtain such insight in silico were developed over the decades. A computationally efficient protocol approximates the molecular dynamics around its native state by a harmonic potential. In this paper, we introduce a new methodology to combine the various harmonic approaches to understand the folding/unfolding dynamics and the dynamics around the native structure of the protein in a temperature dependent way. We apply this new protocol to the HIV1-protease and discuss the results in the light of events in the adaptive evolution towards drug resistance, which is a major problem in HIV infection.
KeywordsHIV1-protease Elastic network models Self-consistent pair-contact probability method Statistical mechanics Molecular dynamics
Parts of this work were supported through a Liebig-Fellowship of the Fonds der chemischen Industrie. Additional financial support of the Fonds der chemischen Industrie is also acknowledged. Figures of molecular structures were generated using VMD (Humphrey et al. 1996).
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