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Biophys J, July 2001, p. 473-489, Vol. 81, No. 1

HIV-1 Integrase Catalytic Core: Molecular Dynamics and Simulated Fluorescence Decays

Cyril Laboulais,* Eric Deprez,* Hervé Leh,dagger Jean-François Mouscadet,dagger Jean-Claude Brochon,* and Marc Le Bret*

 *Laboratoire de Biotechnologies et de Pharmacologie Génétique Appliquée (UMR8532 Centre National de la Recherche Scientifique), Ecole Normale Supérieure de Cachan, 94235 Cachan, and  dagger Laboratoire de Physicochimie et de Pharmacologie des Macromolécules Biologiques (UMR8532 Centre National de la Recherche Scientifique), Institut Gustave Roussy, 94805 Villejuif, France

Two molecular dynamics simulations have been carried out on the HIV-1 integrase catalytic core starting from fully determined crystal structures. During the first one, performed in the absence of divalent cation (6-ns long), the catalytic core took on two main conformations. The conformational transition occurs at approximately 3.4 ns. In contrast, during the second one, in the presence of Mg2+ (4-ns long), there were no such changes. The molecular dynamics simulations were used to compute the fluorescence intensity decays emitted by the four tryptophan residues considered as the only chromophores. The decay was computed by following, frame by frame, the amount of chromophores that remained excited at a certain time after light absorption. The simulation took into account the quenching through electron transfer to the peptide bond and the fluorescence resonance energy transfer between the chromophores. The fit to the experimental intensity decays obtained at 5°C and at 30°C is very good. The fluorescence anisotropy decays were also simulated. Interestingly, the fit to the experimental anisotropy decay was excellent at 5°C and rather poor at 30°C. Various hypotheses such as dimerization and abnormal increase of uncorrelated internal motions are discussed.

Biophys J, July 2001, p. 473-489, Vol. 81, No. 1
© 2001 by the Biophysical Society   0006-3495/01/07/473/17  $2.00


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