Abstract:
: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 Mg(2+) (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 degrees C and at 30 degrees C is very good. The fluorescence anisotropy decays were also simulated. Interestingly, the fit to the experimental anisotropy decay was excellent at 5 degrees C and rather poor at 30 degrees C. Various hypotheses such as dimerization and abnormal increase of uncorrelated internal motions are discussed.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Laboulais C,Deprez E,Leh H,Mouscadet JF,Brochon JC,Le Bret Mdoi
10.1016/S0006-3495(01)75715-3subject
Has Abstractpub_date
2001-07-01 00:00:00pages
473-89issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(01)75715-3journal_volume
81pub_type
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