Collective motions in HIV-1 reverse transcriptase: Examination of flexibility and enzyme function

In order to study the inferences of structure for mechanism, the collective motions of the retroviral reverse transcriptase HIV-1 RT (RT) are examined using the Gaussian network model (GNM) of proteins. This model is particul arly suitable for elucidating the global dynamic characteristics of large p roteins such as the presently investigated heterodimeric RT comprising a to tal of 982 residues. Local packing density and coordination order of amino acid residues is inspected by the GNM to determine the type and range of mo tions, both at the residue level and on a global scale, such as the correla ted movements of entire subdomains. Of the two subunits, p66 and p51, formi ng the RT, only p66 has a DNA-binding cleft and a functional polymerase act ive site. This difference in the structure of the two subunits is shown her e to be reflected in their dynamic characteristics: only p66 has the potent ial to undergo large-scale cooperative motions in the heterodimer, while p5 1 is essentially rigid. Taken together, the global motion of the RT heterod imer is comprised of movements of the p66 thumb subdomain perpendicular to those of the p66 fingers, accompanied by anticorrelated fluctuations of the RNase H domain and p51 thumb, thus providing information about the details of one processivity mechanism. A few clusters of residues, generally dista nt in sequence but close in space, are identified in the p66 palm and conne ction subdomains, which form the hinge-bending regions that control the hig hly concerted motion of the subdomains. These regions include the catalytic ally active site and the non-nucleoside inhibitor binding pocket of p66 pol ymerase, as well as sites whose mutations have been shown to impair enzyme activity. It is easily conceivable that this hinge region, indicated by GNM analysis to play a critical role in modulating the global motion, is locke d into an inactive conformation upon binding of an inhibitor. Comparative a nalysis of the dynamic characteristics of the unliganded and liganded dimer s indicates severe repression of the mobility of the p66 thumb in RT's glob al mode, upon binding of non-nucleoside inhibitors. (C) 1999 Academic Press .