Molecular dynamics of substrate recognition and co-evolution in HIV-1 protease

Abstract

Human Immunodeficiency Virus Type 1 (HIV-1) protease recognizes at least ten cleavage sites as its natural substrates. There is little sequence homology between these substrates and they are asymmetric around the cleavage site in both charge and size distribution. Thus, understanding of the molecular determinants of substrate recognition is a challenging task as well as of great importance in design of effective drugs. The protease-substrate complex crystal structures indicate that the substrates occupy a remarkable uniform region within the binding site, which has been termed as the substrate envelope. Nevertheless, the activities of proteins are intimately related to the dynamics, from local to global motion of the structure. To this end, an elaborated analysis on both structural and dynamic features of seven HIV-1 protease-substrate complex structures are carried out by molecular dynamics (MD) simulations in the present thesis. The conformations of the complex structures in time have been analyzed with respect to the interaction of the substrate with the protease in terms of the substrate volume, the changes in the van der Waals (vdW) contacts between the two, and the dynamics of both substrate and the protease in general. On the other hand, the co-evolution of the substrate peptides with the drug-resistant protease variants is also analyzed. The MD simulations for the p1-p6 substrates (wild-type and LP1’F) in complex with the protease variants (D30N, N88D, and D30N/N88D) were run and similar analysis to those in wild-type complex structures were made. In this work, the substrate recognition has been observed to be an interdependent event and the recognition mechanism may not be the same for all natural substrates. Also, the dynamic substrate envelope has been found to be smaller than the crystal structures suggest. The analyses of the mutant structures have shown that the substrate recognition is altered when there is drug resistance and this alteration is compensated by co-evolution. The results reveal that the conservation of the peptide conformational preferences and dynamic behavior of the complex structure appears to be important for protease substrate recognition.