Using Molecular Dynamics to Investigate 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 challenging as well as of great importance in design of effective drugs. The protease-substrate complex crystal structures indicate that substrates occupy a remarkable uniform region within the binding site, which has been termed as the substrate envelope. Nevertheless, protein activity is 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 complexes have been carried out by molecular dynamics (MD) simulations. Conformations of the complex structures in time were analyzed with respect to the interaction of substrate with protease in terms of the substrate volume, changes in van der Waals contacts between the two, and dynamics of both substrate and protease. Co-evolution of substrate peptides with the drug-resistant protease variants was also analyzed. Similar analysis to those in wild-type complex structures were done for MD simulations for p1-p6 substrates (wild-type and LP1'F) in complex with protease variants (D30N, N88D, and D30N/N88D). The substrate recognition was observed to be an interdependent event and the recognition mechanism may not be the same for all natural substrates. The dynamic substrate envelope was found to be smaller than the crystal structures suggest. The substrate recognition is altered when there is drug resistance and this alteration is compensated by co-evolution. The results reveal that conservation of the peptide conformational preferences and dynamic behavior of the complex structure appears to be important for substrate recognition.