Intra- and Inter-Molecular Coevolution: The Case of HIV1 Protease and Reverse Transcriptase

The stability, fold, and the function of proteins need to be maintained throughout the evolution of these molecules – inducing a selective pressure, that can be revealed in sequence data sets. The conservation of structure and function implies coevolution of amino acids within the protein. To understand such selective pressure in the evolution of the human immunodeficiency virus (HIV), we apply information theoretical measures to the two most important enzymes for the progression of viral infection: the reverse transcriptase and the protease. We computed the mutual information to derive insight into the selective pressure acting locally and globally on the enzymes. We found intra- and inter-protein co-evolution of residues in these enzymes and annotate important structural-evolutionary correlations. We discuss a signal indicating a potential co-evolution between the protease and the reverse transcriptase.