Mutational scan of self-cleavage by HIV-1 protease provides new views of a conformationally dynamic mechanism

The mechanism of conformationally dynamic proteins remains understudied because they are difficult to analyze structurally. For HIV-1 protease the mechanism of cleavage by mature protease is well understood in large part because it forms a stable structure that is amenable to x-ray crystallography. However, self-cleavage or autoproteolysis of protease from the viral polyprotein involves transiently populated structures and is poorly understood. We probed autoproteolysis in HIV-1 using a yeast reporter and mutational scanning. We compared our results with mutational scanning of protease on viral fitness, which integrates both autocleavage and cutting by mature enzyme. We identified 220 mutations that were well tolerated for self-cleavage but not fitness. We analyzed three of these mutations (D30E, W42M and P44L) using independent approaches. All three were capable of efficient self-cleavage in a bacterial assay of autoproteolysis, but had strong defects in mature form for cleavage of a peptide substrate. These separation of function mutations from the mutational scan clustered at hot-spot locations that do not impact autoproteolysis likely because they are conformationally dynamic during self-cleavage. We used the mutational scanning results and molecular simulations to provide models of autoproteolysis conformations. These models provide new views of a structurally dynamic mechanism.