Biology subjects

Swanstrom, R.

Publications and source records attributed to Swanstrom, R..

2 recordsLinked to original sources

bioRxiv2018

HIV-1 Protease Uses Bi-Specific S2/S2’ Subsites To Optimize Cleavage of Two Classes of Target Sites

Retroviral proteases (PR) have a unique specificity that allows cleavage of sites with or without a P1 proline. A P1 proline is required at the MA/CA cleavage site due to its role in a post-cleavage conformational change in the capsid protein. However, the HIV-1 PR prefers to have large hydrophobic amino acids flanking the scissile bond, suggesting PR recognizes two different classes of substrate sequences. We analyzed the cleavage rate of over 150 iterations of six different HIV-1 cleavage sites to explore rate determinants of cleavage. We found that cleavage rates are strongly influenced by the two amino acids flanking the amino acids at the scissile bond (P2-P1/P1-P2), with two complementary sets of rules. When P1 is proline, the P2 side chain interacts with a polar region in the S2 subsite of the PR, while the P2 amino acid interacts with a hydrophobic region of the S2 subsite. When P1 is not proline, the orientations of the P2 and P2 side chains with respect to the scissile bond are reversed; P2 residues interact with a hydrophobic face of the S2 subsite while the P2 amino acid usually engages hydrophilic amino acids in the S2 subsite. These results reveal that the HIV-1 PR has evolved bi-functional S2 and S2 subsites to accommodate the steric effects imposed by a P1 proline on the orientation of P2 and P2 substrate side chains. These results also suggest a new strategy for inhibitor design to engage the multiple specificities in these subsites.

biochemistry↗

bioRxiv2018

Constrained mutational sampling of amino acids in HIV-1 protease evolution

The evolution of HIV-1 protein sequences should be governed by a combination of factors including nucleotide mutational probabilities, the genetic code, and fitness. The impact of these factors on protein sequence evolution are interdependent, making it challenging to infer the individual contribution of each factor from phylogenetic analyses alone. We investigated the protein sequence evolution of HIV-1 by determining an experimental fitness landscape of all individual amino acid changes in protease. We compared our experimental results to the frequency of protease variants in a publicly available dataset of 32,163 sequenced isolates from drug-naive individuals. The most common amino acids in sequenced isolates supported robust experimental fitness, indicating that the experimental fitness landscape captured key features of selection acting on protease during viral infections of hosts. Amino acid changes requiring multiple mutations from the likely ancestor were slightly less likely to support robust experimental fitness than single mutations, consistent with the genetic code favoring chemically conservative amino acid changes. Amino acids that were common in sequenced isolates were predominantly accessible by single mutations from the likely protease ancestor. Multiple mutations commonly observed in isolates were accessible by mutational walks with highly fit single mutation intermediates. Our results indicate that the prevalence of multiple base mutations in HIV-1 protease is strongly influenced by mutational sampling.

evolutionary biology↗