Abstract
HIV-1 protease represents an appealing system for directed enzyme re-design, since it has various different endogenous targets, a relatively simple structure and it is well studied. Recently Chaudhury and Gray (Structure (2009) 17: 1636–1648) published a computational algorithm to discern the specificity determining residues of HIV-1 protease. In this paper we present two computational tools aimed at re-designing HIV-1 protease, derived from the algorithm of Chaudhuri and Gray. First, we present an energy-only based methodology to discriminate cleavable and non cleavable peptides for HIV-1 proteases, both wild type and mutant. Secondly, we show an algorithm we developed to predict mutant HIV-1 proteases capable of cleaving a new target substrate peptide, different from the natural targets of HIV-1 protease. The obtained in silico mutant enzymes were analyzed in terms of cleavability and specificity towards the target peptide using the energy-only methodology. We found two mutant proteases as best candidates for specificity and cleavability towards the target sequence.
Highlights
Proteases represent a class of enzymes ubiquitous in all living organisms, with multiple applications in industry and biotechnology research [1,2,3]
In the following paragraphs we evaluate our methodology in terms of binding energies versus cleavability for: (1) Wild type PR (WT-PR) and its endogenous substrates and known cleavable and non-cleavable peptides, (2) the Pr3 set of mutant PRs and endogenous substrates and (3) the DR set with wild type and mutated endogenous peptides
In the first part of this study we developed a methodology to test the cleavability of a peptide by HIV-1 protease (Tables 1 and S6 in File S1), solely based on the binding energy between the enzyme and the substrate
Summary
Proteases represent a class of enzymes ubiquitous in all living organisms, with multiple applications in industry and biotechnology research [1,2,3]. HIV1 protease (PR) represents an attractive starting structure for directed enzyme re-design, since it is known to cleave a variety of sequences. Wild type PR (WT-PR) is very specific for the endogenous cleavage sequences of the polyprotein (endogenous substrate peptides, Table S1 in File S1), even if the source of this specificity is still not completely clear. There is no clear trend in amino acid sequence (e.g. a negatively charged amino acid in position P1 or a hydrophobic one in position P29). This suggests that with few mutations PR could be made to cleave other target peptide sequences in a specific manner
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
