Studies on the symmetry and sequence context dependence of the HIV-1 proteinase specificity

Two major types of cleavage sites with different sequence preferences have been proposed for the human immunodeficiency virus type 1 (HIV-1) proteinase, To understand the nature of these sequence preferences better, single and multiple amino acid substitutions were introduced into a type 1 cleavage site peptide, thus changing it to a naturally occurring type 2 cleavage site sequence, Our results indicated that the previous classification of the retroviral cleavage sites may not be generally valid and that the preference for a residue at a particular position in the substrate depends strongly on the neighboring residues, including both those at the same side and at the opposite side of the peptide backbone of the substrate, Based on these results, pseudosymmetric (palindromic) substrates were designed, The retroviral proteinases are symmetrical dimers of two identical subunits; however, the residues of naturally occurring cleavage sites do not show symmetrical arrangements, and no obvious symmetrical substrate preference has been observed for the specificity of HIV proteinase, To examine the role of the asymmetry created by the peptide bonds on the specificity of the respective primed and nonprimed halves of the binding site, amino acid substitutions were introduced into a palindromic sequence, In general, the results suggested that the asymmetry does not result in substantial differences in specificity of the S-3 and S-3' subsites, whereas its effect is more pronounced for the S-2 and S-2' subsites, Although it was possible to design several good palindromic substrates, asymmetrical arrangements may be preferred by the HIV proteinase.