Kinetic and modeling studies of subsites S4-S3' of Moloney murine leukemia virus protease.

The substrate specificity of the Moloney murine leukemia virus protease (Mo-MuLV PR) was analyzed by using the oligopeptide substrate Val-Ser-Gln-Asn-Tyr decreases Pro-Ile-Val-Gln-NH2 and a series of analogs containing single amino acid substitutions in the P4-P3' positions. Mo-MuLV PR appears to act similarly to the human immunodeficiency virus (HIV) PRs, except for peptides having substitutions at P4 and P2 positions. Mo-MuLV PR shows a strong preference for the analogs having hydrophobic residues, such as Val or Ile at P4, and Ile and Leu at P2, in contrast to HIV-1 and HIV-2 PRs, which prefer smaller or more polar residues at both positions. We built a molecular model of Mo-MuLV PR on the basis of the crystal structure of the related HIV PR. Although the overall structure of Mo-MuLV PR is predicted to be close to that of HIV-1 PR, almost all of the residues forming the subsites are different. The increased hydrophobicity due to the Pro12 insertion and the presence of more aromatic residues in the S4 subsite of Mo-MuLV PR compared to HIV-1 and HIV-2 PRs can be correlated with the observed differences using P4-substituted analogs of VSQNYPIVQ. The preference of Mo-MuLV PR for larger hydrophobic residues at the P2 position can be correlated with the larger size of its S2 subsite, due in part to the presence of Val39, Ala57, and His84 in Mo-MuLV PR, instead of Ile32, Ile50, and Met76, respectively, as occurs in HIV-2 PR.