Retroviral proteases

The HIV-1 protease, like other retroviral proteases, is a homodimeric aspartyl protease (see Fig. 1). The active site is formed at the dimer interface, with the two aspartic acids located at the base of the active site. The enzymatic mechanism is thought to be a classic acid-base catalysis involving a water molecule and what is called a push-pull mechanism. The water molecule is thought to transfer a proton to the dyad of the carboxyl groups of the aspartic acids, and then a proton from the dyad is transferred to the peptide bond that is being cleaved. In this mechanism, a tetrahedral intermediate transiently exists, which is nonconvalent and which is mimicked in most of the currently used FDA approved inhibitors. 

Matayoshi, E. D., Wang, G. T., Krafft, G. A. and Erickson, J. (1990). Novel fluorogenic substrates for assaying retroviral proteases by resonance energy transfer. Science 247, 954-958. 

A. Wlodawer, and A. Gustchina, Structural and biochemical studies of retroviral proteases, Biochim. Biophys. Acta. 1477 16(2000). 

Selk, L. Clawson, J. Schneider, and S. Kent, Conserved folding in retroviral Protease Crystal structure of a synthetic HIV-1 protease, Science 245 616 (1989). 

FI/F2/F3, triad of RING-finger-like domains F, F-box domain USP, deubiquitinase catalytic domain OTU, a particular class of cystein protease domains RVP, retroviral protease domain DBA, ubiquitin-associated domain Pkinase, protein kinase catalytic domain. 

Selected entries from Methods in Enzymology [vol, page(s)] Association constant determination, 259, 444-445 buoyant mass determination, 259, 432-433, 438, 441, 443, 444 cell handling, 259, 436-437 centerpiece selection, 259, 433-434, 436 centrifuge operation, 259, 437-438 concentration distribution, 259, 431 equilibration time, estimation, 259, 438-439 molecular weight calculation, 259, 431-432, 444 nonlinear least-squares analysis of primary data, 259, 449-451 oligomerization state of proteins [determination, 259, 439-441, 443 heterogeneous association, 259, 447-448 reversibility of association, 259, 445-447] optical systems, 259, 434-435 protein denaturants, 259, 439-440 retroviral protease, analysis, 241, 123-124 sample preparation, 259, 435-436 second virial coefficient [determination, 259, 443, 448-449 nonideality contribution, 259, 448-449] sensitivity, 259, 427 stoichiometry of reaction, determination, 259, 444-445 terms and symbols, 259, 429-431 thermodynamic parameter determination, 259, 427, 443-444, 449-451. 

HIV PR and other retroviral proteases are not enzymes that have evolved to carry out a single reaction at a rapid rate, but rather enzymes with minimum specificity required to cleave the viral precursors in a specific and orderly manner. 

Toh H, Ono M, Saigo K, Miyata T. Retroviral protease-like sequence in the yeast transposon TY1. Nature 1985 315 691-693. 

Pearl LN, Taylor WR. A structural model for the retroviral protease. Nature 1987 329 351-354. 

GA Krafft, GT Wang. Synthetic approaches to continuous assays of retroviral proteases. Meth Enzymol 241 70-86, 1994. 

Wlodawer A, Miller M, Jaskdlski M, Sathyanarayana BK, Baldwin E, Weber IT, et al. Conserved folding in retroviral proteases crystal structure of a synthetic HlV-1 protease. Science 1989 245 616-621. 

Retroviruses encode a protease (PR) responsible for cleaving polyprotein precursors, and such processing is essential for proper virion assembly and maturation. Based on the presence of a sequence Asp-Ser/Thr-Gly in the active sites of retroviral proteases (1) and their inhibition in vitro by pepstatin (2-7), these enzymes have been classified as members of the aspartic protease family. Crystal structures have been determined for the proteases from Rous sarcoma virus (RSV PR) (8), from two variants and several mutants of the human immunodeficiency vims (HIV PR) (9-11), from feline immunodeficiency virus (FIV PR) (12) and from equine infectious anemia vims (EIAV PR) (13). Aspartic proteases contain a single active site which includes two aspartates. In apoenzymes, the two catalytic Asp residues from the active site triad have been found to be in hydrogen bond contact with a water molecule (10). Mutations of the active site Asp25 in HIV-1 PR into Asn (14,15), Thr (3) or Ala (4,16,17) led to an inactive enzyme. Similarly, the RSV PR was inactivated by mutation of its active site Asp to He (18). 

Miller, M., Jaskolski, M., Rao, J. K, M., Leis, J., and Wlodawer, A.( 1989). Crystal structure of a retroviral protease proves relationship to aspartic protease family. Nature 337, 576-579. 

In another example, p-nitrophenyl chloroformate was required to introduce a sophisticated carbamate function in a multi-steps synthesis of retroviral protease inhibiting compounds (Ref. 26). The structure of the intermediate carbonate is given in scheme 30. 

Scheme 30 Preparation of a key intermediate for the synthesis of retroviral protease inhibitors.

L. H. Pearl andW. R. Taylor, Nature (London), 329, 351 (1987). A Structural Model for the Retroviral Proteases. 

Retroviral protease Xentronics MWPC 88.95 78.90 P3j21 3.0 Miller et al (1989)... 

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