Comparative Studies on the Substrate Specificity of Avian Myeloblastosis Virus Proteinase and Lentiviral Proteinases

Tőzsér, József; Bagossi, Péter; Weber, Irene T.; Copeland, Terry D.; Oroszlan, Stephen

doi:10.1074/jbc.271.12.6781

Cited by 30 publications

(34 citation statements)

References 43 publications

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“…Nevertheless, the specificity constants obtained for the HIV-2, EIAV, AMV, and BLV PRs were within the range of those obtained with peptides representing their naturally occurring cleavage sites (27,31).…”

Section: Discussionsupporting

confidence: 60%

“…HFV PR was also unable to hydrolyze the substituted peptides except for the one containing P3-Val; therefore, this enzyme was omitted from further analysis. Our previous studies established that the relative activities measured under the given conditions correlated well with the specificity constants (k cat /K m ) (31).…”

Section: Resultsmentioning

confidence: 67%

“…The expression forms of the enzymes used in this study are summarized in Table 1. Active site titration for the HIV-1, HIV-2, EIAV, AMV, HTLV-1, BLV, and MMLV PRs was performed as described previously (6,13,31,34,37,40). Active site titration of the MPMV PR was performed using the phenylstatine (Pst)-containing inhibitor PYVPstAMT.…”

Section: Retroviralmentioning

confidence: 99%

“…1. Previously, a large set of peptides containing single amino acid substitutions in the P4-to-P3Ј region of the Val-Ser-Gln-Asn-Tyr2Pro-Ile-Val-Gln oligopeptide, a typical type 1 substrate representing the matrix/ capsid cleavage site of HIV-1 (where the arrow denotes the site of the cleavage), was used to characterize the specificity of the PRs of various retroviruses, including HIV-1, HIV-2 (32, 34), equine infectious anemia virus (EIAV) (37), Moloney murine leukemia virus (MMLV) (18), and avian myeloblastosis virus (AMV) (31). Based on these studies, the P2 position was found to be critical for determining the substrate specificity differences of retroviral PRs.…”

mentioning

confidence: 99%

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Amino Acid Preferences of Retroviral Proteases for Amino-Terminal Positions in a Type 1 Cleavage Site

Eizert

Bander

Bagossi

et al. 2008

J Virol

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The specificities of the proteases of 11 retroviruses were studied using a series of oligopeptides with amino acid substitutions in the P1, P3, and P4 positions of a naturally occurring type 1 cleavage site (Val-Ser-GlnAsn-Tyr2Pro-Ile-Val-Gln) in human immunodeficiency virus type 1 (HIV-1). Previously, the substrate specificity of the P2 site was studied for the same representative set of retroviral proteases, which included at least one member from each of the seven genera of the family Retroviridae (P. Bagossi, T. Sperka, A. Fehér, J. Kádas, G. Zahuczky, G. Miklóssy, P. Boross, and J. Tözsér, J. Virol. 79:4213-4218, 2005). Our enzyme set comprised the proteases of HIV-1, HIV-2, equine infectious anemia virus, avian myeloblastosis virus (AMV), Mason-Pfizer monkey virus, mouse mammary tumor virus (MMTV), Moloney murine leukemia virus, human T-lymphotropic virus type 1, bovine leukemia virus, walleye dermal sarcoma virus, and human foamy virus. Molecular models were used to interpret the similarities and differences in specificity between these retroviral proteases. The results showed that the retroviral proteases had similar preferences (Phe and Tyr) for the P1 position in this sequence context, but differences were found for the P3 and P4 positions. Importantly, the sizes of the P3 and P4 residues appear to be a major contributor for specificity. The substrate specificities correlated well with the phylogenetic tree of the retroviruses. Furthermore, while the specificities of some enzymes belonging to different genera appeared to be very similar (e.g., those of AMV and MMTV), the specificities of the primate lentiviral proteases substantially differed from that observed for a nonprimate lentiviral protease.

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Section: Discussionsupporting

confidence: 60%

Section: Resultsmentioning

confidence: 67%

Section: Retroviralmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Amino Acid Preferences of Retroviral Proteases for Amino-Terminal Positions in a Type 1 Cleavage Site

Eizert

Bander

Bagossi

et al. 2008

J Virol

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“…Previously, a large series of peptides containing singleamino-acid substitutions in the P4-P3Ј (nomenclature according to reference 29) region of the Val-Ser-Gln-Asn-Tyr2Pro-Ile-Val-Gln oligopeptide (the arrow indicates the site of cleavage) were used to characterize the specificities of the proteases of various retroviruses, including those of HIV-1, HIV-2 (38,40), equine infectious anemia virus (EIAV) (44), Moloney murine leukemia virus (MMLV) (22), and avian myeloblastosis virus (AMV) (34). Activities relative to the unmodified peptide were determined for substituted peptides (except for MMLV PR) to compare the specificities of the enzymes.…”

mentioning

confidence: 99%

Amino Acid Preferences for a Critical Substrate Binding Subsite of Retroviral Proteases in Type 1 Cleavage Sites

Bagossi

Sperka

Fehér

et al. 2005

J Virol

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The specificities of the proteases of 11 retroviruses representing each of the seven genera of the family Retroviridae were studied using a series of oligopeptides with amino acid substitutions in the P2 position of a naturally occurring type 1 cleavage site (Val-Ser-Gln-Asn-Tyr2Pro-Ile-Val-Gln; the arrow indicates the site of cleavage) in human immunodeficiency virus type 1 (HIV-1). This position was previously found to be one of the most critical in determining the substrate specificity differences of retroviral proteases. Specificities at this position were compared for HIV-1, HIV-2, equine infectious anemia virus, avian myeloblastosis virus, MasonPfizer monkey virus, mouse mammary tumor virus, Moloney murine leukemia virus, human T-cell leukemia virus type 1, bovine leukemia virus, human foamy virus, and walleye dermal sarcoma virus proteases. Three types of P2 preferences were observed: a subgroup of proteases preferred small hydrophobic side chains (Ala and Cys), and another subgroup preferred large hydrophobic residues (Ile and Leu), while the protease of HIV-1 preferred an Asn residue. The specificity distinctions among the proteases correlated well with the phylogenetic tree of retroviruses prepared solely based on the protease sequences. Molecular models for all of the proteases studied were built, and they were used to interpret the results. While size complementarities appear to be the main specificity-determining features of the S2 subsite of retroviral proteases, electrostatic contributions may play a role only in the case of HIV proteases. In most cases the P2 residues of naturally occurring type 1 cleavage site sequences of the studied proteases agreed well with the observed P2 preferences.

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Molecular mechanics calculations on rous sarcoma virus protease with peptide substrates

Weber

Harrison

1997

Protein Science

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Molecular models of Rous sarcoma virus (RSV) protease and 20 peptide substrates with single amino acid substitutions at positions from P4 to P3', where the scissile bond is between P1 and Pl', were built and compared with kinetic measurements. The unsubstituted peptide substrate, Pro-Ala-Val-Ser-Leu-Ala-Met-Thr, represents the NC-PR cleavage site of RSV protease. Models were built of two intermediates in the catalytic reaction, RSV protease with peptide substrate and with the tetrahedral intermediate. The energy minimization used an algorithm that increased the speed and eliminated a cutoff for nonbonded interactions. The calculated protease-substrate interaction energies showed correlation with the relative catalytic efficiency of peptide hydrolysis. The calculated interaction energies for the 8 RSV protease-substrate models with changes in P1 to P1' next to the scissile bond gave the highest correlation coefficient of 0.79 with the kinetic measurements, whereas all 20 substrates showed the lower, but still significant correlation of 0.46. Models of the tetrahedral reaction intermediates gave a correlation of 0.72 for the 8 substrates with changes next to the scissile bond, whereas a correlation coefficient of only 0.34 was observed for all 20 substrates. The differences between the energies calculated for the tetrahedral intermediate and the bound peptide gave the most significant correlation coefficients of 0.90 for models with changes in PI and Pl', and 0.56 for all substrates. These results are compared to those from similar calculations on HIV-1 protease and discussed in relation to the rate-limiting steps in the catalytic mechanism and the entropic contributions.Keywords: aspartic proteases; calculated interaction energies; RSV protease; substrate binding; transition state The Rous sarcoma virus (RSV) protease is a member of the aspartic protease family and is enzymatically active as a dimer. The crystal structure of RSV protease Jaskolski et al., 1991) has a three-dimensional fold similar to that of HIV-1 protease Weber, 1990). Although there are many crystal structures of HIV protease with different inhibitors (for review, see Wlodawer & Erickson, 1993), there is no crystal structure of RSV protease in the complex with an inhibitor. Instead, the structure of the RSV protease-substrate complex has been modeled by analogy to the structures of HIV protease with peptide-like inhibitors, as described in Grinde et al. (1992). RSV and HIV-1 proteases hydrolyze different cleavage sites in their viral polyprotein substrates (Oroszlan & Luftig, 1990), and RSV protease does not cleave peptides representing the natural substrates of HIV-I protease . The molecular basis of substrate specificity of RSV and HIV-1 proteases is not obvious, due to the lack of a clear consensus sequence in the different cleavage sites. The substrate specificity of RSV protease has been analyzed by kinetic measurements of hydrolysis of peptides that represent the natural cleavage sites, and variations of these peptides with dif...

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Comparative Studies on the Substrate Specificity of Avian Myeloblastosis Virus Proteinase and Lentiviral Proteinases

Cited by 30 publications

References 43 publications

Amino Acid Preferences of Retroviral Proteases for Amino-Terminal Positions in a Type 1 Cleavage Site

Amino Acid Preferences of Retroviral Proteases for Amino-Terminal Positions in a Type 1 Cleavage Site

Amino Acid Preferences for a Critical Substrate Binding Subsite of Retroviral Proteases in Type 1 Cleavage Sites

Molecular mechanics calculations on rous sarcoma virus protease with peptide substrates

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