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Journal articles on the topic 'RETROVIRAL PROTEASE'

Author: Grafiati

Published: 6 September 2023

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1

Blusch, Jürgen H., Sigrid Seelmeir, and Klaus von der Helm. "Molecular and Enzymatic Characterization of the Porcine Endogenous Retrovirus Protease." Journal of Virology 76, no. 15 (August 1, 2002): 7913–17. http://dx.doi.org/10.1128/jvi.76.15.7913-7917.2002.

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ABSTRACT The protease of the porcine endogenous retrovirus (PERV) subtypes A/B and C was recombinantly expressed in Escherichia coli as proteolytically active enzyme and characterized. The PERV Gag precursor was also recombinantly produced and used as the substrate in an in vitro enzyme assay in parallel with synthetic nonapeptide substrates designed according to cleavage site sequences identified in the PERV Gag precursor. The proteases of all PERV subtypes consist of 127 amino acid residues with an M r of 14,000 as revealed by determining the protease N and C termini. The PERV proteases have a high specificity for PERV substrates and do not cleave human immunodeficiency virus (HIV)-specific substrates, nor are they inhibited by specific HIV protease inhibitors. Among the known retroviral proteases, the PERV proteases resemble most closely the protease of the murine leukemia retrovirus.

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2

Lehmann-Che, Jacqueline, Marie-Lou Giron, Olivier Delelis, Martin Löchelt, Patricia Bittoun, Joelle Tobaly-Tapiero, Hugues de Thé, and Ali Saïb. "Protease-Dependent Uncoating of a Complex Retrovirus." Journal of Virology 79, no. 14 (July 2005): 9244–53. http://dx.doi.org/10.1128/jvi.79.14.9244-9253.2005.

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ABSTRACT Although retrovirus egress and budding have been partly unraveled, little is known about early stages of the replication cycle. In particular, retroviral uncoating, a process during which incoming retroviral cores are altered to allow the integration of the viral genome into host chromosomes, is poorly understood. To get insights into these early events of the retroviral cycle, we have used foamy complex retroviruses as a model. In this report, we show that a protease-defective foamy retrovirus is noninfectious, although it is still able to bud and enter target cells efficiently. Similarly, a retrovirus mutated in an essential viral protease-dependent cleavage site in the central part of Gag is noninfectious. Following entry, wild-type and mutant retroviruses are able to traffic along microtubules towards the microtubule-organizing center (MTOC). However, whereas nuclear import of Gag and of the viral genome was observed for the wild-type virus as early as 8 hours postinfection, incoming capsids and genome from mutant viruses remained at the MTOC. Interestingly, a specific viral protease-dependent Gag cleavage product was detected only for the wild-type retrovirus early after infection, demonstrating that cleavage of Gag by the viral protease at this stage of the virus life cycle is absolutely required for productive infection, an unprecedented observation among retroviruses.

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3

Davis, David A., Cara A. Brown, Fonda M. Newcomb, Emily S. Boja, Henry M. Fales, Joshua Kaufman, Stephen J. Stahl, Paul Wingfield, and Robert Yarchoan. "Reversible Oxidative Modification as a Mechanism for Regulating Retroviral Protease Dimerization and Activation." Journal of Virology 77, no. 5 (March 1, 2003): 3319–25. http://dx.doi.org/10.1128/jvi.77.5.3319-3325.2003.

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ABSTRACT Human immunodeficiency virus protease activity can be regulated by reversible oxidation of a sulfur-containing amino acid at the dimer interface. We show here that oxidation of this amino acid in human immunodeficiency virus type 1 protease prevents dimer formation. Moreover, we show that human T-cell leukemia virus type 1 protease can be similarly regulated through reversible glutathionylation of its two conserved cysteine residues. Based on the known three-dimensional structures and multiple sequence alignments of retroviral proteases, it is predicted that the majority of retroviral proteases have sulfur-containing amino acids at the dimer interface. The regulation of protease activity by the modification of a sulfur-containing amino acid at the dimer interface may be a conserved mechanism among the majority of retroviruses.

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4

Weber, Irene T., Yuan-Fang Wang, and Robert W. Harrison. "HIV Protease: Historical Perspective and Current Research." Viruses 13, no. 5 (May 6, 2021): 839. http://dx.doi.org/10.3390/v13050839.

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The retroviral protease of human immunodeficiency virus (HIV) is an excellent target for antiviral inhibitors for treating HIV/AIDS. Despite the efficacy of therapy, current efforts to control the disease are undermined by the growing threat posed by drug resistance. This review covers the historical background of studies on the structure and function of HIV protease, the subsequent development of antiviral inhibitors, and recent studies on drug-resistant protease variants. We highlight the important contributions of Dr. Stephen Oroszlan to fundamental knowledge about the function of the HIV protease and other retroviral proteases. These studies, along with those of his colleagues, laid the foundations for the design of clinical inhibitors of HIV protease. The drug-resistant protease variants also provide an excellent model for investigating the molecular mechanisms and evolution of resistance.

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5

Pettit, Steven C., Sergei Gulnik, Lori Everitt, and Andrew H. Kaplan. "The Dimer Interfaces of Protease and Extra-Protease Domains Influence the Activation of Protease and the Specificity of GagPol Cleavage." Journal of Virology 77, no. 1 (January 1, 2003): 366–74. http://dx.doi.org/10.1128/jvi.77.1.366-374.2003.

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ABSTRACT Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation.

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6

Youngren, S. D., J. D. Boeke, N. J. Sanders, and D. J. Garfinkel. "Functional organization of the retrotransposon Ty from Saccharomyces cerevisiae: Ty protease is required for transposition." Molecular and Cellular Biology 8, no. 4 (April 1988): 1421–31. http://dx.doi.org/10.1128/mcb.8.4.1421-1431.1988.

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We used several mutations generated in vitro to further characterize the functions of the products encoded by the TyB gene of the transpositionally active retrotransposon TyH3 from Saccharomyces cerevisiae. Mutations close to a core protein domain of TyB, which is homologous to retroviral proteases, have striking effects on Ty protein processing, the physiology of Ty viruslike particles, and transposition. The Ty protease is required for processing of both TyA and TyB proteins. Mutations in the protease resulted in the synthesis of morphologically and functionally aberrant Ty viruslike particles. The mutant particles displayed reverse transcriptase activity, but did not synthesize Ty DNA in vitro. Ty RNA was present in the mutant particles, but at very low levels. Transposition of a genetically tagged element ceased when the protease domain was mutated, demonstrating that Ty protease is essential for transposition. One of these mutations also defined a segment of TyB encoding an active reverse transcriptase. These results indicate that the Ty protease, like its retroviral counterpart, plays an important role in particle assembly, replication, and transposition of these elements.

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7

Youngren, S. D., J. D. Boeke, N. J. Sanders, and D. J. Garfinkel. "Functional organization of the retrotransposon Ty from Saccharomyces cerevisiae: Ty protease is required for transposition." Molecular and Cellular Biology 8, no. 4 (April 1988): 1421–31. http://dx.doi.org/10.1128/mcb.8.4.1421.

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We used several mutations generated in vitro to further characterize the functions of the products encoded by the TyB gene of the transpositionally active retrotransposon TyH3 from Saccharomyces cerevisiae. Mutations close to a core protein domain of TyB, which is homologous to retroviral proteases, have striking effects on Ty protein processing, the physiology of Ty viruslike particles, and transposition. The Ty protease is required for processing of both TyA and TyB proteins. Mutations in the protease resulted in the synthesis of morphologically and functionally aberrant Ty viruslike particles. The mutant particles displayed reverse transcriptase activity, but did not synthesize Ty DNA in vitro. Ty RNA was present in the mutant particles, but at very low levels. Transposition of a genetically tagged element ceased when the protease domain was mutated, demonstrating that Ty protease is essential for transposition. One of these mutations also defined a segment of TyB encoding an active reverse transcriptase. These results indicate that the Ty protease, like its retroviral counterpart, plays an important role in particle assembly, replication, and transposition of these elements.

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8

Álvarez, Enrique, Luis Menéndez-Arias, and Luis Carrasco. "The Eukaryotic Translation Initiation Factor 4GI Is Cleaved by Different Retroviral Proteases." Journal of Virology 77, no. 23 (December 1, 2003): 12392–400. http://dx.doi.org/10.1128/jvi.77.23.12392-12400.2003.

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ABSTRACT The initiation factor eIF4G plays a central role in the regulation of translation. In picornaviruses, as well as in human immunodeficiency virus type 1 (HIV-1), cleavage of eIF4G by the viral protease leads to inhibition of protein synthesis directed by capped cellular mRNAs. In the present work, cleavage of both eIF4GI and eIF4GII has been analyzed by employing the proteases encoded within the genomes of several members of the family Retroviridae, e.g., Moloney murine leukemia virus (MoMLV), mouse mammary tumor virus, human T-cell leukemia virus type 1, HIV-2, and simian immunodeficiency virus. All of the retroviral proteases examined were able to cleave the initiation factor eIF4GI both in intact cells and in cell-free systems, albeit with different efficiencies. The eIF4GI hydrolysis patterns obtained with HIV-1 and HIV-2 proteases were very similar to each other but rather different from those obtained with MoMLV protease. Both eIF4GI and eIF4GII were cleaved very efficiently by the MoMLV protease. However, eIF4GII was a poor substrate for HIV proteases. Proteolytic cleavage of eIF4G led to a profound inhibition of cap-dependent translation, while protein synthesis driven by mRNAs containing internal ribosome entry site elements remained unaffected or was even stimulated in transfected cells.

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9

Hartl, Maximilian J., Kristian Schweimer, Martin H. Reger, Stephan Schwarzinger, Jochen Bodem, Paul Rösch, and Birgitta M. Wöhrl. "Formation of transient dimers by a retroviral protease." Biochemical Journal 427, no. 2 (March 29, 2010): 197–203. http://dx.doi.org/10.1042/bj20091451.

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Retroviral proteases have been shown previously to be only active as homodimers. They are essential to form the separate and active proteins from the viral precursors. Spumaretroviruses produce separate precursors for Gag and Pol, rather than a Gag and a Gag–Pol precursor. Nevertheless, processing of Pol into a PR (protease)–RT (reverse transcriptase) and integrase is essential in order to obtain infectious viral particles. We showed recently that the PR–RT from a simian foamy virus, as well as the separate PRshort (protease) domain, exhibit proteolytic activities, although only monomeric forms could be detected. In the present study, we demonstrate that PRshort and PR–RT can be inhibited by the putative dimerization inhibitor cholic acid. Various other inhibitors, including darunavir and tipranavir, known to prevent HIV-1 PR dimerization in cells, had no effect on foamy virus protease in vitro. 1H-15N HSQC (heteronuclear single quantum coherence) NMR analysis of PRshort indicates that cholic acid binds in the proposed PRshort dimerization interface and appears to impair formation of the correct dimer. NMR analysis by paramagnetic relaxation enhancement resulted in elevated transverse relaxation rates of those amino acids predicted to participate in dimer formation. Our results suggest transient PRshort homodimers are formed under native conditions but are only present as a minor transient species, which is not detectable by traditional methods.

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10

Golda, Mária, János András Mótyán, Mohamed Mahdi, and József Tőzsér. "Functional Study of the Retrotransposon-Derived Human PEG10 Protease." International Journal of Molecular Sciences 21, no. 7 (March 31, 2020): 2424. http://dx.doi.org/10.3390/ijms21072424.

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Paternally expressed gene 10 (PEG10) is a human retrotransposon-derived imprinted gene. The mRNA of PEG10 encodes two protein isoforms: the Gag-like protein (RF1PEG10) is coded by reading frame 1, while the Gag-Pol-like polyprotein (RF1/RF2PEG10) is coded by reading frames 1 and 2. The proteins are translated by a typical retroviral frameshift mechanism. The protease (PR) domain of RF2PEG10 contains an -Asp-Ser-Gly- sequence, which corresponds to the consensus -Asp-Ser/Thr-Gly- active-site motif of retroviral aspartic proteases. The function of the aspartic protease domain of RF2PEG10 remains unclear. To elucidate the function of PEG10 protease (PRPEG10), we designed a frameshift mutant (fsRF1/RF2PEG10) for comparison with the RF1/RF2PEG10 form. To study the effects of PRPEG10 on cellular proliferation and viability, mammalian HEK293T and HaCaT cells were transfected with plasmids coding for either RF1/RF2PEG10, the frameshift mutant (fsRF1/RF2PEG10), or a PR active-site (D370A) mutant fsRF1/RF2PEG10. Our results indicate that fsRF1/RF2PEG10 overexpression results in increased cellular proliferation. Remarkably, transfection with fsRF1/RF2PEG10 had a detrimental effect on cell viability. We hypothesize that PRPEG10 plays an important role in the function of this retroviral remnant, mediating the proliferation of cells and possibly implicating it in the inhibition of apoptosis.

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11

Mótyán, János András, Márió Miczi, and József Tőzsér. "Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases." International Journal of Molecular Sciences 21, no. 4 (February 17, 2020): 1352. http://dx.doi.org/10.3390/ijms21041352.

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The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

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12

Kelleher, Anthony D., Andrew K. Sewell, and David A. Price. "Dyslipidemia due to retroviral protease inhibitors." Nature Medicine 8, no. 4 (April 1, 2002): 308. http://dx.doi.org/10.1038/nm0402-308a.

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13

Weber, Irene T. "Structural alignment of retroviral protease sequences." Gene 85, no. 2 (December 1989): 565–66. http://dx.doi.org/10.1016/0378-1119(89)90453-8.

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14

Yip, Matthew C. J., Nicholas O. Bodnar, and Tom A. Rapoport. "Ddi1 is a ubiquitin-dependent protease." Proceedings of the National Academy of Sciences 117, no. 14 (March 19, 2020): 7776–81. http://dx.doi.org/10.1073/pnas.1902298117.

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TheSaccharomyces cerevisiaeprotein Ddi1 and its homologs in higher eukaryotes have been proposed to serve as shuttling factors that deliver ubiquitinated substrates to the proteasome. Although Ddi1 contains both ubiquitin-interacting UBA and proteasome-interacting UBL domains, the UBL domain is atypical, as it binds ubiquitin. Furthermore, unlike other shuttling factors, Ddi1 and its homologs contain a conserved helical domain (helical domain of Ddi1, HDD) and a retroviral-like protease (RVP) domain. The RVP domain is probably responsible for cleavage of the precursor of the transcription factor Nrf1 in higher eukaryotes, which results in the up-regulation of proteasomal subunit genes. However, enzymatic activity of the RVP domain has not yet been demonstrated, and the function of Ddi1 remains poorly understood. Here, we show that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains (longer than about eight ubiquitins). The RVP domain is inactive in isolation, in contrast to its retroviral counterpart. Proteolytic activity of Ddi1 requires the HDD domain and is stimulated by the UBL domain, which mediates high-affinity interaction with the polyubiquitin chain. Compromising the activity of Ddi1 in yeast cells results in the accumulation of polyubiquitinated proteins. Aside from the proteasome, Ddi1 is the only known endoprotease that acts on polyubiquitinated substrates. Ddi1 and its homologs likely cleave polyubiquitinated substrates under conditions where proteasome function is compromised.

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15

Golda, Mária, János András Mótyán, Mohamed Mahdi, and József Tőzsér. "Study of the Retrotransposon-Derived Human PEG10 Protease." Proceedings 50, no. 1 (July 1, 2020): 110. http://dx.doi.org/10.3390/proceedings2020050110.

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Paternally expressed gene 10 (PEG10) is a human retrotransposon-derived imprinted gene. Previous works have demonstrated that a mutation in the coding sequence of this gene is lethal with regard to embryological age due to defects of placental development. In addition, PEG10 is implicated in several malignancies, such as pancreatic cancer and hepatocellular carcinoma. The PEG10 gene encodes two protein isoforms, which are translated by a typical retroviral frameshift mechanism. The Gag-like protein (RF1PEG10) is encoded by reading frame 1, whilst reading frames 1 and 2 accounts for the Gag-Pol-like polyprotein (RF1/RF2PEG10). The protease (PR) domain of RF2PEG10 contains an -Asp-Ser-Gly- sequence, which refers to the conservative -Asp-Ser/Thr-Gly- active-site motif of retroviral aspartic proteases. The function of the aspartic protease domain of RF2PEG10 remains unclear. In order to further investigate the function of the PEG10 protease (PRPEG10), a frameshift mutant was generated (fsRF1/RF2PEG10) for comparison with the RF1/RF2PEG10 form. To study the effects of PRPEG10 on cellular proliferation and viability, mammalian HEK293T and HaCaT cells were transfected with plasmids encoding for either the frameshift mutant (fsRF1/RF2PEG10) or a PR active-site (D370A) mutant fsRF1/RF2PEG10. Based on our findings, an fsRF1/RF2PEG10 overexpression resulted in an increased cellular proliferation, compared to the mutant form. Interestingly, transfection with fsRF1/RF2PEG10 had a detrimental effect on cell viability. We hypothesize that PRPEG10 may play a cardinal role in the function of this retroviral remnant, possibly implicated in cellular proliferation and the inhibition of apoptosis.

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16

Miller, Maria, Jonathan Leis, and Alexander Wlodawer. "Preliminary crystallographic study of a retroviral protease." Journal of Molecular Biology 204, no. 1 (November 1988): 211–12. http://dx.doi.org/10.1016/0022-2836(88)90610-9.

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17

Horáková, Dana, Michaela Rumlová, Iva Pichová, and Tomáš Ruml. "Luminometric method for screening retroviral protease inhibitors." Analytical Biochemistry 345, no. 1 (October 2005): 96–101. http://dx.doi.org/10.1016/j.ab.2005.07.013.

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18

Wang, Shainn-Wei, Kristin Noonan, and Anna Aldovini. "Nucleocapsid-RNA Interactions Are Essential to Structural Stability but Not to Assembly of Retroviruses." Journal of Virology 78, no. 2 (January 15, 2004): 716–23. http://dx.doi.org/10.1128/jvi.78.2.716-723.2004.

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ABSTRACT The process of RNA incorporation into nascent virions is thought to be critical for efficient retroviral particle assembly and production. Here we show that human immunodeficiency virus type 1 mutant particles (which are highly unstable and break down soon after release from the cell) lacking nucleocapsid (NC) core protein-mediated RNA incorporation are produced efficiently and can be recovered at the normal density when viral protease function is abolished. These results demonstrate that RNA binding by Gag is not necessary for retroviral particle assembly. Rather, the RNA interaction with NC is critical for retroviral particle structural stability subsequent to release from the membrane and protease-mediated Gag cleavage. Thus, the NC-RNA interaction, and not simply the presence of RNA, provides the virus with a structural function that is critical for stable retroviral particle architecture.

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19

Davis, David A., Haydar Bulut, Prabha Shrestha, Hiroaki Mitsuya, and Robert Yarchoan. "Regulation of Retroviral and SARS-CoV-2 Protease Dimerization and Activity through Reversible Oxidation." Antioxidants 11, no. 10 (October 18, 2022): 2054. http://dx.doi.org/10.3390/antiox11102054.

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Most viruses encode their own proteases to carry out viral maturation and these often require dimerization for activity. Studies on human immunodeficiency virus type 1 (HIV-1), type 2 (HIV-2) and human T-cell leukemia virus (HTLV-1) proteases have shown that the activity of these proteases can be reversibly regulated by cysteine (Cys) glutathionylation and/or methionine oxidation (for HIV-2). These modifications lead to inhibition of protease dimerization and therefore loss of activity. These changes are reversible with the cellular enzymes, glutaredoxin or methionine sulfoxide reductase. Perhaps more importantly, as a result, the maturation of retroviral particles can also be regulated through reversible oxidation and this has been demonstrated for HIV-1, HIV-2, Mason-Pfizer monkey virus (M-PMV) and murine leukemia virus (MLV). More recently, our group has learned that SARS-CoV-2 main protease (Mpro) dimerization and activity can also be regulated through reversible glutathionylation of Cys300. Overall, these studies reveal a conserved way for viruses to regulate viral polyprotein processing particularly during oxidative stress and reveal novel targets for the development of inhibitors of dimerization and activity of these important viral enzyme targets.

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20

Bagossi, Péter, Tamás Sperka, Anita Fehér, János Kádas, Gábor Zahuczky, Gabriella Miklóssy, Péter Boross, and József Tözsér. "Amino Acid Preferences for a Critical Substrate Binding Subsite of Retroviral Proteases in Type 1 Cleavage Sites." Journal of Virology 79, no. 7 (April 1, 2005): 4213–18. http://dx.doi.org/10.1128/jvi.79.7.4213-4218.2005.

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ABSTRACT 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-Tyr↓Pro-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, Mason-Pfizer 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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21

Miller, Maria, Mariusz Jaskólski, J. K. Mohana Rao, Jonathan Leis, and Alexander Wlodawer. "Crystal structure of a retroviral protease proves relationship to aspartic protease family." Nature 337, no. 6207 (February 1989): 576–79. http://dx.doi.org/10.1038/337576a0.

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22

Sadiq, S. Kashif. "Reaction–diffusion basis of retroviral infectivity." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, no. 2080 (November 13, 2016): 20160148. http://dx.doi.org/10.1098/rsta.2016.0148.

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Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env 3 ) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env 3 molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env 3 diffuses comparably to Gag-absent Env 3 . Initial immobility of Env 3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env 3 diffusion, and permits Env 3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.

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23

Wosicki, Stanislaw, Miroslaw Gilski, Helena Zabranska, Iva Pichova, and Mariusz Jaskolski. "Comparison of a retroviral protease in monomeric and dimeric states." Acta Crystallographica Section D Structural Biology 75, no. 10 (September 20, 2019): 904–17. http://dx.doi.org/10.1107/s2059798319011355.

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Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason–Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 Å, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S—S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.

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Bühler, Bernd, Ying-Chuan Lin, Garrett Morris, Arthur J. Olson, Chi-Huey Wong, Douglas D. Richman, John H. Elder, and Bruce E. Torbett. "Viral Evolution in Response to the Broad-Based Retroviral Protease Inhibitor TL-3." Journal of Virology 75, no. 19 (October 1, 2001): 9502–8. http://dx.doi.org/10.1128/jvi.75.19.9502-9508.2001.

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ABSTRACT TL-3 is a protease inhibitor developed using the feline immunodeficiency virus protease as a model. It has been shown to efficiently inhibit replication of human, simian, and feline immunodeficiency viruses and therefore has broad-based activity. We now demonstrate that TL-3 efficiently inhibits the replication of 6 of 12 isolates with confirmed resistance mutations to known protease inhibitors. To dissect the spectrum of molecular changes in protease and viral properties associated with resistance to TL-3, a panel of chronological in vitro escape variants was generated. We have virologically and biochemically characterized mutants with one (V82A), three (M46I/F53L/V82A), or six (L24I/M46I/F53L/L63P/V77I/V82A) changes in the protease and structurally modeled the protease mutant containing six changes. Virus containing six changes was found to be 17-fold more resistant to TL-3 in cell culture than was wild-type virus but maintained similar in vitro replication kinetics compared to the wild-type virus. Analyses of enzyme activity of protease variants with one, three, and six changes indicated that these enzymes, compared to wild-type protease, retained 40, 47, and 61% activity, respectively. These results suggest that deficient protease enzymatic activity is sufficient for function, and the observed protease restoration might imply a selective advantage, at least in vitro, for increased protease activity.

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DAVIS, David A., Fonda M. NEWCOMB, Jackob MOSKOVITZ, Paul T. WINGFIELD, Stephen J. STAHL, Joshua KAUFMAN, Henry M. FALES, Rodney L. LEVINE, and Robert YARCHOAN. "HIV-2 protease is inactivated after oxidation at the dimer interface and activity can be partly restored with methionine sulphoxide reductase." Biochemical Journal 346, no. 2 (February 22, 2000): 305–11. http://dx.doi.org/10.1042/bj3460305.

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Human immunodeficiency viruses encode a homodimeric protease that is essential for the production of infectious virus. Previous studies have shown that HIV-1 protease is susceptible to oxidative inactivation at the dimer interface at Cys-95, a process that can be reversed both chemically and enzymically. Here we demonstrate a related yet distinct mechanism of reversible inactivation of the HIV-2 protease. Exposure of the HIV-2 protease to H2O2 resulted in conversion of the two methionine residues (Met-76 and Met-95) to methionine sulphoxide as determined by amino acid analysis and mass spectrometry. This oxidation completely inactivated protease activity. However, the activity could be restored (up to 40%) after exposure of the oxidized protease to methionine sulphoxide reductase. This treatment resulted in the reduction of methionine sulphoxide 95 but not methionine sulphoxide 76 to methionine, as determined by peptide mapping/mass spectrometry. We also found that exposure of immature HIV-2 particles to H2O2 led to the inhibition of polyprotein processing in maturing virus particles comparable to that demonstrated for HIV-1 particles. Thus oxidative inactivation of the HIV protease in vitro and in maturing viral particles is not restricted to the type 1 proteases. These studies indicate that two distinct retroviral proteases are susceptible to inactivation after a very minor modification at residue 95 of the dimer interface and suggest that the dimer interface might be a viable target for the development of novel protease inhibitors.

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Raugi, Dana N., Robert A. Smith, and Geoffrey S. Gottlieb. "Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors." Journal of Virology 90, no. 2 (November 11, 2015): 1062–69. http://dx.doi.org/10.1128/jvi.01772-15.

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ABSTRACTProtease is essential for retroviral replication, and protease inhibitors (PI) are important for treating HIV infection. HIV-2 exhibits intrinsic resistance to most FDA-approved HIV-1 PI, retaining clinically useful susceptibility only to lopinavir, darunavir, and saquinavir. The mechanisms for this resistance are unclear; although HIV-1 and HIV-2 proteases share just 38 to 49% sequence identity, all critical structural features of proteases are conserved. Structural studies have implicated four amino acids in the ligand-binding pocket (positions 32, 47, 76, and 82). We constructed HIV-2ROD9molecular clones encoding the corresponding wild-type HIV-1 amino acids (I32V, V47I, M76L, and I82V) either individually or together (clone PRΔ4) and compared the phenotypic sensitivities (50% effective concentration [EC50]) of mutant and wild-type viruses to nine FDA-approved PI. Single amino acid replacements I32V, V47I, and M76L increased the susceptibility of HIV-2 to multiple PI, but no single change conferred class-wide sensitivity. In contrast, clone PRΔ4 showed PI susceptibility equivalent to or greater than that of HIV-1 for all PI. We also compared crystallographic structures of wild-type HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir to models of the PRΔ4 enzyme. These models suggest that the amprenavir sensitivity of PRΔ4 is attributable to stabilizing enzyme-inhibitor interactions in the P2 and P2′ pockets of the protease dimer. Together, our results show that the combination of four amino acid changes in HIV-2 protease confer a pattern of PI susceptibility comparable to that of HIV-1, providing a structural rationale for intrinsic HIV-2 PI resistance and resolving long-standing questions regarding the determinants of differential PI susceptibility in HIV-1 and HIV-2.IMPORTANCEProteases are essential for retroviral replication, and HIV-1 and HIV-2 proteases share a great deal of structural similarity. However, only three of nine FDA-approved HIV-1 protease inhibitors (PI) are active against HIV-2. The underlying reasons for intrinsic PI resistance in HIV-2 are not known. We examined the contributions of four amino acids in the ligand-binding pocket of the enzyme that differ between HIV-1 and HIV-2 by constructing HIV-2 clones encoding the corresponding HIV-1 amino acids and testing the PI susceptibilities of the resulting viruses. We found that the HIV-2 clone containing all four changes (PRΔ4) was as susceptible as HIV-1 to all nine PI. We also modeled the PRΔ4 enzyme structure and compared it to existing crystallographic structures of HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir. Our findings demonstrate that four positions in the ligand-binding cleft of protease are the primary cause of HIV-2 PI resistance.

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Sturley, Stephen L., Oliver Distler, Jun-Shan Liang, David A. Cooper, Richard J. Deckelbaum, and Henry N. Ginsberg. "Reply to 'Dyslipidemia due to retroviral protease inhibitors'." Nature Medicine 8, no. 4 (April 1, 2002): 308–9. http://dx.doi.org/10.1038/nm0402-308b.

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Germinario, Ralph. "Anti-Retroviral Protease Inhibitors -'A Two Edged Sword?'." IUBMB Life 55, no. 2 (February 1, 2003): 67–70. http://dx.doi.org/10.1080/1521654031000090922.

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Miller, Maria. "The early years of retroviral protease crystal structures." Biopolymers 94, no. 4 (June 30, 2010): 521–29. http://dx.doi.org/10.1002/bip.21387.

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30

Germinario, Ralph J. "Anti-Retroviral Protease Inhibitors - ‘A Two Edged Sword?’." IUBMB Life 55, no. 2 (February 13, 2008): 67–70. http://dx.doi.org/10.1002/tbmb.718540874.

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31

Golda, Mária, János András Mótyán, Katalin Nagy, Krisztina Matúz, Tibor Nagy, and József Tőzsér. "Biochemical Characterization of Human Retroviral-Like Aspartic Protease 1 (ASPRV1)." Biomolecules 10, no. 7 (July 6, 2020): 1004. http://dx.doi.org/10.3390/biom10071004.

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The human retroviral-like aspartic protease 1 (ASPRV1) is a mammalian retroviral-like enzyme that catalyzes a critical proteolytic step during epidermal differentiation; therefore, it is also referred to as skin-specific aspartic protease (SASPase). Neutrophil granulocytes were also found recently to express ASPRV1 that is involved in the progression of acute chronic inflammation of the central nervous system, especially in autoimmune encephalomyelitis. Thus, investigation of ASPRV1 is important due to its therapeutic or diagnostic potential. We investigated the structural characteristics of ASPRV1 by homology modeling; analysis of the proposed structure was used for interpretation of in vitro specificity studies. For in-vitro characterization, activities of SASP28 and SASP14 enzyme forms were measured using synthetic oligopeptide substrates. We demonstrated that self-processing of SASP28 precursor causes autoactivation of the protease. The highest activity was measured for GST-SASP14 at neutral pH and at high ionic strength, and we proved that pepstatin A and acetyl-pepstatin can also inhibit the protease. In agreement with the structural characteristics, the relatively lower urea dissociation constant implied lower dimer stability of SASP14 compared to that of HIV-1 protease. The obtained structural and biochemical characteristics support better understanding of ASPRV1 function in the skin and central nervous system.

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Wlodawer, A., M. Miller, M. Jaskolski, B. Sathyanarayana, E. Baldwin, I. Weber, L. Selk, L. Clawson, J. Schneider, and S. Kent. "Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease." Science 245, no. 4918 (August 2, 1989): 616–21. http://dx.doi.org/10.1126/science.2548279.

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Onchieku, Noah Machuki, Sonam Kumari, Rajan Pandey, Vaibhav Sharma, Mohit Kumar, Arunaditya Deshmukh, Inderjeet Kaur, et al. "Artemisinin Binds and Inhibits the Activity of Plasmodium falciparum Ddi1, a Retroviral Aspartyl Protease." Pathogens 10, no. 11 (November 11, 2021): 1465. http://dx.doi.org/10.3390/pathogens10111465.

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Reduced sensitivity of the human malaria parasite, Plasmodium falciparum, to Artemisinin and its derivatives (ARTs) threatens the global efforts towards eliminating malaria. ARTs have been shown to cause ubiquitous cellular and genetic insults, which results in the activation of the unfolded protein response (UPR) pathways. The UPR restores protein homeostasis, which otherwise would be toxic to cellular survival. Here, we interrogated the role of DNA-damage inducible protein 1 (PfDdi1), a unique proteasome-interacting retropepsin in mediating the actions of the ARTs. We demonstrate that PfDdi1 is an active A2 family protease that hydrolyzes ubiquitinated proteasome substrates. Treatment of P. falciparum parasites with ARTs leads to the accumulation of ubiquitinated proteins in the parasites and blocks the destruction of ubiquitinated proteins by inhibiting the PfDdi1 protease activity. Besides, whereas the PfDdi1 is predominantly localized in the cytoplasm, exposure of the parasites to ARTs leads to DNA fragmentation and increased recruitment of the PfDdi1 into the nucleus. Furthermore, we show that Ddi1 knock-out Saccharomycescerevisiae cells are more susceptible to ARTs and the PfDdI1 protein robustly restores the corresponding functions in the knock-out cells. Together, these results show that ARTs act in multiple ways; by inducing DNA and protein damage and might be impairing the damage recovery by inhibiting the activity of PfDdi1, an essential ubiquitin-proteasome retropepsin.

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34

Rein, Alan. "Murine Leukemia Viruses: Objects and Organisms." Advances in Virology 2011 (2011): 1–14. http://dx.doi.org/10.1155/2011/403419.

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Murine leukemia viruses (MLVs) are among the simplest retroviruses. Prototypical gammaretroviruses encode only the three polyproteins that will be used in the assembly of progeny virus particles. These are the Gag polyprotein, which is the structural protein of a retrovirus particle, the Pol protein, comprising the three retroviral enzymes—protease, which catalyzes the maturation of the particle, reverse transcriptase, which copies the viral RNA into DNA upon infection of a new host cell, and integrase, which inserts the DNA into the chromosomal DNA of the host cell, and the Env polyprotein, which induces the fusion of the viral membrane with that of the new host cell, initiating infection. In general, a productive MLV infection has no obvious effect upon host cells. Although gammaretroviral structure and replication follow the same broad outlines as those of other retroviruses, we point out a number of significant differences between different retroviral genera.

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35

Eizert, Helga, Pálma Bander, Péter Bagossi, Tamás Sperka, Gabriella Miklóssy, Péter Boross, Irene T. Weber, and József Tözsér. "Amino Acid Preferences of Retroviral Proteases for Amino-Terminal Positions in a Type 1 Cleavage Site." Journal of Virology 82, no. 20 (August 13, 2008): 10111–17. http://dx.doi.org/10.1128/jvi.00418-08.

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ABSTRACT 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-Gln-Asn-Tyr↓Pro-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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36

Kotler, M., W. Danho, R. A. Katz, J. Leis, and A. M. Skalka. "Avian Retroviral Protease and Cellular Aspartic Proteases are Distinguished by Activities on Peptide Substrates." Journal of Biological Chemistry 264, no. 6 (February 1989): 3428–35. http://dx.doi.org/10.1016/s0021-9258(18)94085-8.

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37

Swanstrom, Ronald, and Wesley I. Sundquist. "Stephan Oroszlan and the Proteolytic Processing of Retroviral Proteins: Following A Pro." Viruses 13, no. 11 (November 4, 2021): 2218. http://dx.doi.org/10.3390/v13112218.

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Steve Oroszlan determined the sequences at the ends of virion proteins for a number of different retroviruses. This work led to the insight that the amino-terminal amino acid of the mature viral CA protein is always proline. In this remembrance, we review Steve’s work that led to this insight and show how that insight was a necessary precursor to the work we have done in the subsequent years exploring the cleavage rate determinants of viral protease processing sites and the multiple roles the amino-terminal proline of CA plays after protease cleavage liberates it from its position in a protease processing site.

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38

Kotler, M., R. A. Katz, and A. M. Skalka. "Activity of avian retroviral protease expressed in Escherichia coli." Journal of Virology 62, no. 8 (1988): 2696–700. http://dx.doi.org/10.1128/jvi.62.8.2696-2700.1988.

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39

Sirkis, Roy, Jeffrey E. Gerst, and Deborah Fass. "Ddi1, a Eukaryotic Protein With the Retroviral Protease Fold." Journal of Molecular Biology 364, no. 3 (December 2006): 376–87. http://dx.doi.org/10.1016/j.jmb.2006.08.086.

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40

Hafenrichter, Rudolf, Frank Weiland, Josef Schneider, and Heinz-Jürgen Thiel. "Properties of retroviral protease responsible for gag precursor cleavage." Virology 172, no. 1 (September 1989): 355–58. http://dx.doi.org/10.1016/0042-6822(89)90139-6.

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41

Slabaugh, M. B., and N. A. Roseman. "Retroviral protease-like gene in the vaccinia virus genome." Proceedings of the National Academy of Sciences 86, no. 11 (June 1, 1989): 4152–55. http://dx.doi.org/10.1073/pnas.86.11.4152.

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42

Li, Mi, Alla Gustchina, Rui Cruz, Marisa Simões, Pedro Curto, Juan Martinez, Carlos Faro, Isaura Simões, and Alexander Wlodawer. "Structure of RC1339/APRc fromRickettsia conorii, a retropepsin-like aspartic protease." Acta Crystallographica Section D Biological Crystallography 71, no. 10 (September 30, 2015): 2109–18. http://dx.doi.org/10.1107/s1399004715013905.

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The crystal structures of two constructs of RC1339/APRc fromRickettsia conorii, consisting of either residues 105–231 or 110–231 followed by a His tag, have been determined in three different crystal forms. As predicted, the fold of a monomer of APRc resembles one-half of the mandatory homodimer of retroviral pepsin-like aspartic proteases (retropepsins), but the quaternary structure of the dimer of APRc differs from that of the canonical retropepsins. The observed dimer is most likely an artifact of the expression and/or crystallization conditions since it cannot support the previously reported enzymatic activity of this bacterial aspartic protease. However, the fold of the core of each monomer is very closely related to the fold of retropepsins from a variety of retroviruses and to a single domain of pepsin-like eukaryotic enzymes, and may represent a putative common ancestor of monomeric and dimeric aspartic proteases.

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43

Onchieku, Noah Machuki, Reagan Mogire, Loise Ndung'u, Peter Mwitari, Francis Kimani, Damaris Matoke-Muhia, Daniel Kiboi, and Gabriel Magoma. "Deciphering the targets of retroviral protease inhibitors in Plasmodium berghei." PLOS ONE 13, no. 8 (August 1, 2018): e0201556. http://dx.doi.org/10.1371/journal.pone.0201556.

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44

Kontijevskis, Aleksejs, Peteris Prusis, Ramona Petrovska, Sviatlana Yahorava, Felikss Mutulis, Ilze Mutule, Jan Komorowski, and Jarl E. S. Wikberg. "A Look Inside HIV Resistance through Retroviral Protease Interaction Maps." PLoS Computational Biology 3, no. 3 (March 9, 2007): e48. http://dx.doi.org/10.1371/journal.pcbi.0030048.

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45

Kontijevskis, Aleksejs, Peteris Prusis, Ramona Petrovska, Sviatlana Yahorava, Felikss Mutulis, Ilze Mutule, Jan Komorowski, and Jarl E. Wikberg. "A Look inside HIV Resistance through Retroviral Protease Interaction Maps." PLoS Computational Biology preprint, no. 2007 (2005): e48. http://dx.doi.org/10.1371/journal.pcbi.0030048.eor.

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46

TOH, HIROYUKI, MASAO ONO, KAORU SAIGO, and TAKASHI MIYATA. "Retroviral protease-like sequence in the yeast transposon Ty 1." Nature 315, no. 6021 (June 1985): 691. http://dx.doi.org/10.1038/315691a0.

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47

Katoh, Iyoko, Teruo Yasunaga, Yoji Ikawa, and Yoshiyuki Yoshinaka. "Inhibition of retroviral protease activity by an aspartyl proteinase inhibitor." Nature 329, no. 6140 (October 1987): 654–56. http://dx.doi.org/10.1038/329654a0.

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48

Llido, S., B. Langlois d"Estaintot, A. Dautant, S. Geoffre, P. Picard, and G. Precigoux. "Conformational study of a putative HLTV-1 retroviral protease inhibitor." Acta Crystallographica Section D Biological Crystallography 49, no. 3 (May 1, 1993): 344–48. http://dx.doi.org/10.1107/s0907444992013623.

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49

Kotler, M., R. A. Katz, W. Danho, J. Leis, and A. M. Skalka. "Synthetic peptides as substrates and inhibitors of a retroviral protease." Proceedings of the National Academy of Sciences 85, no. 12 (June 1, 1988): 4185–89. http://dx.doi.org/10.1073/pnas.85.12.4185.

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50

MELLOR, J., S. M. FULTON, M. J. DOBSON, W. WILSON, S. M. KINGSMAN, and A. J. KINGSMAN. "Retroviral protease-like sequence in the yeast transposon Ty 1(reply)." Nature 315, no. 6021 (June 1985): 691–92. http://dx.doi.org/10.1038/315691b0.

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