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Minshawi F, Lanvermann S, McKenzie E, Jeffery R, Couper K, Papoutsopoulou S, Roers A, Muller W. The Generation of an Engineered Interleukin-10 Protein With Improved Stability and Biological Function. Front Immunol 2020; 11:1794. [PMID: 32849644 PMCID: PMC7431522 DOI: 10.3389/fimmu.2020.01794] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Interleukin-10 (IL-10) is an immunoregulatory cytokine that plays a pivotal role in modulating inflammation. IL-10 has inhibitory effects on proinflammatory cytokine production and function in vitro and in vivo; as such, IL-10 is viewed as a potential treatment for various inflammatory diseases. However, a significant drawback of using IL-10 in clinical application is the fact that the biologically active form of IL-10 is an unstable homodimer, which has a short half-life and is easily degraded in vivo. Consequently, IL-10 therapy using recombinant native IL-10 has had only limited success in the treatment of human disease. To improve the therapeutic potential of IL-10, we have generated a novel form of IL-10, which consists of two IL-10 monomer subunits linked in a head to tail fashion by a flexible linker. We show that the linker length per se did not affect the expression and biological activity of the stable IL-10 molecule, which was more active than natural IL-10, both in vitro and in vivo. We confirmed that the new form of IL-10 had a much-improved temperature- and pH-dependent biological stability compared to natural IL-10. The IL-10 dimer protein binds to the IL-10 receptor similarly to the natural IL-10 protein, as shown by antibody blocking and through the genetic modifications of one monomer in the IL-10 dimer specifically at the IL-10 receptor binding site. Finally, we showed that stable IL-10 is more effective at suppressing LPS-induced-inflammation in vivo compared to the natural IL-10. In conclusion, we have developed a new stable dimer version of the IL-10 protein with improved stability and efficacy to suppress inflammation. We propose that this novel stable IL-10 dimer could serve as the basis for the development of targeted anti-inflammatory drugs.
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Affiliation(s)
- Faisal Minshawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Sebastian Lanvermann
- Centre for Translational Medicine, Thomas Jefferson University, Philadelphia, PA, United States
| | - Edward McKenzie
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Rebecca Jeffery
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Kevin Couper
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Stamatia Papoutsopoulou
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom.,Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, United Kingdom
| | - Axel Roers
- Institute of Immunology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Dresden, Germany
| | - Werner Muller
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
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2
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Wapling J, Srivastava S, Shehu-Xhilaga M, Tachedjian G. Targeting Human Immunodeficiency Virus Type 1 Assembly, Maturation and Budding. Drug Target Insights 2017. [DOI: 10.1177/117739280700200020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Johanna Wapling
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Seema Srivastava
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
| | - Miranda Shehu-Xhilaga
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
- Infectious Diseases Unit, Alfred Hospital, Prahran, Victoria 3181, Australia
| | - Gilda Tachedjian
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
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3
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Hodge CN, Aldrich PE, Fernandez CH, Otto MJ, Rayner MM, Wong YN, Erickson-Viitanen S. Studies on Orally Available Inhibitors of HIV Protease. Peptidyl Aldehydes and Trifluoromethyl Ketones. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Low-molecular-weight peptidyl aldehyde inhibitors of HIV protease that reach in vivo plasma concentrations after oral administration substantiailly in excess of the antiviral IC90 are described. We also report efforts to improve the potency and stability of these compounds that culminated in a series of peptidyl trifluoromethyl ketones with increased potency but decreased bioavailability.
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Affiliation(s)
- C. N. Hodge
- Department of Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - P. E. Aldrich
- Department of Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - C. H. Fernandez
- Department of Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - M. J. Otto
- Department of Virology Research, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - M. M. Rayner
- Department of Virology Research, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - Y. N. Wong
- Department of Drug Metabolism, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - S. Erickson-Viitanen
- Department of Virology Research, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
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Kovrigina EA, Galiakhmetov AR, Kovrigin EL. The Ras G Domain Lacks the Intrinsic Propensity to Form Dimers. Biophys J 2016; 109:1000-8. [PMID: 26331257 DOI: 10.1016/j.bpj.2015.07.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 05/27/2015] [Accepted: 07/07/2015] [Indexed: 12/24/2022] Open
Abstract
Ras GTPase is a molecular switch controlling a number of cellular pathways including growth, proliferation, differentiation, and apoptosis. Recent reports indicated that Ras undergoes dimerization at the membrane surface through protein-protein interactions. If firmly established this property of Ras would require profound reassessment of a large amount of published data and modification of the Ras signaling paradigm. One proposed mechanism of dimerization involves formation of salt bridges between the two GTPase domains (G domains) leading to formation of a compact dimer as observed in Ras crystal structures. In this work, we interrogated the intrinsic ability of Ras to self-associate in solution by creating conditions of high local concentration through irreversibly tethering the two G domains together at their unstructured C-terminal tails. We evaluated possible self-association in this inverted tandem conjugate via analysis of the time-domain fluorescence anisotropy and NMR chemical shift perturbations. We did not observe the increased rotational correlation time expected for the G domain dimer. Variation of the ionic strength (to modulate stability of the salt bridges) did not affect the rotational correlation time in the tandem further supporting independent rotational diffusion of two G domains. In a parallel line of experiments to detect and map weak self-association of the G domains, we analyzed NMR chemical shifts perturbations at a number of sites near the crystallographic dimer interface. The nearly complete lack of chemical shift perturbations in the tandem construct supported a simple model with the independent G domains repelled from each other by their overall negative charge. These results lead us to the conclusion that self-association of the G domains cannot be responsible for homodimerization of Ras reported in the literature.
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Wiley AP, Williams SL, Essex JW. Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics. J Chem Theory Comput 2015; 5:1117-28. [PMID: 26609621 DOI: 10.1021/ct800152d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 protease performs a vital step in the propagation of the HIV virus and is therefore an important drug target in the treatment of AIDS. It consists of a homodimer, with access to the active site limited by two protein flaps. NMR studies have identified two time scales of motions that occur in these flaps, and it is thought that the slower of these is responsible for a conformational change that makes the protein ligand-accessible. This motion occurs on a time scale outside that achievable using traditional molecular dynamics simulations. Reversible Digitally Filtered Molecular Dynamics (RDFMD) is a method that amplifies low frequency motions associated with conformational change and has recently been applied to, among others, E. coli dihydrofolate reductase, inducing a conformational change between known crystal structures. In this paper, the conformational motions of HIV-1 protease produced during MD and RDFMD simulations are presented, including movement between the known semiopen and closed conformations, and the opening and closing of the protein flaps.
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Affiliation(s)
- Adrian P Wiley
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K
| | - Sarah L Williams
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K
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6
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Kobe B, Ve T, Williams SJ. Fusion-protein-assisted protein crystallization. Acta Crystallogr F Struct Biol Commun 2015; 71:861-9. [PMID: 26144231 PMCID: PMC4498707 DOI: 10.1107/s2053230x15011061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/07/2015] [Indexed: 01/29/2023] Open
Abstract
Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.
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Affiliation(s)
- Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
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7
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Potempa M, Nalivaika E, Ragland D, Lee SK, Schiffer CA, Swanstrom R. A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro. J Mol Biol 2015; 427:2360-78. [PMID: 25986307 DOI: 10.1016/j.jmb.2015.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 01/09/2023]
Abstract
Though the steps of human immunodeficiency virus type 1 (HIV-1) virion maturation are well documented, the mechanisms regulating the proteolysis of the Gag and Gag-Pro-Pol polyproteins by the HIV-1 protease (PR) remain obscure. One proposed mechanism argues that the maturation intermediate p15NC must interact with RNA for efficient cleavage by the PR. We investigated this phenomenon and found that processing of multiple substrates by the HIV-1 PR was enhanced in the presence of RNA. The acceleration of proteolysis occurred independently from the substrate's ability to interact with nucleic acid, indicating that a direct interaction between substrate and RNA is not necessary for enhancement. Gel-shift assays demonstrated the HIV-1 PR is capable of interacting with nucleic acids, suggesting that RNA accelerates processing reactions by interacting with the PR rather than the substrate. All HIV-1 PRs examined have this ability; however, the HIV-2 PR does not interact with RNA and does not exhibit enhanced catalytic activity in the presence of RNA. No specific sequence or structure was required in the RNA for a productive interaction with the HIV-1 PR, which appears to be principally, though not exclusively, driven by electrostatic forces. For a peptide substrate, RNA increased the kinetic efficiency of the HIV-1 PR by an order of magnitude, affecting both turnover rate (k(cat)) and substrate affinity (K(m)). These results suggest that an allosteric binding site exists on the HIV-1 PR and that HIV-1 PR activity during maturation could be regulated in part by the juxtaposition of the enzyme with virion-packaged RNA.
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Affiliation(s)
- Marc Potempa
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ellen Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Debra Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ronald Swanstrom
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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8
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Inhibitor and substrate binding induced stability of HIV-1 protease against sequential dissociation and unfolding revealed by high pressure spectroscopy and kinetics. PLoS One 2015; 10:e0119099. [PMID: 25781460 PMCID: PMC4362767 DOI: 10.1371/journal.pone.0119099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 01/28/2015] [Indexed: 01/10/2023] Open
Abstract
High-pressure methods have become an interesting tool of investigation of structural stability of proteins. They are used to study protein unfolding, but dissociation of oligomeric proteins can be addressed this way, too. HIV-1 protease, although an interesting object of biophysical experiments, has not been studied at high pressure yet. In this study HIV-1 protease is investigated by high pressure (up to 600 MPa) fluorescence spectroscopy of either the inherent tryptophan residues or external 8-anilino-1-naphtalenesulfonic acid at 25°C. A fast concentration-dependent structural transition is detected that corresponds to the dimer-monomer equilibrium. This transition is followed by a slow concentration independent transition that can be assigned to the monomer unfolding. In the presence of a tight-binding inhibitor none of these transitions are observed, which confirms the stabilizing effect of inhibitor. High-pressure enzyme kinetics (up to 350 MPa) also reveals the stabilizing effect of substrate. Unfolding of the protease can thus proceed only from the monomeric state after dimer dissociation and is unfavourable at atmospheric pressure. Dimer-destabilizing effect of high pressure is caused by negative volume change of dimer dissociation of -32.5 mL/mol. It helps us to determine the atmospheric pressure dimerization constant of 0.92 μM. High-pressure methods thus enable the investigation of structural phenomena that are difficult or impossible to measure at atmospheric pressure.
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9
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Stead MA, Wright SC. Structures of heterodimeric POZ domains of Miz1/BCL6 and Miz1/NAC1. Acta Crystallogr F Struct Biol Commun 2014; 70:1591-6. [PMID: 25484205 PMCID: PMC4259219 DOI: 10.1107/s2053230x14023449] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/24/2014] [Indexed: 12/22/2022] Open
Abstract
The POZ domain is an evolutionarily conserved protein-protein interaction domain that is found in approximately 40 mammalian transcription factors. POZ domains mediate both homodimerization and the heteromeric interactions of different POZ-domain transcription factors with each other. Miz1 is a POZ-domain transcription factor that regulates cell-cycle arrest and DNA-damage responses. The activities of Miz1 are altered by its interaction with the POZ-domain transcriptional repressors BCL6 and NAC1, and these interactions have been implicated in tumourigenesis in B-cell lymphomas and in ovarian serous carcinomas that overexpress BCL6 and NAC1, respectively. A strategy for the purification of tethered POZ domains that form forced heterodimers is described, and crystal structures of the heterodimeric POZ domains of Miz1/BCL6 and of Miz1/NAC1 are reported. These structures will be relevant for the design of therapeutics that target POZ-domain interaction interfaces.
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10
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Naicker P, Stoychev S, Dirr HW, Sayed Y. Amide hydrogen exchange in HIV-1 subtype B and C proteases - insights into reduced drug susceptibility and dimer stability. FEBS J 2014; 281:5395-410. [DOI: 10.1111/febs.13084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/29/2014] [Accepted: 09/29/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Previn Naicker
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
| | - Stoyan Stoychev
- Council for Scientific and Industrial Research; Biosciences; Pretoria South Africa
| | - Heini W. Dirr
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
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11
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Oliveira JCCD, Oliveira CHD, Oliveira HED, Pereira A, Maraschin M, d'Acâmpora AJ. Effects of perioperative hypothermia and reactive oxygen species in the healing of colonic anastomosis in rats. Acta Cir Bras 2014; 29:742-7. [DOI: 10.1590/s0102-86502014001800008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/24/2014] [Indexed: 12/19/2022] Open
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12
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Cella LN, Biswas P, Yates MV, Mulchandani A, Chen W. Quantitative assessment of in vivo HIV protease activity using genetically engineered QD-based FRET probes. Biotechnol Bioeng 2014; 111:1082-7. [PMID: 24473897 DOI: 10.1002/bit.25199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/09/2014] [Accepted: 01/21/2014] [Indexed: 11/09/2022]
Abstract
HIV protease plays a central role in its life cycle leading to release of functional viral particles. It has been successfully used as a therapeutic target to block HIV infection. Several protease inhibitors (PIs) are currently being employed as a part of anti-HIV therapy. However, the constant genetic drift in the virus leads to accumulation of mutations in both cleavage site and the protease, resulting in resistance and failure of therapy. We reported the use of a quantum dot (QD)-based protein probe for the in vivo monitoring of HIV-1 protease activity based on fluorescence resonance energy transfer. In the current study, we demonstrate the utility of this approach by quantifying the in vivo cleavage rates of three known protease and cleavage site mutations in the presence or absence of different PIs. The changes in IC50 values for the different PIs were similar to that observed in patients, validating our assay as a rapid platform for PI screening.
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Affiliation(s)
- Lakshmi N Cella
- Department of Chemical and Environmental Engineering, University of California, Riverside, California
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13
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de Oliveira JCC, de Oliveira CH, de Oliveira HE, Colombeli GL, De Bona Heck N, Pereira A, D'Acâmpora AJ. Effects of perioperative hypothermia on healing of anastomosis of the colon in rats. Int J Colorectal Dis 2013; 28:705-12. [PMID: 23588874 DOI: 10.1007/s00384-013-1695-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/27/2013] [Indexed: 02/04/2023]
Abstract
OBJECTIVE We evaluated the hypothesis that induced perioperative hypothermia in rats causes adverse effects on the healing of colonic anastomosis. MATERIALS AND METHODS Forty-eight Wistar rats were divided into eight groups of six animals that underwent laparotomy, sigmoid section, and anastomosis. Four groups were operated under normothermic conditions (36 ± 1 °C) and four under hypothermic conditions (32 ± 1 °C). The reoperations were performed on days 3, 7, and 14 post-surgery, and two groups where SHAM reoperated on day 3. We evaluated anastomotic bursting pressure and tissue hydroxyproline content; performed a histological analysis of inflammatory parameters and healing (inflammatory cell infiltrate, edema, fibrin, collagen deposition and apoptotic cells) with categorization scores = 0, 1, 2, 3; and examined the relative quantification gene expression (cDNA) of inflammatory cytokines [interleukin 1 (IL-1), interleukin 6 (IL-6), and interleukin 10 (IL-10)] and growth factors [vascular endothelial growth factor and insulin-like growth factor 1 (IGF-1)] by reverse transcription polymerase chain reaction. RESULTS Both of the hypothermic groups showed lower anastomotic burst pressure on days 7 and 14 post-surgery, reduced hydroxyproline content on day 14, reduction of inflammatory infiltrates and edema at day 3, and less collagen deposition on day 14. In animals that were hypothermic, the cytokine gene expression showed reduced IL-1 on day 3, reduced IL-6 on days 7 and 14, and reduced IL-10 on days 7 and 14 and a reduction in the growth factor IGF-1 on day 7. CONCLUSION Perioperative hypothermia had detrimental effects on the healing of colonic anastomosis in rats.
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Affiliation(s)
- João Carlos Costa de Oliveira
- Department of Surgery, Health Sciences Center, Federal University of Santa Catarina, Rua Prof. Maria Flora Pausewang, s/n, 88036-800 Trindade, Florianópolis, SC, Brazil.
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Reddy Chichili VP, Kumar V, Sivaraman J. Linkers in the structural biology of protein-protein interactions. Protein Sci 2013; 22:153-67. [PMID: 23225024 DOI: 10.1002/pro.2206] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/08/2012] [Accepted: 11/13/2012] [Indexed: 12/14/2022]
Abstract
Linkers or spacers are short amino acid sequences created in nature to separate multiple domains in a single protein. Most of them are rigid and function to prohibit unwanted interactions between the discrete domains. However, Gly-rich linkers are flexible, connecting various domains in a single protein without interfering with the function of each domain. The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers. Often, independent proteins may not exist as stable or structured proteins until they interact with their binding partner, following which they gain stability and the essential structural elements. Gly-rich linkers have been proven useful for these types of unstable interactions, particularly where the interaction is weak and transient, by creating a covalent link between the proteins to form a stable protein-protein complex. Gly-rich linkers are also employed to form stable covalently linked dimers, and to connect two independent domains that create a ligand-binding site or recognition sequence. The lengths of linkers vary from 2 to 31 amino acids, optimized for each condition so that the linker does not impose any constraints on the conformation or interactions of the linked partners. Various structures of covalently linked protein complexes have been described using X-ray crystallography, nuclear magnetic resonance and cryo-electron microscopy techniques. In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein-protein complexes, and to obtain protein dimers.
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15
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Yang H, Nkeze J, Zhao RY. Effects of HIV-1 protease on cellular functions and their potential applications in antiretroviral therapy. Cell Biosci 2012; 2:32. [PMID: 22971934 PMCID: PMC3490751 DOI: 10.1186/2045-3701-2-32] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 08/31/2012] [Indexed: 11/10/2022] Open
Abstract
Human Immunodeficiency Virus Type 1 (HIV-1) protease inhibitors (PIs) are the most potent class of drugs in antiretroviral therapies. However, viral drug resistance to PIs could emerge rapidly thus reducing the effectiveness of those drugs. Of note, all current FDA-approved PIs are competitive inhibitors, i.e., inhibitors that compete with substrates for the active enzymatic site. This common inhibitory approach increases the likelihood of developing drug resistant HIV-1 strains that are resistant to many or all current PIs. Hence, new PIs that move away from the current target of the active enzymatic site are needed. Specifically, allosteric inhibitors, inhibitors that prohibit PR enzymatic activities through non-competitive binding to PR, should be sought. Another common feature of current PIs is they were all developed based on the structure-based design. Drugs derived from a structure-based strategy may generate target specific and potent inhibitors. However, this type of drug design can only target one site at a time and drugs discovered by this method are often associated with strong side effects such as cellular toxicity, limiting its number of target choices, efficacy, and applicability. In contrast, a cell-based system may provide a useful alternative strategy that can overcome many of the inherited shortcomings associated with structure-based drug designs. For example, allosteric PIs can be sought using a cell-based system without considering the site or mechanism of inhibition. In addition, a cell-based system can eliminate those PIs that have strong cytotoxic effect. Most importantly, a simple, economical, and easy-to-maintained eukaryotic cellular system such as yeast will allow us to search for potential PIs in a large-scaled high throughput screening (HTS) system, thus increasing the chances of success. Based on our many years of experience in using fission yeast as a model system to study HIV-1 Vpr, we propose the use of fission yeast as a possible surrogate system to study the effects of HIV-1 protease on cellular functions and to explore its utility as a HTS system to search for new PIs to battle HIV-1 resistant strains.
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Affiliation(s)
- Hailiu Yang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA.
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16
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Alvizo O, Mittal S, Mayo SL, Schiffer CA. Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease. Protein Sci 2012; 21:1029-41. [PMID: 22549928 DOI: 10.1002/pro.2086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/23/2012] [Accepted: 04/10/2012] [Indexed: 02/02/2023]
Abstract
HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease.
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Affiliation(s)
- Oscar Alvizo
- Division of Biology, Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, California 91125, USA
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Identification of broad-based HIV-1 protease inhibitors from combinatorial libraries. Biochem J 2010; 429:527-32. [PMID: 20507280 DOI: 10.1042/bj20091645] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Clinically approved inhibitors of the HIV-1 protease function via a competitive mechanism. A particular vulnerability of competitive inhibitors is their sensitivity to increases in substrate concentration, as may occur during virion assembly, budding and processing into a mature infectious viral particle. Advances in chemical synthesis have led to the development of new high-diversity chemical libraries using rapid in-solution syntheses. These libraries have been shown previously to be effective at disrupting protein-protein and protein-nucleic acid interfaces. We have screened 44000 compounds from such a library to identify inhibitors of the HIV-1 protease. One compound was identified that inhibits wild-type protease, as well as a drug-resistant protease with six mutations. Moreover, analysis of this compound suggests an allosteric non-competitive mechanism of inhibition and may represent a starting point for an additional strategy for anti-retroviral therapy.
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18
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Prashar V, Bihani SC, Das A, Rao DR, Hosur MV. Insights into the mechanism of drug resistance: X-ray structure analysis of G48V/C95F tethered HIV-1 protease dimer/saquinavir complex. Biochem Biophys Res Commun 2010; 396:1018-23. [PMID: 20471372 DOI: 10.1016/j.bbrc.2010.05.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 05/10/2010] [Indexed: 11/28/2022]
Abstract
The mutation G48V in HIV-1 protease is a major resistance mutation against the drug saquinavir. Recently, G48V mutation is found to co-exist with the mutation C95F in AIDS patients treated with saquinavir. We report here the three-dimensional crystal structure of G48V/C95F tethered HIV-1 protease/saquinavir complex. The structure indicates following as the possible causes of drug resistance: (1) loss of direct van der Waals interactions between saquinavir and enzyme residues PHE-53 and PRO-1081, (2) loss of water-mediated hydrogen bonds between the carbonyl oxygen atoms in saquinavir and amide nitrogen atoms of flap residues 50 and 1050, (3) changes in inter-monomer interactions, which could affect the energetics of domain movements associated with inhibitor-binding, and (4) significant reduction in the stability of the mutant dimer. The present structure also provides a rationale for the clinical observation that the resistance mutations C95F/G48V/V82A occur as a cluster in AIDS patients.
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Affiliation(s)
- Vishal Prashar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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19
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Das A, Mahale S, Prashar V, Bihani S, Ferrer JL, Hosur MV. X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrahedral Intermediate and Short Ionic Hydrogen Bond SIHB with Catalytic Aspartate. J Am Chem Soc 2010; 132:6366-73. [DOI: 10.1021/ja100002b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Amit Das
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Smita Mahale
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Vishal Prashar
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Subhash Bihani
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - J.-L. Ferrer
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - M. V. Hosur
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
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20
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Current and Novel Inhibitors of HIV Protease. Viruses 2009; 1:1209-39. [PMID: 21994591 PMCID: PMC3185513 DOI: 10.3390/v1031209] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 12/07/2009] [Accepted: 12/07/2009] [Indexed: 12/25/2022] Open
Abstract
The design, development and clinical success of HIV protease inhibitors represent one of the most remarkable achievements of molecular medicine. This review describes all nine currently available FDA-approved protease inhibitors, discusses their pharmacokinetic properties, off-target activities, side-effects, and resistance profiles. The compounds in the various stages of clinical development are also introduced, as well as alternative approaches, aiming at other functional domains of HIV PR. The potential of these novel compounds to open new way to the rational drug design of human viruses is critically assessed.
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21
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Prashar V, Bihani S, Das A, Ferrer JL, Hosur M. Catalytic water co-existing with a product peptide in the active site of HIV-1 protease revealed by X-ray structure analysis. PLoS One 2009; 4:e7860. [PMID: 19924250 PMCID: PMC2775671 DOI: 10.1371/journal.pone.0007860] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 10/15/2009] [Indexed: 11/18/2022] Open
Abstract
Background It is known that HIV-1 protease is an important target for design of antiviral compounds in the treatment of Acquired Immuno Deficiency Syndrome (AIDS). In this context, understanding the catalytic mechanism of the enzyme is of crucial importance as transition state structure directs inhibitor design. Most mechanistic proposals invoke nucleophilic attack on the scissile peptide bond by a water molecule. But such a water molecule coexisting with any ligand in the active site has not been found so far in the crystal structures. Principal Findings We report here the first observation of the coexistence in the active site, of a water molecule WAT1, along with the carboxyl terminal product (Q product) peptide. The product peptide has been generated in situ through cleavage of the full-length substrate. The N-terminal product (P product) has diffused out and is replaced by a set of water molecules while the Q product is still held in the active site through hydrogen bonds. The position of WAT1, which hydrogen bonds to both the catalytic aspartates, is different from when there is no substrate bound in the active site. We propose WAT1 to be the position from where catalytic water attacks the scissile peptide bond. Comparison of structures of HIV-1 protease complexed with the same oligopeptide substrate, but at pH 2.0 and at pH 7.0 shows interesting changes in the conformation and hydrogen bonding interactions from the catalytic aspartates. Conclusions/Significance The structure is suggestive of the repositioning, during substrate binding, of the catalytic water for activation and subsequent nucleophilic attack. The structure could be a snap shot of the enzyme active site primed for the next round of catalysis. This structure further suggests that to achieve the goal of designing inhibitors mimicking the transition-state, the hydrogen-bonding pattern between WAT1 and the enzyme should be replicated.
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Affiliation(s)
- Vishal Prashar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Subhash Bihani
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Amit Das
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Jean-Luc Ferrer
- Laboratoire de Cristallographie et Cristallogenèse des Protéines/Le Groupe Synchrotron, Institut de Biologie Structurale, Grenoble, France
| | - Madhusoodan Hosur
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- * E-mail:
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22
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Bihani SC, Das A, Prashar V, Ferrer JL, Hosur MV. Resistance mechanism revealed by crystal structures of unliganded nelfinavir-resistant HIV-1 protease non-active site mutants N88D and N88S. Biochem Biophys Res Commun 2009; 389:295-300. [PMID: 19720046 DOI: 10.1016/j.bbrc.2009.08.138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 08/24/2009] [Indexed: 11/30/2022]
Abstract
Nelfinavir is an inhibitor of HIV-1 protease, and is used for treatment of patients suffering from HIV/AIDS. However, treatment results in drug resistant mutations in HIV-1 protease. N88D and N88S are two such mutations which occur in the non-active site region of the enzyme. We have determined crystal structures of unliganded N88D and N88S mutants of HIV-1 protease to resolution of 1.65A and 1.8A, respectively. These structures refined against synchrotron data lead to R-factors of 0.1859 and 0.1780, respectively. While structural effects of N88D are very subtle, the mutation N88S has caused a significant conformational change in D30, an active site residue crucial for substrate and inhibitor binding.
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Affiliation(s)
- Subhash C Bihani
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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23
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Bihani S, Das A, Prashar V, Ferrer JL, Hosur MV. X-ray structure of HIV-1 protease in situ product complex. Proteins 2009; 74:594-602. [DOI: 10.1002/prot.22174] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Zhang S, Kaplan AH, Tropsha A. HIV-1 protease function and structure studies with the simplicial neighborhood analysis of protein packing method. Proteins 2008; 73:742-53. [PMID: 18498108 DOI: 10.1002/prot.22094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method was used to predict the effect of mutagenesis on the enzymatic activity of the HIV-1 protease (HIVP). SNAPP relies on a four-body statistical scoring function derived from the analysis of spatially nearest neighbor residue compositional preferences in a diverse and representative subset of protein structures from the Protein Data Bank. The method was applied to the analysis of HIVP mutants with residue substitutions in the hydrophobic core as well as at the interface between the two protease monomers. Both wild-type and tethered structures were employed in the calculations. We obtained a strong correlation, with R(2) as high as 0.96, between DeltaSNAPP score (i.e., the difference in SNAPP scores between wild-type and mutant proteins) and the protease catalytic activity for tethered structures. However, a weaker but significant correlation was obtained for nontethered structures. Our analysis identified residues both in the hydrophobic core and at the dimeric interface that are very important for the protease function. This study demonstrates a potential utility of the SNAPP method for rational design of mutagenesis studies and protein engineering.
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Affiliation(s)
- Shuxing Zhang
- Department of Experimental Therapeutics, M. D. Anderson Cancer Center, Unit 36, Houston, Texas 77030, USA
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25
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Bartoňová V, Král V, Sieglová I, Brynda J, Fábry M, Hořejší M, Kožíšek M, Šašková KG, Konvalinka J, Sedláček J, Řezáčová P. Potent inhibition of drug-resistant HIV protease variants by monoclonal antibodies. Antiviral Res 2008; 78:275-7. [DOI: 10.1016/j.antiviral.2008.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 12/17/2007] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
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26
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Imamura D, Zhou R, Feig M, Kroos L. Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease. J Biol Chem 2008; 283:15287-99. [PMID: 18378688 PMCID: PMC2397457 DOI: 10.1074/jbc.m708962200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 03/25/2008] [Indexed: 11/06/2022] Open
Abstract
The bacterium Bacillus subtilis undergoes endospore formation in response to starvation. sigma factors play a key role in spatiotemporal regulation of gene expression during development. Activation of sigma factors is coordinated by signal transduction between the forespore and the mother cell. sigma(E) is produced as pro-sigma(E), which is activated in the mother cell by cleavage in response to a signal from the forespore. We report that expression of SpoIIR, a putative signaling protein normally made in the forespore, and SpoIIGA, a putative protease, is necessary and sufficient for accurate, rapid, and abundant processing of pro-sigma(E) to sigma(E) in Escherichia coli. Modeling and mutational analyses provide evidence that SpoIIGA is a novel type of aspartic protease whose C-terminal half forms a dimer similar to the human immunodeficiency virus type 1 protease. Previous studies suggest that the N-terminal half of SpoIIGA is membrane-embedded. We found that SpoIIGA expressed in E. coli is membrane-associated and that after detergent treatment SpoIIGA was self-associated. Also, SpoIIGA interacts with SpoIIR. The results support a model in which SpoIIGA forms inactive dimers or oligomers, and interaction of SpoIIR with the N-terminal domain of SpoIIGA on one side of a membrane causes a conformational change that allows formation of active aspartic protease dimer in the C-terminal domain on the other side of the membrane, where it cleaves pro-sigma(E).
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Affiliation(s)
- Daisuke Imamura
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and Faculty of Pharmaceutical Sciences, Setsunan University, Osaka 573-0101, Japan
| | - Ruanbao Zhou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and Faculty of Pharmaceutical Sciences, Setsunan University, Osaka 573-0101, Japan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and Faculty of Pharmaceutical Sciences, Setsunan University, Osaka 573-0101, Japan
| | - Lee Kroos
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and Faculty of Pharmaceutical Sciences, Setsunan University, Osaka 573-0101, Japan
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27
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Popov EM. Current advances in the X-ray crystallography of proteins. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1995v064n12abeh000194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Sun JP, Luo Y, Yu X, Wang WQ, Zhou B, Liang F, Zhang ZY. Phosphatase activity, trimerization, and the C-terminal polybasic region are all required for PRL1-mediated cell growth and migration. J Biol Chem 2007; 282:29043-29051. [PMID: 17656357 DOI: 10.1074/jbc.m703537200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phosphatase of regenerating liver (PRL) phosphatases are implicated in a number of tumorigenesis and metastasis processes. The PRLs are unique among protein-tyrosine phosphatases in that they have extremely low phosphatase activity, a high propensity for trimer formation, and a polybasic region that precedes the C-terminal prenylation motif. To investigate the functional significance of these distinctive biochemical and structural features, we established a cell-based system in which ectopic PRL1 expression increased cell proliferation and migration, whereas knockdown of endogenous PRL1 abrogated these cellular activities. We showed that the intrinsic PRL1 phosphatase activity is obligatory for its biological function. We provided evidence that trimerization may be a general property for all PRL enzymes, and that PRL1 trimer formation is essential for the PRL1-mediated cell growth and migration. This finding indicates a novel mechanism for phosphatase regulation. We further demonstrated that the conserved C-terminal polybasic region is important for specific phosphoinositide recognition by PRL1. Both the polybasic residues and the adjacent prenylation motif are required for proper PRL1 subcellular localization and full biological activity.
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Affiliation(s)
- Jin-Peng Sun
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Yong Luo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Xiao Yu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Wei-Qing Wang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Bo Zhou
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Fubo Liang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202.
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29
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Wapling J, Srivastava S, Shehu-Xhilaga M, Tachedjian G. Targeting human immunodeficiency virus type 1 assembly, maturation and budding. Drug Target Insights 2007; 2:159-82. [PMID: 21901072 PMCID: PMC3155237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The targets for licensed drugs used for the treatment of human immunodeficiency virus type 1 (HIV-1) are confined to the viral reverse transcriptase (RT), protease (PR), and the gp41 transmembrane protein (TM). While currently approved drugs are effective in controlling HIV-1 infections, new drug targets and agents are needed due to the eventual emergence of drug resistant strains and drug toxicity. Our increased understanding of the virus life-cycle and how the virus interacts with the host cell has unveiled novel mechanisms for blocking HIV-1 replication. This review focuses on inhibitors that target the late stages of virus replication including the synthesis and trafficking of the viral polyproteins, viral assembly, maturation and budding. Novel approaches to blocking the oligomerization of viral enzymes and the interactions between viral proteins and host cell factors, including their feasibility as drug targets, are discussed.
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Affiliation(s)
- Johanna Wapling
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia,Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Seema Srivastava
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
| | - Miranda Shehu-Xhilaga
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia,Infectious Diseases Unit, Alfred Hospital, Prahran, Victoria 3181, Australia
| | - Gilda Tachedjian
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia,Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia,Department of Medicine, Monash University, Prahran, Victoria 3181, Australia,Correspondence: Gilda Tachedjian, Ph.D., Molecular Interactions Group, The Macfarlane Burnet Institute for Medical Research and Public Health, GPO Box 2284, Melbourne, Victoria, 3001, Australia. Tel: 61 3 9282 2256; Fax: 61 3 9282 2100;
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30
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Torbeev VY, Kent SBH. Convergent chemical synthesis and crystal structure of a 203 amino acid "covalent dimer" HIV-1 protease enzyme molecule. Angew Chem Int Ed Engl 2007; 46:1667-70. [PMID: 17397076 DOI: 10.1002/anie.200604087] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vladimir Yu Torbeev
- Department of Chemistry, Institute for Biophysical Dynamics, Gordon Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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31
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Torbeev V, Kent S. Convergent Chemical Synthesis and Crystal Structure of a 203 Amino Acid “Covalent Dimer” HIV-1 Protease Enzyme Molecule. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604087] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Das A, Prashar V, Mahale S, Serre L, Ferrer JL, Hosur MV. Crystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates. Proc Natl Acad Sci U S A 2006; 103:18464-9. [PMID: 17116869 PMCID: PMC1693685 DOI: 10.1073/pnas.0605809103] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Indexed: 11/18/2022] Open
Abstract
HIV-1 protease is an effective target for designing drugs against AIDS, and structural information about the true transition state and the correct mechanism can provide important inputs. We present here the three-dimensional structure of a bi-product complex between HIV-1 protease and the two cleavage product peptides AETF and YVDGAA. The structure, refined against synchrotron data to 1.65 A resolution, shows the occurrence of the cleavage reaction in the crystal, with the product peptides still held in the enzyme active site. The separation between the scissile carbon and nitrogen atoms is 2.67 A, which is shorter than a normal van der Waal separation, but it is much longer than a peptide bond length. The substrate is thus in a stage just past the G'Z intermediate described in Northrop's mechanism [Northrop DB (2001) Acc Chem Res 34:790-797]. Because the products are generated in situ, the structure, by extrapolation, can give insight into the mechanism of the cleavage reaction. Both oxygens of the generated carboxyl group form hydrogen bonds with atoms at the catalytic center: one to the OD2 atom of a catalytic aspartate and the other to the scissile nitrogen atom. The latter hydrogen bond may have mediated protonation of scissile nitrogen, triggering peptide bond cleavage. The inner oxygen atoms of the catalytic aspartates in the complex are 2.30 A apart, indicating a low-barrier hydrogen bond between them at this stage of the reaction, an observation not included in Northrop's proposal. This structure forms a template for designing mechanism-based inhibitors.
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Affiliation(s)
- Amit Das
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Vishal Prashar
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Smita Mahale
- National Institute for Research in Reproductive Health, Parel, Mumbai 400012, India; and
| | - L. Serre
- Institute de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Joseph Fourier, 38027 Grenoble Cedex 1, France
| | - J.-L. Ferrer
- Institute de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Joseph Fourier, 38027 Grenoble Cedex 1, France
| | - M. V. Hosur
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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33
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Cheng YSE, Lo KH, Hsu HH, Shao YM, Yang WB, Lin CH, Wong CH. Screening for HIV protease inhibitors by protection against activity-mediated cytotoxicity in Escherichia coli. J Virol Methods 2006; 137:82-7. [PMID: 16849028 DOI: 10.1016/j.jviromet.2006.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2006] [Revised: 05/28/2006] [Accepted: 06/05/2006] [Indexed: 11/15/2022]
Abstract
Expressed retroviral proteases are often cytotoxic to the hosts. The cytotoxicity of a tethered dimer HIV protease described previously is particularly severe that transformed Escherichia coli cells could not survive the bactericidal activity of the low-level protease produced under uninduced conditions. The presence of HIV protease inhibitors protected the transformed cells from cytotoxic effects and allowed the growth of these cells on plates and in broth. A high throughput screening method was developed to seek compounds that served as "growth factors" for the HIV protease restricted cells. Several compounds identified by this screening supported the growth of these cells, preserved their viability, and inhibited HIV protease. This assay could be used as a general method for screening for inhibitors of recombinant enzymes that produce a cytotoxic phenotype in host cells.
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Affiliation(s)
- Yih-Shyun E Cheng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan, ROC.
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34
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Takahashi T, Yana D, Mihara H. Utilization of L-alpha-nucleobase amino acids (NBAs) as protein engineering tools: construction of NBA-modified HIV-1 protease analogues and enhancement of dimerization induced by nucleobase interaction. Chembiochem 2006; 7:729-32. [PMID: 16550624 DOI: 10.1002/cbic.200500422] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tsuyoshi Takahashi
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Yokohama 226-8501, Japan.
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35
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Broglia RA, Tiana G, Sutto L, Provasi D, Simona F. Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers. Protein Sci 2005; 14:2668-81. [PMID: 16195553 PMCID: PMC2253289 DOI: 10.1110/ps.051670905] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The main problems found in designing drugs are those of optimizing the drug-target interaction and of avoiding the insurgence of resistance. We suggest a scheme for the design of inhibitors that can be used as leads for the development of a drug and that do not face either of these problems, and then apply it to the case of HIV-1-PR. It is based on the knowledge that the folding of single-domain proteins, such as each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting, and highly conserved amino acids that play a central role in the folding process. Because LES have evolved over many generations to recognize and strongly interact with each other so as to make the protein fold fast and avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding-inhibitor molecules suggest themselves: short peptides (or eventually their mimetic molecules) displaying the same amino acid sequence of that of LES (p-LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance; in fact, mutations in HIV-1-PR that successfully avoid the action of p-LES imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations, we first identify the LES of the HIV-1-PR and then show that the corresponding p-LES peptides act as effective inhibitors of the folding of the protease.
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Kumar M, Prashar V, Mahale S, Hosur M. Observation of a tetrahedral reaction intermediate in the HIV-1 protease-substrate complex. Biochem J 2005; 389:365-71. [PMID: 15794743 PMCID: PMC1175113 DOI: 10.1042/bj20041804] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Revised: 03/17/2005] [Accepted: 03/24/2005] [Indexed: 11/17/2022]
Abstract
HIV-1 protease is an effective target for the design of drugs against AIDS. To help this process of drug design, three-dimensional structures have been determined of complexes between HIV-1 protease and a variety of transition-state analogue inhibitors. The true transition state, however, has not been structurally characterized. The crystal structure of the C95M/C1095A HIV-1 protease tethered dimer shows a distinctive feature in which the two flaps of the enzyme are in a 'closed conformation' even in the unliganded state. This unique feature has been utilized here to study the structure of HIV-1 protease complexed to an oligopeptide substrate of amino acid sequence His-Lys-Ala-Arg-Val-Leu*NPhe-Glu-Ala-Nle-Ser (where * denotes the cleavage site, and NPhe and Nle denote p-nitrophenylalanine and norleucine residues respectively). The X-ray structure of the complex refined against 2.03 A (0.203 nm) resolution synchrotron data shows that the substrate is trapped as a tetrahedral reaction intermediate in the crystal. The hydrogen-bonding interactions between the reaction intermediate and the catalytic aspartates are different from those observed previously using transition-state analogues. The reaction intermediate did not dissociate to release the products, possibly due to the inflexibility introduced in the flaps when the enzyme is packed inside crystals.
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Affiliation(s)
- Mukesh Kumar
- *Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Vishal Prashar
- *Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Smita Mahale
- †National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India
| | - Madhusoodan V. Hosur
- *Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
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Sperka T, Pitlik J, Bagossi P, Tözsér J. Beta-lactam compounds as apparently uncompetitive inhibitors of HIV-1 protease. Bioorg Med Chem Lett 2005; 15:3086-90. [PMID: 15893929 DOI: 10.1016/j.bmcl.2005.04.020] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Revised: 03/31/2005] [Accepted: 04/14/2005] [Indexed: 10/25/2022]
Abstract
Compounds of a combinatorial monocyclic beta-lactam library were found to be apparently uncompetitive inhibitors of HIV-1 protease, providing lead compounds for a new class of HIV protease inhibitors.
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Affiliation(s)
- Tamás Sperka
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Faculty of Medicine, H-4012 Debrecen, Hungary
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38
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Kovalskyy D, Dubyna V, Mark AE, Kornelyuk A. A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the active site. Proteins 2004; 58:450-8. [DOI: 10.1002/prot.20304] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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39
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Prashar V, Hosur MV. 1.8A X-ray structure of C95M/C1095F double mutant of tethered HIV-1 protease dimer complexed with acetyl pepstatin. Biochem Biophys Res Commun 2004; 323:1229-35. [PMID: 15451428 DOI: 10.1016/j.bbrc.2004.08.226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Indexed: 11/21/2022]
Abstract
Under the selection pressure of drugs, mutations appear in HIV-1 protease even at the sites, which are conserved in the untreated individuals. Cysteine 95 is a highly conserved residue and is believed to be involved in regulation of HIV-1 protease. In some of the virus isolates from patients undergoing heavy treatment with anti-HIV protease drugs, C95F mutation has appeared. The present study reports 1.8A X-ray structure of C95M/C1095F double mutant of tethered HIV-1 protease dimer complexed with acetyl pepstatin. It is found that in this mutant, dimer interface has become more rigid and that the packing at the interface of terminal and core domains is altered. These alterations may be relevant to C95F mutation conferring drug resistance to HIV-1 protease.
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Affiliation(s)
- Vishal Prashar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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40
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Cheng TJ, Brik A, Wong CH, Kan CC. Model system for high-throughput screening of novel human immunodeficiency virus protease inhibitors in Escherichia coli. Antimicrob Agents Chemother 2004; 48:2437-47. [PMID: 15215092 PMCID: PMC434161 DOI: 10.1128/aac.48.7.2437-2447.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Novel human immunodeficiency virus (HIV) protease inhibitors are urgently needed for combating the drug-resistance problem in the fight against AIDS. To facilitate lead discovery of HIV protease inhibitors, we have developed a safe, convenient, and cost-effective Escherichia coli-based assay system. This E. coli-based system involves coexpression of an engineered beta-galactosidase as an HIV protease substrate and the HIV protease precursor comprising the transframe region and the protease domain. Autoprocessing of the HIV protease precursor releases the mature HIV protease. Subsequently, the HIV protease cleaves beta-galactosidase, resulting in a loss of the beta-galactosidase activity, which can be detected in high-throughput screens. Using Food and Drug Administration-approved HIV protease inhibitors, this E. coli-based system is validated as a surrogate screening system for identifying inhibitors that not only possess inhibitory activity against HIV protease but also have solubility and permeability for in vivo activity. The usefulness of the E. coli-based system was demonstrated with the identification of a novel HIV protease inhibitor from a library of compounds that were prepared by an amide-forming reaction with transition-state analog cores. A novel inhibitor with a sulfonamide core of amprenavir, E2, has shown good correlation with the in vitro enzymatic assay and in vivo E. coli-based system. This system can also be used to generate drug resistance profiles that could be used to suggest therapeutic uses of HIV protease inhibitors to treat the drug-resistant HIV strains. This simple yet efficient E. coli system not only represents a screening platform for high-throughput identification of leads targeting the HIV proteases but also can be adapted to all other classes of proteases.
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Affiliation(s)
- Ting-Jen Cheng
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA
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41
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Ingr M, Uhlíková T, Strísovský K, Majerová E, Konvalinka J. Kinetics of the dimerization of retroviral proteases: the "fireman's grip" and dimerization. Protein Sci 2004; 12:2173-82. [PMID: 14500875 PMCID: PMC2366921 DOI: 10.1110/ps.03171903] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
All retroviral proteases belong to the family of aspartic proteases. They are active as homodimers, each unit contributing one catalytic aspartate to the active site dyad. An important feature of all aspartic proteases is a conserved complex scaffold of hydrogen bonds supporting the active site, called the "fireman's grip," which involves the hydroxyl groups of two threonine (serine) residues in the active site Asp-Thr(Ser)-Gly triplets. It was shown previously that the fireman's grip is indispensable for the dimer stability of HIV protease. The retroviral proteases harboring Ser in their active site triplet are less active and, under natural conditions, are expressed in higher enzyme/substrate ratio than those having Asp-Thr-Gly triplet. To analyze whether this observation can be attributed to the different influence of Thr or Ser on dimerization, we prepared two pairs of the wild-type and mutant proteases from HIV and myeloblastosis-associated virus harboring either Ser or Thr in their Asp-Thr(Ser)-Gly triplet. The equilibrium dimerization constants differed by an order of magnitude within the relevant pairs. The proteases with Thr in their active site triplets were found to be approximately 10 times more thermodynamically stable. The dimer association contributes to this difference more than does the dissociation. We propose that the fireman's grip might be important in the initial phases of dimer formation to help properly orientate the two subunits of a retroviral protease. The methyl group of threonine might contribute significantly to fixing such an intermediate conformation.
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Affiliation(s)
- Marek Ingr
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, 166 10 Praha 6, Czech Republic
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42
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Fehér A, Boross P, Sperka T, Oroszlan S, Tözsér J. Expression of the murine leukemia virus protease in fusion with maltose-binding protein in Escherichia coli. Protein Expr Purif 2004; 35:62-8. [PMID: 15039067 DOI: 10.1016/j.pep.2004.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Revised: 01/12/2004] [Indexed: 01/15/2023]
Abstract
The protease of murine leukemia virus (MLV) was cloned into pMal-c2 vector, expressed in fusion with maltose-binding protein (MBP), and purified to homogeneity after Factor Xa cleavage of the chimeric protein. Substantial degradation of the fusion protein was observed during expression, which severely diminished the yield. The degree of degradation of the fusion protein was even more pronounced when a single-chain form of the MLV protease was cloned after the gene coding for MBP. To increase the yield, a hexahistidine tag with an additional Factor Xa cleavage site was cloned after the protease and nickel chelate affinity chromatography was used as the first purification step. The modified procedure resulted in substantially higher yield as compared to the original procedure. The degradation of hexahistidine-tagged active site mutant MLV protease was very low and comparable to that obtained with hexahistidine-tagged MBP, but purified MLV protease alone was not able to degrade purified MBP, suggesting that during expression the active MLV protease may activate bacterial proteases which appear to be responsible for the degradation of the fusion proteins.
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Affiliation(s)
- Anita Fehér
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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Abstract
Perioperative hypothermia triples the incidence of adverse myocardial outcomes in high-risk patients. Mild hypothermia significantly increases blood loss and augments allogeneic transfusion requirement, but the molecular pathophysiology of this effect remains to be elucidated. Only 1.9 degrees C core hypothermia triples the incidence of surgical wound infection following colon resection and increases the duration of hospitalization by 20%. Hypothermia adversely affects antibody- and cell-mediated immune defences, as well as the oxygen availability in the peripheral wound tissues. Mild perioperative hypothermia changes the kinetics and action of various anaesthetic and paralysing agents, increases thermal discomfort, and is associated with delayed post-anaesthetic recovery. Finally, mild core hypothermia influences pulse oximetry monitoring and various electrophysiological indices of the nervous system, with questionable clinical significance, as yet.
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Affiliation(s)
- Anthony G Doufas
- Department of Anesthesiology/Neuroscience and Anesthesia ICU, and Outcomes Research Institute, University of Louisville Hospital, 530 South Jackson Street, Louisville, KY 40202, USA.
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44
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Dautin N, Karimova G, Ladant D. Human immunodeficiency virus (HIV) type 1 transframe protein can restore activity to a dimerization-deficient HIV protease variant. J Virol 2003; 77:8216-26. [PMID: 12857890 PMCID: PMC165233 DOI: 10.1128/jvi.77.15.8216-8226.2003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The protease (PR) from human immunodeficiency virus (HIV) is essential for viral replication: this aspartyl protease, active only as a dimer, is responsible for cleavage of the viral polyprotein precursors (Gag and Gag-Pol), to release the functional mature proteins. In this work, we have studied the structure-function relationships of the HIV PR by combining a genetic test to detect proteolytic activity in Escherichia coli and a bacterial two-hybrid assay to analyze PR dimerization. We showed that a drug-resistant PR variant isolated from a patient receiving highly active antiretroviral therapy is impaired in its dimerization capability and, as a consequence, is proteolytically inactive. We further showed that the polypeptide regions adjacent to the PR coding sequence in the Gag-Pol polyprotein precursor, and in particular, the transframe polypeptide (TF), located at the N terminus of PR, can facilitate the dimerization of this variant PR and restore its enzymatic activity. We propose that the TF protein could help to compensate for folding and/or dimerization defects in PR arising from certain mutations within the PR coding sequence and might therefore function to buffer genetic variations in PR.
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Affiliation(s)
- Nathalie Dautin
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, CNRS URA 2185, Institut Pasteur, 75724 Paris Cedex 15, France.
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45
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Abstract
Topological linking of proteins is a new approach for stabilizing and controlling the oligomerization state of proteins that fold in an interwined manner. The recent design of a backbone cyclized protein catenane based on the p53tet domain suggested that topological cross-linking provided increased stability against thermal and chemical denaturation. However, the tetrameric structure complicated detailed biophysical analysis of this protein. Here, we describe the design, synthesis and thermodynamic characterization of a protein catenane based on a dimeric mutant of the p53tet domain (M340E/L344K). The formation of the catenane proceeded efficiently, and the overall structure and oligomerization of the domain was not affected by the formation of the topological link. Unfolding and refolding of the catenane was consistent with a two-state process. The topological link stabilized the dimer against thermal and chemical denaturation considerably, raising the apparent melting temperature by 59 degrees C and the midpoint of denaturation by 4.5M GuHCl at a concentration of 50 microM. The formation of the topological link increased the resistance of the dimer to proteolysis. However, the m value decreased by 1.7kcalmol(-1)M(-1), suggesting a decrease in accessible surface area in the unfolded state. This implies that the stabilization from the topological link is largely due to a destabilization of the unfolded state, similar to other cross-links in proteins. Topological linking therefore provides a powerful and orthogonal tool for the stabilization of peptide and protein oligomers.
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Affiliation(s)
- John W Blankenship
- Department of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MC CVN-6, La Jolla, CA 92037, USA
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46
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Choudhury S, Everitt L, Pettit SC, Kaplan AH. Mutagenesis of the dimer interface residues of tethered and untethered HIV-1 protease result in differential activity and suggest multiple mechanisms of compensation. Virology 2003; 307:204-12. [PMID: 12667791 DOI: 10.1016/s0042-6822(02)00080-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
As is the case for all retroviruses, the protease of HIV-1 is only functional as a homodimer; dimerization of two protease monomers results in the formation of the enzyme active site. This dimer structure is supported primarily by interactions between the first four amino-terminal and the last four carboxy-terminal amino acids. These eight amino acids form a beta-sheet in which hydrophobic residues are oriented towards the core of the molecule and polar residues are directed towards the solvent. Although the structure of the dimer interface has been determined, the forces that support dimerization have not been fully characterized. Here, we describe a tethered construct in which two protease monomers are joined by a 5 amino acid linker. We evaluate the relative role of each dimer interface residue in functional homo- and heterodimers. Our studies indicate that the hydrophobic residues of the dimer interface are particularly important in maintaining enzyme activity and that enzyme activity is more sensitive to substitutions of the C-terminal amino acids. Further, we demonstrate that the presence of the tether is able to compensate for mutations within the dimer interface that inactivate the enzyme.
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Affiliation(s)
- Sumana Choudhury
- Department of Medicine, UNC School of Medicine, Chapel Hill, NC 27599-7030, USA
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47
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Abstract
The total synthesis, at will, of a wide variety of protein and enzyme molecules is made feasible by modem chemical ligation methods. As Emil Fischer intuitively understood, synthetic access to the enzyme molecule enables the power of chemical science to be applied to elucidating the molecular basis of catalytic function in unprecedented detail.
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Affiliation(s)
- Stephen Kent
- Institute for Biophysical Dynamics, Department of Chemistry, The University of Chicago, IL 60637, USA.
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48
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Abstract
Eukaryotic initiation factor (eIF) 4GI is efficiently cleaved during picornaviral replication. eIF4GI processing has also recently been observed during HIV-1 replication. We have compared the efficiency of eIF4GI proteolysis in rabbit reticulocyte lysates during translation of mRNAs encoding the foot-and-mouth disease virus leader proteinase (L(pro)) or the HIV-1 proteinase (HIV-1(pro)). L(pro) cleaved 50% eIF4GI within 12 min whereas HIV-1(pro) required 4 h; the concentrations were 2 pg/microl (0.1 nM) for L(pro) and 60 pg/microl (2.66 nM) for HIV-1(pro). HIV-1(pro) processing of eIF4GI is therefore not quantitatively analogous to that of L(pro), suggesting that the primary function of eIF4GI cleavage in HIV-1 replication may not be protein synthesis inhibition.
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Affiliation(s)
- Petra Schlick
- Institute for Medical Biochemistry, Division of Biochemistry, University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
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49
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Kumar M, Kannan KK, Hosur MV, Bhavesh NS, Chatterjee A, Mittal R, Hosur RV. Effects of remote mutation on the autolysis of HIV-1 PR: X-ray and NMR investigations. Biochem Biophys Res Commun 2002; 294:395-401. [PMID: 12051725 DOI: 10.1016/s0006-291x(02)00482-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Autolysis rates of the C95M and C95M/C1095A mutants of a HIV-1 protease tethered dimer have been determined by real time NMR and it is observed that the double mutant has approximately two times higher rate. X-ray structure of the C95M/C1095A double mutant has been solved and refined to 2.1 A resolution. Comparison of the double mutant structure with that of C95M single mutant reveals that there is a shift in the position of the catalytic aspartates and the bound catalytic water. The mutation also causes a loss of hydrophobic packing near the dimerization domain of the protein. These observations demonstrate that subtle changes are adequate to cause significant changes in the rate of autolysis of the double mutant. This provides a rationale for the effects of remote mutations on the activity and drug resistance of the enzyme.
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Affiliation(s)
- Mukesh Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 005, India
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50
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Bhavesh NS, Panchal SC, Mittal R, Hosur RV. NMR identification of local structural preferences in HIV-1 protease tethered heterodimer in 6 M guanidine hydrochloride. FEBS Lett 2001; 509:218-24. [PMID: 11741592 DOI: 10.1016/s0014-5793(01)03066-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding protein folding requires complete characterization of all the states of the protein present along the folding pathways. For this purpose nuclear magnetic resonance (NMR) has proved to be a very powerful technique because of the great detail it can unravel regarding the structure and dynamics of protein molecules. We report here NMR identification of local structural preferences in human immunodeficiency virus-1 protease in the 'unfolded state'. Analyses of the chemical shifts revealed the presence of local structural preferences many of which are native-like, and there are also some non-native structural elements. Three-bond H(N)-H(alpha) coupling constants that could be measured for some of the N-terminal and C-terminal residues are consistent with the native-like beta-structure. Unusually shifted 15N and amide proton chemical shifts of residues adjacent to some prolines and tryptophans also indicate the presence of some structural elements. These conclusions are supported by amide proton temperature coefficients and nuclear Overhauser enhancement data. The locations of the residues exhibiting preferred structural propensities on the crystal structure of the protein, give useful insights into the folding mechanism of this protein.
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Affiliation(s)
- N S Bhavesh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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