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Kassay N, Mótyán JA, Matúz K, Golda M, Tőzsér J. Biochemical Characterization, Specificity and Inhibition Studies of HTLV-1, HTLV-2, and HTLV-3 Proteases. Life (Basel) 2021; 11:life11020127. [PMID: 33562087 PMCID: PMC7915765 DOI: 10.3390/life11020127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/03/2023] Open
Abstract
The human T-lymphotropic viruses (HTLVs) are causative agents of severe diseases including adult T-cell leukemia. Similar to human immunodeficiency viruses (HIVs), the viral protease (PR) plays a crucial role in the viral life-cycle via the processing of the viral polyproteins. Thus, it is a potential target of anti-retroviral therapies. In this study, we performed in vitro comparative analysis of human T-cell leukemia virus type 1, 2, and 3 (HTLV-1, -2, and -3) proteases. Amino acid preferences of S4 to S1′ subsites were studied by using a series of synthetic oligopeptide substrates representing the natural and modified cleavage site sequences of the proteases. Biochemical characteristics of the different PRs were also determined, including catalytic efficiencies and dependence of activity on pH, temperature, and ionic strength. We investigated the effects of different HIV-1 PR inhibitors (atazanavir, darunavir, DMP-323, indinavir, ritonavir, and saquinavir) on enzyme activities, and inhibitory potentials of IB-268 and IB-269 inhibitors that were previously designed against HTLV-1 PR. Comparative biochemical analysis of HTLV-1, -2, and -3 PRs may help understand the characteristic similarities and differences between these enzymes in order to estimate the potential of the appearance of drug-resistance against specific HTLV-1 PR inhibitors.
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Affiliation(s)
- Norbert Kassay
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
| | - Mária Golda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
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2
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Kneller DW, Agniswamy J, Harrison RW, Weber IT. Highly drug-resistant HIV-1 protease reveals decreased intra-subunit interactions due to clusters of mutations. FEBS J 2020; 287:3235-3254. [PMID: 31920003 PMCID: PMC7343616 DOI: 10.1111/febs.15207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/16/2019] [Accepted: 01/08/2020] [Indexed: 01/07/2023]
Abstract
Drug-resistance is a serious problem for treatment of the HIV/AIDS pandemic. Potent clinical inhibitors of HIV-1 protease show several orders of magnitude worse inhibition of highly drug-resistant variants. Hence, the structure and enzyme activities were analyzed for HIV protease mutant HIV-1 protease (EC 3.4.23.16) (PR) with 22 mutations (PRS5B) from a clinical isolate that was selected by machine learning to represent high-level drug-resistance. PRS5B has 22 mutations including only one (I84V) in the inhibitor binding site; however, clinical inhibitors had poor inhibition of PRS5B activity with kinetic inhibition value (Ki ) values of 4-1000 nm or 18- to 8000-fold worse than for wild-type PR. High-resolution crystal structures of PRS5B complexes with the best inhibitors, amprenavir (APV) and darunavir (DRV) (Ki ~ 4 nm), revealed only minor changes in protease-inhibitor interactions. Instead, two distinct clusters of mutations in distal regions induce coordinated conformational changes that decrease favorable internal interactions across the entire protein subunit. The largest structural rearrangements are described and compared to other characterized resistant mutants. In the protease hinge region, the N83D mutation eliminates a hydrogen bond connecting the hinge and core of the protease and increases disorder compared to highly resistant mutants PR with 17 mutations and PR with 20 mutations with similar hinge mutations. In a distal β-sheet, mutations G73T and A71V coordinate with accessory mutations to bring about shifts that propagate throughout the subunit. Molecular dynamics simulations of ligand-free dimers show differences consistent with loss of interactions in mutant compared to wild-type PR. Clusters of mutations exhibit both coordinated and antagonistic effects, suggesting PRS5B may represent an intermediate stage in the evolution of more highly resistant variants. DATABASES: Structural data are available in Protein Data Bank under the accession codes 6P9A and 6P9B for PRS5B/DRV and PRS5B/APV, respectively.
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Affiliation(s)
- Daniel W. Kneller
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States of America,Author of correspondence:
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Donovan M, Salamito M, Thomas-Collignon A, Simonetti L, Desbouis S, Rain JC, Formstecher E, Bernard D. Filaggrin and filaggrin 2 processing are linked together through skin aspartic acid protease activation. PLoS One 2020; 15:e0232679. [PMID: 32437351 PMCID: PMC7241785 DOI: 10.1371/journal.pone.0232679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 04/21/2020] [Indexed: 12/16/2022] Open
Abstract
Skin aspartic acid protease (SASPase) is believed to be a key enzyme involved in filaggrin processing during epidermal terminal differentiation. Since little is known about the regulation of SASPase function, the aim of this study was to identify involved protein partners in the process. Yeast two hybrid analyses using SASPase as bait against a human reconstructed skin library identified that the N-terminal domain of filaggrin 2 binds to the N-terminal fragment of SASPase. This interaction was confirmed in reciprocal yeast two hybrid screens and by Surface Plasmon Resonance analyses. Immunohistochemical studies in human skin, using specific antibodies to SASPase and the N-terminal domain of filaggrin 2, showed that the two proteins partially co-localized to the stratum granulosum. In vitro enzymatic assays showed that the N-terminal domain of filaggrin 2 enhanced the autoactivation of SASPase to its 14 kDa active form. Taken together, the data suggest that the N-terminal domain of filaggrin 2 regulates the activation of SASPase that may be a key event upstream of filaggrin processing to natural moisturizing factors in the human epidermis.
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Affiliation(s)
- Mark Donovan
- L’Oréal Research & Innovation, Aulnay-sous-Bois, France
- * E-mail:
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4
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Potempa M, Lee SK, Kurt Yilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW, Schiffer CA, Swanstrom R. HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites. J Mol Biol 2018; 430:5182-5195. [PMID: 30414407 DOI: 10.1016/j.jmb.2018.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 11/16/2022]
Abstract
Retroviral proteases (PRs) have a unique specificity that allows cleavage of sites with or without a P1' proline. A P1' proline is required at the MA/CA cleavage site due to its role in a post-cleavage conformational change in the capsid protein. However, the HIV-1 PR prefers to have large hydrophobic amino acids flanking the scissile bond, suggesting that PR recognizes two different classes of substrate sequences. We analyzed the cleavage rate of over 150 combinations of six different HIV-1 cleavage sites to explore rate determinants of cleavage. We found that cleavage rates are strongly influenced by the two amino acids flanking the amino acids at the scissile bond (P2-P1/P1'-P2'), with two complementary sets of rules. When P1' is proline, the P2 side chain interacts with a polar region in the S2 subsite of the PR, while the P2' amino acid interacts with a hydrophobic region of the S2' subsite. When P1' is not proline, the orientations of the P2 and P2' side chains with respect to the scissile bond are reversed; P2 residues interact with a hydrophobic face of the S2 subsite, while the P2' amino acid usually engages hydrophilic amino acids in the S2' subsite. These results reveal that the HIV-1 PR has evolved bi-functional S2 and S2' subsites to accommodate the steric effects imposed by a P1' proline on the orientation of P2 and P2' substrate side chains. These results also suggest a new strategy for inhibitor design to engage the multiple specificities in these subsites.
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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
| | - Sook-Kyung Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amy Rogers
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ean Spielvogel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles W Carter
- Department of Biochemistry and Biophysics, 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
- Lineberger Comprehensive Cancer Center, 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.
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5
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Wang J, Zhang R, Yang X, Liu X, Zhang H. Facile synthesis of copper(II)-decorated functional mesoporous material for specific adsorption of histidine-rich proteins. Talanta 2018; 176:308-317. [DOI: 10.1016/j.talanta.2017.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/30/2017] [Accepted: 08/05/2017] [Indexed: 12/29/2022]
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6
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Rodriguez-Siordia I, Rojo-Arreola L, Navarrete Del Toro MDLA, García-Carreño F. American lobster Cathepsin D, an aspartic peptidase resistant to proteolysis and active in organic solvents, non-ionic detergents and salts. Int J Biol Macromol 2017; 107:1501-1509. [PMID: 28987802 DOI: 10.1016/j.ijbiomac.2017.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/29/2017] [Accepted: 10/02/2017] [Indexed: 11/16/2022]
Abstract
Suitable peptidases for biotechnological applications are those active at low temperature, in organic solvents, detergents or proteolytic additives. American lobster cathepsin D1 (CD1) is an enzyme highly efficient at 5-50°C and at pH 2.5-5.5. We assessed the effect of common industrial additives on CD1 activity. CD1 was isolated from lobster gastric fluid by chromatography. The proteolytic activity was measured using a fluorogenic specific substrate and the conformation by intrinsic fluorescence. Non-ionic detergents Tween-20 and Triton X-100 stabilize the peptidase activity. Ethanol, methanol and isopropanol [5-15% (v/v)] increased the enzyme activity up to 80%. The enzyme is active until 2.5M urea and is resistant to proteolysis by papain and renin. In this work, a crustacean peptidase that remains active when exposed to different chemical and proteolytic additives is reported, evincing that crustaceans are a good model for discovery of novel stable peptidases for future pharmaceutical, cosmetic and alimentary applications.
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Affiliation(s)
- Ivan Rodriguez-Siordia
- Centro de Investigaciones Biologicas del Noroeste, Instituto Politecnico Nacional 195, Col., Playa Palo de Santa Rita Sur, 23096, La Paz, Baja California Sur, Mexico
| | - Liliana Rojo-Arreola
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, Instituto Politecnico Nacional 195, Col., Playa Palo de Santa Rita Sur, 23096, La Paz, Baja California Sur, Mexico
| | - María de Los Angeles Navarrete Del Toro
- Centro de Investigaciones Biologicas del Noroeste, Instituto Politecnico Nacional 195, Col., Playa Palo de Santa Rita Sur, 23096, La Paz, Baja California Sur, Mexico
| | - Fernando García-Carreño
- Centro de Investigaciones Biologicas del Noroeste, Instituto Politecnico Nacional 195, Col., Playa Palo de Santa Rita Sur, 23096, La Paz, Baja California Sur, Mexico.
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7
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Maseko SB, Padayachee E, Govender T, Sayed Y, Kruger G, Maguire GEM, Lin J. I36T↑T mutation in South African subtype C (C-SA) HIV-1 protease significantly alters protease-drug interactions. Biol Chem 2017; 398:1109-1117. [PMID: 28525359 DOI: 10.1515/hsz-2017-0107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022]
Abstract
The efficacy of HIV-1 protease (PR) inhibition therapies is often compromised by the emergence of mutations in the PR molecule that reduces the binding affinity of inhibitors while maintaining viable catalytic activity and affinity for natural substrates. In the present study, we used a recombinant HIV-1 C-SA PR and a recently reported variant for inhibition (Ki, IC50) and thermodynamic studies against nine clinically used inhibitors. This is the first time that binding free energies for C-SA PR and the mutant are reported. This variant PR harbours a mutation and insertion (I36T↑T) at position 36 of the C-SA HIV-1 PR, and did not show a significant difference in the catalytic effect of the HIV-1 PR. However, the nine clinically approved HIV PR drugs used in this study demonstrated weaker inhibition and lower binding affinities toward the variant when compared to the wild type HIV-1 PR. All the protease inhibitors (PIs), except Amprenavir and Ritonavir exhibited a significant decrease in binding affinity (p<0.0001). Darunavir and Nelfinavir exhibited the weakest binding affinity, 155- and 95-fold decreases respectively, toward the variant. Vitality values for the variant PR, against the seven selected PIs, confirm the impact of the mutation and insertion on the South African HIV-1 subtype C PR. This information has important clinical implications for thousands of patients in Sub-Saharan Africa.
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8
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Herpoldt KL, Artzy-Schnirman A, Christofferson AJ, Makarucha AJ, de la Rica R, Yarovsky I, Stevens MM. Designing Fluorescent Peptide Sensors with Dual Specificity for the Detection of HIV-1 Protease. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2015; 27:7187-7195. [PMID: 28479671 PMCID: PMC5419500 DOI: 10.1021/acs.chemmater.5b03651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
HIV-1 protease is a key enzyme in the life cycle of HIV/AIDS, as it is responsible for the formation of the mature virus particle. We demonstrate here that phage-display peptides raised against this enzyme can be used as peptide sensors for the detection of HIV-1 protease in a simple, one-pot assay. The presence of the enzyme is detected through an energy transfer between two peptide sensors when simultaneously complexed with the target protein. The multivalent nature of this assay increases the specificity of the detection by requiring all molecules to be interacting in order for there to be a FRET signal. We also perform molecular dynamics simulations to explore the interaction between the protease and the peptides in order to guide the design of these peptide sensors and to understand the mechanisms which cause these simultaneous binding events. This approach aims to facilitate the development of new assays for enzymes that are not dependent on the cleavage of a substrate and do not require multiple washing steps.
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Affiliation(s)
- Karla-Luise Herpoldt
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Arbel Artzy-Schnirman
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | | | - Adam J. Makarucha
- Health Innovations Research Institute, RMIT University, GPO Box 2476, Victoria 3001, Australia
| | - Roberto de la Rica
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Irene Yarovsky
- Health Innovations Research Institute, RMIT University, GPO Box 2476, Victoria 3001, Australia
| | - Molly M. Stevens
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
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9
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Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK. Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models. J Chem Theory Comput 2015; 11:4555-64. [PMID: 26574247 DOI: 10.1021/acs.jctc.5b00676] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.
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Affiliation(s)
- Kaifu Gao
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Andrew T Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
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10
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Jadhav SB, Bankar SB, Granström T, Ojamo H, Singhal RS, Survase SA. Interaction of carbohydrates with alcohol dehydrogenase: Effect on enzyme activity. J Biosci Bioeng 2015; 120:252-6. [DOI: 10.1016/j.jbiosc.2015.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/09/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
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11
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Samukange V, Kamo M, Yasukawa K, Inouye K. Effects of salts on the interaction of 8-anilinonaphthalene 1-sulphonate and thermolysin. Biosci Biotechnol Biochem 2014; 78:1522-8. [PMID: 25209499 DOI: 10.1080/09168451.2014.923299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Neutral salts activate and stabilize thermolysin. In this study, to explore the mechanism, we analyzed the interaction of 8-anilinonaphthalene 1-sulphonate (ANS) and thermolysin by ANS fluorescence. At pH 7.5, the fluorescence of ANS increased and blue-shifted with increasing concentrations (0-2.0 μM) of thermolysin, indicating that the anilinonaphthalene group of ANS binds with thermolysin through hydrophobic interaction. ANS did not alter thermolysin activity. The dissociation constants (Kd) of the complex between ANS and thermolysin was 33 ± 2 μM at 0 M NaCl at pH 7.5, decreased with increasing NaCl concentrations, and reached 9 ± 3 μM at 4 M NaCl. The Kd values were not varied (31-34 μM) in a pH range of 5.5-8.5. This suggests that at high NaCl concentrations, Na(+) and/or Cl(-) ions bind with thermolysin and affect the binding of ANS with thermolysin. Our results also suggest that the activation and stabilization of thermolysin by NaCl are partially brought about by the binding of Na(+) and/or Cl(-) ions with thermolysin.
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Affiliation(s)
- Vimbai Samukange
- a Division of Food Science and Biotechnology, Graduate School of Agriculture , Kyoto University , Sakyo-ku , Japan
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12
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Louis JM, Tözsér J, Roche J, Matúz K, Aniana A, Sayer JM. Enhanced stability of monomer fold correlates with extreme drug resistance of HIV-1 protease. Biochemistry 2013; 52:7678-88. [PMID: 24079831 PMCID: PMC3888107 DOI: 10.1021/bi400962r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During treatment, mutations in HIV-1 protease (PR) are selected rapidly that confer resistance by decreasing affinity to clinical protease inhibitors (PIs). As these unique drug resistance mutations can compromise the fitness of the virus to replicate, mutations that restore conformational stability and activity while retaining drug resistance are selected on further evolution. Here we identify several compensating mechanisms by which an extreme drug-resistant mutant bearing 20 mutations (PR20) with >5-fold increased Kd and >4000-fold decreased affinity to the PI darunavir functions. (1) PR20 cleaves, albeit poorly, Gag polyprotein substrates essential for viral maturation. (2) PR20 dimer, which exhibits distinctly enhanced thermal stability, has highly attenuated autoproteolysis, thus likely prolonging its lifetime in vivo. (3) The enhanced stability of PR20 results from stabilization of the monomer fold. Both monomeric PR20(T26A) and dimeric PR20 exhibit Tm values 6-7.5 °C higher than those for their PR counterparts. Two specific mutations in PR20, L33F and L63P at sites of autoproteolysis, increase the Tm of monomeric PR(T26A) by ~8 °C, similar to PR20(T26A). However, without other compensatory mutations as seen in PR20, L33F and L63P substitutions, together, neither restrict autoproteolysis nor significantly reduce binding affinity to darunavir. To determine whether dimer stability contributes to binding affinity for inhibitors, we examined single-chain dimers of PR and PR(D25N) in which the corresponding identical monomer units were covalently linked by GGSSG sequence. Linking of the subunits did not appreciably change the ΔTm on inhibitor binding; thus stabilization by tethering appears to have little direct effect on enhancing inhibitor affinity.
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Affiliation(s)
- John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - József Tözsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary H-4012
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary H-4012
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Jane M. Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
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13
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Pokorná J, Heyda J, Konvalinka J. Ion specific effects of alkali cations on the catalytic activity of HIV-1 protease. Faraday Discuss 2013; 160:359-70; discussion 389-403. [PMID: 23795510 DOI: 10.1039/c2fd20094e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human immunodeficiency virus 1 protease (HIV-1 PR), an important therapeutic target for the treatment of AIDS, is one of the most well-studied enzymes. However, there is still much to learn about the regulation of the activity and inhibition of this key viral enzyme. Specifically, the mechanism of activation of HIV-1 PR from the viral polyprotein upon HIV maturation is still not understood. It has been suggested that external factors like pH or salt concentration might contribute to regulation of this crucial step in the viral life cycle. Recently, we analyzed the activity of HIV-1 PR in aqueous solutions of sodium and potassium chloride by experimental determination of enzyme kinetics and molecular dynamics simulations. We showed that the effect of salt concentration is cation-specific [Heyda et al., Phys. Chem. Chem. Phys., 2009 (11), 7599]. In this study, we extended this analysis for other alkali cations and found that the dependence of the initial velocity of peptide substrate hydrolysis on the nature of the cation follows the Hofmeister series, with the exception of caesium. Significantly higher catalytic efficiencies both in terms of substrate binding (K(M)) and turnover number (kcat) are observed in the presence of K+ compared to Na+ or Li+ at corresponding salt concentrations. Molecular dynamics simulations suggest that both lithium and sodium are attracted more strongly than potassium and caesium to the protein surface, mostly due to stronger interactions with carboxylate side chain groups of aspartates and glutamates. Furthermore, we observed a surprising decrease in the K(M) value for a specific substrate at very low salt concentration. The molecular mechanism of this phenomenon will be further analyzed.
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Affiliation(s)
- Jana Pokorná
- Gilead and IOCB Research Center Prague, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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14
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Correlated electrostatic mutations provide a reservoir of stability in HIV protease. PLoS Comput Biol 2012; 8:e1002675. [PMID: 22969420 PMCID: PMC3435258 DOI: 10.1371/journal.pcbi.1002675] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/18/2012] [Indexed: 12/13/2022] Open
Abstract
HIV protease, an aspartyl protease crucial to the life cycle of HIV, is the target of many drug development programs. Though many protease inhibitors are on the market, protease eventually evades these drugs by mutating at a rapid pace and building drug resistance. The drug resistance mutations, called primary mutations, are often destabilizing to the enzyme and this loss of stability has to be compensated for. Using a coarse-grained biophysical energy model together with statistical inference methods, we observe that accessory mutations of charged residues increase protein stability, playing a key role in compensating for destabilizing primary drug resistance mutations. Increased stability is intimately related to correlations between electrostatic mutations – uncorrelated mutations would strongly destabilize the enzyme. Additionally, statistical modeling indicates that the network of correlated electrostatic mutations has a simple topology and has evolved to minimize frustrated interactions. The model's statistical coupling parameters reflect this lack of frustration and strongly distinguish like-charge electrostatic interactions from unlike-charge interactions for of the most significantly correlated double mutants. Finally, we demonstrate that our model has considerable predictive power and can be used to predict complex mutation patterns, that have not yet been observed due to finite sample size effects, and which are likely to exist within the larger patient population whose virus has not yet been sequenced. HIV is incurable because its enzymes evolve rapidly by developing resistance mutations to retroviral inhibitors. Most of these mutations work synergistically, but the biophysical basis behind their cooperation is not well understood. Our work addresses these important issues by bridging the gap between the statistical modeling of HIV protease subtype B sequences with the energetics of mutations involving charged amino acids by showing that electrostatic stability is intimately related to correlations. Moreover, we demonstrate that our statistical model has considerable predictive power and can be used to predict complex mutation patterns that have not yet been observed due to the finite sizes of the current sequence databases. In other words, as the database size increases, our model has the ability to predict the identities of the high probability mutations patterns, which are more likely to be observed. Knowing which currently unobserved mutations are more likely to be observed can be very advantageous in combating the disease.
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Sayer JM, Agniswamy J, Weber IT, Louis JM. Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: relevance to drug resistance. Protein Sci 2011; 19:2055-72. [PMID: 20737578 DOI: 10.1002/pro.486] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mature protease from Group N human immunodeficiency virus Type 1 (HIV-1) (PR1(N)) differs in 20 amino acids from the extensively studied Group M protease (PR1(M)) at positions corresponding to minor drug-resistance mutations (DRMs). The first crystal structure (1.09 Å resolution) of PR1(N) with the clinical inhibitor darunavir (DRV) reveals the same overall structure as PR1(M), but with a slightly larger inhibitor-binding cavity. Changes in the 10s loop and the flap hinge propagate to shift one flap away from the inhibitor, whereas L89F and substitutions in the 60s loop perturb inhibitor-binding residues 29-32. However, kinetic parameters of PR1(N) closely resemble those of PR1(M), and calorimetric results are consistent with similar binding affinities for DRV and two other clinical PIs, suggesting that minor DRMs coevolve to compensate for the detrimental effects of drug-specific major DRMs. A miniprecursor (TFR 1-61-PR1(N)) comprising the transframe region (TFR) fused to the N-terminus of PR1(N) undergoes autocatalytic cleavage at the TFR/PR1(N) site concomitant with the appearance of catalytic activity characteristic of the dimeric, mature enzyme. This cleavage is inhibited at an equimolar ratio of precursor to DRV (∼6 μM), which partially stabilizes the precursor dimer from a monomer. However, cleavage at L34/W35 within the TFR, which precedes the TFR 1-61/PR1(N) cleavage at pH ≤ 5, is only partially inhibited. Favorable properties of PR1(N) relative to PR1(M) include its suitability for column fractionation by size under native conditions and >10-fold higher dimer dissociation constant (150 nM). Exploiting these properties may facilitate testing of potential dimerization inhibitors that perturb early precursor processing steps.
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Affiliation(s)
- Jane M Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, USA
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16
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Dürrschmidt P, Mansfeld J, Ulbrich-Hofmann R. Refolding of the non-specific neutral protease from Bacillus stearothermophilus proceeds via an autoproteolytically sensitive intermediate. Biophys Chem 2010; 147:66-73. [DOI: 10.1016/j.bpc.2010.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/19/2009] [Accepted: 01/05/2010] [Indexed: 10/20/2022]
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Abstract
Progress in understanding protein folding allows to simulate, with atomic detail, the evolution of amino-acid sequences folding to a given native conformation. A particularly attractive example is the HIV-1 protease, main target of therapies to fight AIDS, which under drug pressure is able to develop resistance within few months from the starting of therapy. By comparing the results of simulations of the evolution of the protease with the corresponding proteomic data, one can approximately determine the value of the associated evolution pressure under which the enzyme has become and, as a consequence, map out the energy landscape in sequence space of the HIV-1 protease. It is found that there are several families of sequences folding to the native conformations of the enzyme. Each of these families are characterized by different sets of highly conserved ("hot") amino acids which play a critical role in the folding and stability of the protease. There are two main possibilities for the virus to move from one family to a different one: (a) in a single generation, through the concerted mutations of the hot amino acids, a highly unlikely event, (b) through a folding path (if it exists), again a very improbable event. In fact, the number of generations needed by the virus to change stepwise its sequence from one family to another is astronomically large. These results point to the "hot" segments of the protease as promising targets for a nonconventional inhibition strategy, likely not to create resistance.
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Affiliation(s)
- G Tiana
- Department of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy.
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18
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Anwar T, Ahmad B, Younus H. Cross-linked stem bromelain: A more stabilized active preparation. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701568575] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Abstract
We describe a method for the specific isolation of representative N-terminal peptides of proteins and their proteolytic fragments. Their isolation is based on a gel-free, peptide-centric proteomics approach using the principle of diagonal chromatography. We will indicate that the introduction of an altered chemical property to internal peptides holding a free alpha-N-terminus results in altered column retention of these peptides, thereby enabling the isolation and further characterization by mass spectrometry of N-terminal peptides. Besides pointing to changes in protein expression levels when performing such proteome surveys in a differential modus, protease specificity and substrate repertoires can be allocated since both are specified by neo-N-termini generated after a protease cleavage event. As such, our gel-free proteomics technology is widely applicable and amenable for a variety of proteome-driven protease degradomics research.
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Noel AF, Bilsel O, Kundu A, Wu Y, Zitzewitz JA, Matthews CR. The folding free-energy surface of HIV-1 protease: insights into the thermodynamic basis for resistance to inhibitors. J Mol Biol 2009; 387:1002-16. [PMID: 19150359 DOI: 10.1016/j.jmb.2008.12.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 12/20/2008] [Accepted: 12/22/2008] [Indexed: 11/28/2022]
Abstract
Spontaneous mutations at numerous sites distant from the active site of human immunodeficiency virus type 1 protease enable resistance to inhibitors while retaining enzymatic activity. As a benchmark for probing the effects of these mutations on the conformational adaptability of this dimeric beta-barrel protein, the folding free-energy surface of a pseudo-wild-type variant, HIV-PR(*), was determined by a combination of equilibrium and kinetic experiments on the urea-induced unfolding/refolding reactions. The equilibrium unfolding reaction was well described by a two-state model involving only the native dimeric form and the unfolded monomer. The global analysis of the kinetic folding mechanism reveals the presence of a fully folded monomeric intermediate that associates to form the native dimeric structure. Independent analysis of a stable monomeric version of the protease demonstrated that a small-amplitude fluorescence phase in refolding and unfolding, not included in the global analysis of the dimeric protein, reflects the presence of a transient intermediate in the monomer folding reaction. The partially folded and fully folded monomers are only marginally stable with respect to the unfolded state, and the dimerization reaction provides a modest driving force at micromolar concentrations of protein. The thermodynamic properties of this system are such that mutations can readily shift the equilibrium from the dimeric native state towards weakly folded states that have a lower affinity for inhibitors but that could be induced to bind to their target proteolytic sites. Presumably, subsequent secondary mutations increase the stability of the native dimeric state in these variants and, thereby, optimize the catalytic properties of the resistant human immunodeficiency virus type 1 protease.
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Affiliation(s)
- Amanda F Noel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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21
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Heyda J, Pokorná J, Vrbka L, Vácha R, Jagoda-Cwiklik B, Konvalinka J, Jungwirth P, Vondrášek J. Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease. Phys Chem Chem Phys 2009; 11:7599-604. [DOI: 10.1039/b905462f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Bannwarth L, Rose T, Dufau L, Vanderesse R, Dumond J, Jamart-Grégoire B, Pannecouque C, De Clercq E, Reboud-Ravaux M. Dimer Disruption and Monomer Sequestration by Alkyl Tripeptides Are Successful Strategies for Inhibiting Wild-Type and Multidrug-Resistant Mutated HIV-1 Proteases. Biochemistry 2008; 48:379-87. [DOI: 10.1021/bi801422u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ludovic Bannwarth
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Thierry Rose
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Laure Dufau
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Régis Vanderesse
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Julien Dumond
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Brigitte Jamart-Grégoire
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Christophe Pannecouque
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Erik De Clercq
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Michèle Reboud-Ravaux
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Sinsuwan S, Rodtong S, Yongsawatdigul J. NaCl-activated extracellular proteinase from Virgibacillus sp. SK37 isolated from fish sauce fermentation. J Food Sci 2007; 72:C264-9. [PMID: 17995713 DOI: 10.1111/j.1750-3841.2007.00375.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Virgibacillus sp. SK37 exhibited high extracellular proteolytic activity in skim milk broth containing 10% NaCl. Optimum conditions of the crude proteinase were at pH 8.0 and 65 degrees C. The proteinase was strongly inhibited by phenylmethanesulfonyl fluoride (PMSF) and preferably hydrolyzed Suc-Ala-Ala-Pro-Phe-AMC, suggesting the serine proteinase with a subtilisin-like characteristic. Proteolytic activity increased with NaCl concentration up to 20%. Ca(2+) activated the enzyme activity but reduced enzyme stability at 65 degrees C. Several proteinases with dominant molecular mass (MW) of 81, 67, 63, 50, 38, and 18 kDa were detected on native-polyacrylamide gel electrophoresis (native-PAGE) activity staining in the absence and presence of 25% NaCl. These results demonstrated that Virgibacillus sp. SK37 produced salt-activated extracellular proteinases. Virgibacillus sp. SK37 could be a promising strain for starter culture development used in fish sauce fermentation.
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Affiliation(s)
- S Sinsuwan
- School of Food Technology, Suranaree Univ. of Technology, Nakhon Ratchasima 30000, Thailand
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Ishima R, Torchia DA, Louis JM. Mutational and Structural Studies Aimed at Characterizing the Monomer of HIV-1 Protease and Its Precursor. J Biol Chem 2007; 282:17190-9. [PMID: 17412697 DOI: 10.1074/jbc.m701304200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An experimental protocol for folding the mature human immunodeficiency virus-1 (HIV-1) protease is presented that facilitates NMR studies at a low protein concentration of approximately 20 micoM. Under these conditions, NMR spectra show that the mature protease lacking its terminal beta-sheet residues 1-4 and 96-99 (PR(5-95)) exhibits a stable monomer fold spanning the region 10-90 that is similar to that of the single subunit of the wild-type dimer and the dimer bearing a D25N mutation (PR(D25N)). Urea-induced unfolding monitored both by changes in (1)H-(15)N heteronuclear single quantum correlation spectra and by protein fluorescence indicates that although PR(5-95) monomer displays a transition profile similar to that of the PR(D25N) dimer (50% unfolded (U(50)) = approximately 1.9 M), extending the protease with 4 residues (SFNF) of its N-terminally flanking sequence in the Gag-Pol precursor ((SFNF)PR(D25N)) decreases the stability of the fold (U(50) = approximately 1.5 M). Assigned backbone chemical shifts were used to elucidate differences in the stability of the PR(T26A) (U(50) = 2.5 M) and (SFNF)PR(D25N) monomers and compared with PR(D25N/T26A) monomer. Discernible differences in the backbone chemical shifts were observed for N-terminal protease residues 3-6 of (SFNF)PR(D25N) that may relate to the increase in the equilibrium dissociation constant (K(d)) and the very low catalytic activity of the protease prior to its autoprocessing at its N terminus from the Gag-Pol precursor.
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Affiliation(s)
- Rieko Ishima
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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Louis JM, Ishima R, Torchia DA, Weber IT. HIV-1 protease: structure, dynamics, and inhibition. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2007; 55:261-98. [PMID: 17586318 DOI: 10.1016/s1054-3589(07)55008-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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26
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Kanibolotsky DS, Ivanova OS, Lisnyak VV. Comparison of NMR and MD N–H bond order parameters: example of HIV-1 protease. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020601078489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Raghuraman H, Ganguly S, Chattopadhyay A. Effect of ionic strength on the organization and dynamics of membrane-bound melittin. Biophys Chem 2006; 124:115-24. [PMID: 16831504 DOI: 10.1016/j.bpc.2006.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/19/2006] [Accepted: 06/20/2006] [Indexed: 11/25/2022]
Abstract
Melittin, a cationic hemolytic peptide, is intrinsically fluorescent due to the presence of a single functionally important tryptophan residue. We have previously shown that the sole tryptophan of melittin is localized in a motionally restricted environment in the membrane interface. We have monitored the effect of ionic strength on the organization and dynamics of membrane-bound melittin utilizing fluorescence and circular dichroism (CD) spectroscopic approaches. Our results show that red edge excitation shift (REES) of melittin bound to membranes is sensitive to the change in ionic strength of the medium. This could be attributed to a change in the immediate environment around melittin tryptophan with increasing ionic strength due to differential solvation of ions. Interestingly, the rotational mobility of melittin does not appear to be affected with change in ionic strength. In addition, fluorescence parameters such as lifetime and acrylamide quenching of melittin indicate an increase in water penetration in the membrane interface upon increasing ionic strength. Our results suggest that the solvent dynamics and water penetration in the interfacial region of the membranes are significantly affected at physiologically relevant ionic strength. These results assume significance in the overall context of the influence of ionic strength in the organization and dynamics of membrane proteins and membrane-active peptides.
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Affiliation(s)
- H Raghuraman
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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28
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Morimoto K, Furuta E, Hashimoto H, Inouye K. Effects of High Concentration of Salts on the Esterase Activity and Structure of a Kiwifruit Peptidase, Actinidain. ACTA ACUST UNITED AC 2006; 139:1065-71. [PMID: 16788057 DOI: 10.1093/jb/mvj106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Effects of salts on the activity and stability of actinidain were examined. With increasing salt concentration up to 0.5 M, the activity (kcat/Km) for N-alpha-Cbz-L-lysine p-nitrophenyl ester decreased to 40% of that in the absence of salt. The inhibitor constant Ki of LiCl, NaCl, and KCl was 0.16-0.43 M. With 3 M KCl and NaCl, the specificity constant kcat/Km recovered to 110 and 75%, respectively. No re-activation was observed with LiCl. The inhibition and re-activation were dependent on the changes in both Km and kcat, whereas no CD change was observed. The tryptophan fluorescence of actinidain was not affected by 0-0.5 M salt, but a considerable decrease in its intensity was observed with increasing salt concentration from 0.5 to 3.0 M. These results suggest that the inhibition observed with the lower salt concentration (<0.5 M) is due to attenuation of the electrostatic interaction between the enzyme and substrate, and the higher concentration (0.5-3.0 M) induces structural change in the states of tryptophan residues, which is associated with the re-activation. Actinidain keeps considerably high activity and stability even in the presence of 3 M salts.
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Affiliation(s)
- Koichi Morimoto
- Department of Biotechnological Science, Kinki University, Nishimitani, Kinokawa, Wakayama 649-6493
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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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Shuker SB, Mariani VL, Herger BE, Dennison KJ. Understanding HTLV-I protease. CHEMISTRY & BIOLOGY 2003; 10:373-80. [PMID: 12770819 DOI: 10.1016/s1074-5521(03)00104-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suzanne Beckham Shuker
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Oliveira V, Gatti R, Rioli V, Ferro ES, Spisni A, Camargo ACM, Juliano MA, Juliano L. Temperature and salts effects on the peptidase activities of the recombinant metallooligopeptidases neurolysin and thimet oligopeptidase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:4326-34. [PMID: 12199711 DOI: 10.1046/j.1432-1033.2002.03129.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the recombinant neurolysin and thimet oligopeptidase (TOP) hydrolytic activities towards internally quenched fluorescent peptides derived from the peptide Abz-GGFLRRXQ-EDDnp (Abz, ortho-aminobenzoicacid; EDDnp, N-(2,4-dinitrophenyl) ethylenediamine), in which X was substituted by 11 different natural amino acids. Neurolysin hydrolyzed these peptides at R-R or at R-X bonds, and TOP hydrolyzed at R-R or L-R bonds, showing a preference to cleave at three or four amino acids from the C-terminal end. The kinetic parameters of hydrolysis and the variations of the cleavage sites were evaluated under different conditions of temperature and salt concentration. The relative amount of cleavage varied with the nature of the substitution at the X position as well as with temperature and NaCl concentration. TOP was activated by all assayed salts in the range 0.05-0.2 m for NaCl, KCl, NH4Cl and NaI, and 0.025-0.1 m for Na2SO4. Concentration higher than 0.2 N NH4Cl and NaI reduced TOP activity, while 0.5 N or higher concentration of NaCl, KCl and Na2SO4 increased TOP activity. Neurolysin was strongly activated by NaCl, KCl and Na2SO4, while NH4Cl and NaI have very modest effect. High positive values of enthalpy (DeltaH*) and entropy (DeltaS*) of activation were found together with an unusual temperature dependence upon the hydrolysis of the substrates. The effects of low temperature and high NaCl concentration on the hydrolytic activities of neurolysin and TOP do not seem to be a consequence of large secondary structure variation of the proteins, as indicated by the far-UV CD spectra. However, the modulation of the activities of the two oligopeptidases could be related to variations of conformation, in limited regions of the peptidases, enough to modify their activities.
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Affiliation(s)
- Vitor Oliveira
- Department of Biophysics, Escola Paulista de Medicina, São Paulo, Brazil
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Fehér A, Weber IT, Bagossi P, Boross P, Mahalingam B, Louis JM, Copeland TD, Torshin IY, Harrison RW, Tözsér J. Effect of sequence polymorphism and drug resistance on two HIV-1 Gag processing sites. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:4114-20. [PMID: 12180988 DOI: 10.1046/j.1432-1033.2002.03105.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The HIV-1 proteinase (PR) has proved to be a good target for antiretroviral therapy of AIDS, and various PR inhibitors are now in clinical use. However, there is a rapid selection of viral variants bearing mutations in the proteinase that are resistant to clinical inhibitors. Drug resistance also involves mutations of the nucleocapsid/p1 and p1/p6 cleavage sites of Gag, both in vitro and in vivo. Cleavages at these sites have been shown to be rate limiting steps for polyprotein processing and viral maturation. Furthermore, these sites show significant sequence polymorphism, which also may have an impact on virion infectivity. We have studied the hydrolysis of oligopeptides representing these cleavage sites with representative mutations found as natural variations or that arise as resistant mutations. Wild-type and five drug resistant PRs with mutations within or outside the substrate binding site were tested. While the natural variations showed either increased or decreased susceptibility of peptides toward the proteinases, the resistant mutations always had a beneficial effect on catalytic efficiency. Comparison of the specificity changes obtained for the various substrates suggested that the maximization of the van der Waals contacts between substrate and PR is the major determinant of specificity: the same effect is crucial for inhibitor potency. The natural nucleocapsid/p1 and p1/p6 sites do not appear to be optimized for rapid hydrolysis. Hence, mutation of these rate limiting cleavage sites can partly compensate for the reduced catalytic activity of drug resistant mutant HIV-1 proteinases.
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Affiliation(s)
- Anita Fehér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
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33
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Dürrschmidt P, Mansfeld J, Ulbrich-Hofmann R. Differentiation between conformational and autoproteolytic stability of the neutral protease from Bacillus stearothermophilus containing an engineered disulfide bond. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:3612-8. [PMID: 11422393 DOI: 10.1046/j.1432-1327.2001.02270.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The introduction of a disulfide bond into the neutral protease from Bacillus stearothermophilus by the double mutation G8C/N60C had resulted in an extremely thermostable enzyme with a half-life of 35.9 min at 92.5 degrees C [Mansfeld, J., Vriend, G., Dijkstra, B.W., Veltman, O.R., van den Burg, B., Venema, G., Ulbrich-Hofmann, R. & Eijsink, V.G. (1997) J. Biol. Chem. 272, 11152-11156]. The study in guanidine hydrochloride of this enzyme and the respective wild-type enzyme allowed us to distinguish between the stability toward global unfolding and autoproteolysis. At low protease concentrations (20 microg.mL-1) and short periods of incubation with guanidine hydrochloride (5 min), transition curves without the interference by autoproteolysis could be derived from fluorescence emission measurements. The effect of the disulfide bond on the global unfolding of the protein proved to be smaller than expected. In contrast, the measurement of autoproteolysis at higher protein concentrations (100 microg.mL-1) by quantitative evaluation of the bands of intact protein on SDS/PAGE revealed a strong stabilization toward autoproteolytic degradation by the disulfide bond. The rate of autoproteolysis in guanidine hydrochloride was found to be much lower than that of thermal denaturation, which can be attributed to the inhibition of the proteases by this denaturant. The results suggest that the disulfide bond stabilizes the protease against autoproteolysis more than against global unfolding. Autoproteolysis starts as soon as the cleavage sites in flexible external structural regions become accessible. It is suggested that the stabilizing effect of the disulfide bond is caused by the fixation of the crucial loop region 56-69 or by hindrance of the primary cleavage in this region by the amino acid exchanges.
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Affiliation(s)
- P Dürrschmidt
- Martin-Luther University Halle-Wittenberg, Department of Biochemistry/Biotechnology, Halle/Saale, Federal Republic of Germany
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34
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Park MT, Lee MS, Choi JY, Kim SC, Lee GM. Orthophosphate anion enhances the stability and activity of endoxylanase from Bacillus sp. Biotechnol Bioeng 2001; 72:434-40. [PMID: 11180063 DOI: 10.1002/1097-0290(20000220)72:4<434::aid-bit1005>3.0.co;2-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Endoxylanase, for which the optimum temperature is 60 degrees C (optimum pH 7), is labile to heat. Because the isoelectric point (pI) value of this xylanase is 10.6, the net charge of this enzyme is positive at pH 7. Thus, ions are likely to influence its enzyme structure and the thermal stability of endoxylanase may improve. Among the various ions tested, orthophosphate anion (HPO(4)(2-)) was found to significantly improve not only the stability but the activity of xylanase. When K(2)HPO(4) concentration was increased from 50 mM to 1.2 M, the T(m )value of xylanase was increased from 60.0 degrees C to 74.5 degrees C. The affinity of xylanase on xylan also increased along with K(2)HPO(4) concentration. Thus, the xylanase activity at 0.6 M K(2)HPO(4) was 2.3-fold higher than that at 50 mM K(2)HPO(4), and 120.2-fold higher than that in 40 mM MOPS buffer. This enhanced activity in the presence of K(2)HPO(4 )probably takes place because the orthophosphate anion affects the binding and catalytic residues of endoxylanase.
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Affiliation(s)
- M T Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology 373-1, Kusong-Dong, Yusong-Gu, Taejon 305-701, Korea
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Ullrich B, Laberge M, Tölgyesi F, Szeltner Z, Polgár L, Fidy J. Trp42 rotamers report reduced flexibility when the inhibitor acetyl-pepstatin is bound to HIV-1 protease. Protein Sci 2000; 9:2232-45. [PMID: 11152134 PMCID: PMC2144495 DOI: 10.1110/ps.9.11.2232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Q7K/L331/L631 HIV-1 protease mutant was expressed in Escherichia coli and the effect of binding a substrate-analog inhibitor, acetyl-pepstatin, was investigated by fluorescence spectroscopy and molecular dynamics. The dimeric enzyme has four intrinsic tryptophans, located at positions 6 and 42 in each monomer. Fluorescence spectra and acrylamide quenching experiments show two differently accessible Trp populations in the apoenzyme with k(q1) = 6.85 x 10(9) M(-1) s(-1) and k(q2) = 1.88 x 10(9) M(-1) s(-1), that merge into one in the complex with k(q) = 1.78 x 10(9) M(-1) s(-1). 500 ps trajectory analysis of Trp X1/X2 rotameric interconversions suggest a model to account for the observed Trp fluorescence. In the simulations, Trp6/Trp6B rotameric interconversions do not occur on this timescale for both HIV forms. In the apoenzyme simulations, however, both Trp42s and Trp42Bs are flipping between X1/X2 states; in the complexed form, no such interconverions occur. A detailed investigation of the local Trp environments sampled during the molecular dynamics simulation suggests that one of the apoenzyme Trp42B rotameric interconversions would allow indole-quencher contact, such as with nearby Tyr59. This could account for the short lifetime component. The model thus interprets the experimental data on the basis of the conformational fluctuations of Trp42s alone. It suggests that the rotameric interconversions of these Trps, located relatively far from the active site and at the very start of the flap region, becomes restrained when the apoenzyme binds the inhibitor. The model is thus consistent with associating components of the fluorescence decay in HIV-1 protease to ground state conformational heterogeneity.
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Affiliation(s)
- B Ullrich
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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36
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Strisovsky K, Tessmer U, Langner J, Konvalinka J, Kräusslich HG. Systematic mutational analysis of the active-site threonine of HIV-1 proteinase: rethinking the "fireman's grip" hypothesis. Protein Sci 2000; 9:1631-41. [PMID: 11045610 PMCID: PMC2144712 DOI: 10.1110/ps.9.9.1631] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Aspartic proteinases share a conserved network of hydrogen bonds (termed "fireman's grip"), which involves the hydroxyl groups of two threonine residues in the active site Asp-Thr-Gly triplets (Thr26 in the case of human immunodeficiency virus type 1 (HIV-1) PR). In the case of retroviral proteinases (PRs), which are active as symmetrical homodimers, these interactions occur at the dimer interface. For a systematic analysis of the "fireman's grip," Thr26 of HIV-1 PR was changed to either Ser, Cys, or Ala. The variant enzymes were tested for cleavage of HIV-1 derived peptide and polyprotein substrates. PR(T26S) and PR(T26C) showed similar or slightly reduced activity compared to wild-type HIV-1 PR, indicating that the sulfhydryl group of cysteine can substitute for the hydroxyl of the conserved threonine in this position. PR(T26A), which lacks the "fireman's grip" interaction, was virtually inactive and was monomeric in solution at conditions where wild-type PR exhibited a monomer-dimer equilibrium. All three mutations had little effect when introduced into only one chain of a linked dimer of HIV-1 PR. In this case, even changing both Thr residues to Ala yielded residual activity suggesting that the "fireman's grip" is not essential for activity but contributes significantly to dimer formation. Taken together, these results indicate that the "fireman's grip" is crucial for stabilization of the retroviral PR dimer and for overall stability of the enzyme.
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Affiliation(s)
- K Strisovsky
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Praha, Czech Republic
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Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 1999; 7:1047-55. [PMID: 10508781 DOI: 10.1016/s0969-2126(99)80172-5] [Citation(s) in RCA: 225] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND (1)H and (15)N transverse relaxation measurements on perdeuterated proteins are ideally suited for detecting backbone conformational fluctuations on the millisecond-microsecond timescale. The identification of conformational exchange on this timescale by measuring the relaxation of both (1)H and (15)N holds great promise for the elucidation of functionally relevant conformational changes in proteins. RESULTS We measured the transverse (1)H and (15)N relaxation rates of backbone amides of HIV-1 protease in its free and inhibitor-bound forms. An analysis of these rates, obtained as a function of the effective rotating frame field, provided information about the timescale of structural fluctuations in several regions of the protein. The flaps that cover the active site of the inhibitor-bound protein undergo significant changes of backbone (φ,psi) angles, on the 100 micros timescale, in the free protein. In addition, the intermonomer beta-sheet interface of the bound form, which from protease structure studies appears to be rigid, was found to fluctuate on the millisecond timescale. CONCLUSIONS We present a working model of the flap-opening mechanism in free HIV-1 protease which involves a transition from a semi-open to an open conformation that is facilitated by interaction of the Phe53 ring with the substrate. We also identify a surprising fluctuation of the beta-sheet intermonomer interface that suggests a structural requirement for maturation of the protease. Thus, slow conformational fluctuations identified by (1)H and (15)N transverse relaxation measurements can be related to the biological functions of proteins.
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Affiliation(s)
- R Ishima
- Molecular Structural Biology Unit National Institute of Dental and Craniofacial Research National Institutes of Health Bethesda, MD 20892, USA
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38
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Abstract
The most common strategy in the development of HIV-1 protease inhibitors has been the design of high affinity transition state analogs that effectively compete with natural substrates for the active site. A second approach has been the development of compounds that inactivate the protease by destabilizing its quaternary or tertiary structure. A successful optimization of these strategies requires an accurate knowledge of the energetics of structural stabilization and binding, and the identification of those regions in the protease molecule that are critical to stability and function. Here the energetics of stabilization of the HIV-1 protease has been measured for the first time by high sensitivity differential scanning calorimetry. These studies have permitted the evaluation of the different components of the Gibbs energy of stabilization (the enthalpy, entropy and heat capacity changes). The stability of the protease is pH-dependent and due to its dimeric nature is also concentration-dependent. At pH 3.4 the Gibbs energy of stabilization is close to 10 kcal/mol at 25 degreesC, consistent with a dissociation constant of 5x10(-8) M. The stability of the protease increases at higher pH values. At pH 5, the Gibbs energy of stabilization is 14.5 kcal/mol at 25 degreesC, consistent with a dissociation constant of 2.3x10(-11) M. The pH dependence of the Gibbs energy of stabilization indicates that between pH 3.4 and pH 5 an average of 3-4 ionizable groups per dimer become protonated upon unfolding. A structure-based thermodynamic analysis of the protease molecule indicates that most of the Gibbs energy of stabilization is provided by the dimerization interface and that the isolated subunits are intrinsically unstable. The Gibbs energy, however, is not uniformly distributed along the dimerization interface. The dimer interface is characterized by the presence of clusters of residues (hot spots) that contribute significantly and other regions that contribute very little to subunit association. At the dimerization interface, residues located at the carboxy and amino termini contribute close to 75% of the total Gibbs energy (Cys95, Thr96, Leu97, Asn98 and Phe99 and Pro1, Ile3, Leu5). Residues Thr26, Gly27 and Asp29 located at the base of the active site are also important, and to a lesser extent Gly49, Ile50, Gly51 located at the tip of the flap region. The structure-based thermodynamic analysis also predicts the existence of regions of the protease with only marginal stability and a high propensity to undergo independent local unfolding. In particular, the flap region occupies a very shallow energy minimum and its conformation can easily be affected by relatively small perturbations. This property of the protease can be related to the ability of some mutations to elicit resistance towards certain inhibitors.
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Affiliation(s)
- M J Todd
- Department of Biology and Biocalorimetry Center, The Johns Hopkins University, Baltimore, MD, 21218, USA
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Inouye K, Kuzuya K, Tonomura B. Sodium chloride enhances markedly the thermal stability of thermolysin as well as its catalytic activity. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1388:209-14. [PMID: 9774734 DOI: 10.1016/s0167-4838(98)00189-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermolysin, a thermophilic metalloproteinase, is markedly activated in the presence of high concentrations (1-5 M) of neutral salts. The activity increases in an exponential fashion with increasing salt concentration, and is enhanced 13-15 times with 4 M NaCl at pH 7.0 and 25 degreesC (K. Inouye, Effects of salts on thermolysin: activation of hydrolysis and synthesis of N-carbobenzoxy-l-aspartyl-l-phenylalanine methyl ester, and a unique change in the absorption spectrum of thermolysin, J. Biochem. 112 (1992) 335-340). In this study, the effect of NaCl on the thermal stability of thermolysin has been examined at 60-85 degreesC. The activation energy, Ea, for the thermal inactivation is 15 kcal/mol at 0 M NaCl, and increases up to 30-33 kcal/mol by the addition of 0. 5-1.5 M NaCl. Further increase in [NaCl] decreases the Ea value, and at 4 M NaCl it is almost the same as that at 0 M NaCl. Thermolysin at 0.5-1.5 M NaCl is twice as heat-stable as in the absence of NaCl. The NaCl dependence of the stability is different from that of the activity, suggesting that the effects of NaCl on activity and stability are independent. Thermolysin has been demonstrated to be not only a thermophilic enzyme but also a highly halophilic one.
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Affiliation(s)
- K Inouye
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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40
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Lescar J, Stouracova R, Riottot MM, Chitarra V, Brynda J, Fabry M, Horejsi M, Sedlacek J, Bentley GA. Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody. J Mol Biol 1997; 267:1207-22. [PMID: 9150407 DOI: 10.1006/jmbi.1997.0950] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
F11.2.32, a monoclonal antibody raised against HIV-1 protease (Kd = 5 nM), which inhibits proteolytic activity of the enzyme (K(inh) = 35(+/-3)nM), has been studied by crystallographic methods. The three-dimensional structure of the complex between the Fab fragment and a synthetic peptide, spanning residues 36 to 46 of the protease, has been determined at 2.2 A resolution, and that of the Fab in the free state has been determined at 2.6 A resolution. The refined model of the complex reveals ten well-ordered residues of the peptide (P36 to P45) bound in a hydrophobic cavity at the centre of the antigen-binding site. The peptide adopts a beta hairpin-like structure in which residues P38 to P42 form a type II beta-turn conformation. An intermolecular antiparallel beta-sheet is formed between the peptide and the CDR3-H loop of the antibody; additional polar interactions occur between main-chain atoms of the peptide and hydroxyl groups from tyrosine residues protruding from CDR1-L and CDR3-H. Three water molecules, located at the antigen-antibody interface, mediate polar interactions between the peptide and the most buried hypervariable loops, CDR3-L and CDR1-H. A comparison between the free and complexed Fab fragments shows that significant conformational changes occur in the long hypervariable regions, CDR1-L and CDR3-H, upon binding the peptide. The conformation of the bound peptide, which shows no overall structural similarity to the corresponding segment in HIV-1 protease, suggests that F11.2.32 might inhibit proteolysis by distorting the native structure of the enzyme.
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Affiliation(s)
- J Lescar
- Unité d'Immunologie Structurale (URA 1961 CNRS), Département d'Immunologie, Institut Pasteur, Paris, France
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Szeltner Z, Polgár L. Rate-determining steps in HIV-1 protease catalysis. The hydrolysis of the most specific substrate. J Biol Chem 1996; 271:32180-4. [PMID: 8943273 DOI: 10.1074/jbc.271.50.32180] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The human immunodeficiency virus type-1 (HIV-1) encodes a protease which is essential for the production of infectious virus. The protease prefers substrates that contain glutamic acid or glutamine at the P2' position. The catalytic role of these residues has been studied by using a highly specific fluorogen substrate, 2-aminobenzoyl-Thr-Ile-Nle-Phe(NO2)-Gln-Arg (substrate QR), and its counterpart (substrate ER) containing Glu in place of Gln. The newly designed substrate ER that contains a pair of charged residues at P2' and P3' sites is the most specific substrate described so far for HIV-1 protease. The specificity rate constant (kcat/Km = 2.1 x 10(7) M-1 s-1) approaches, but does not reach, the diffusion limit. This follows from the appreciable solvent kinetic deuterium isotope effects on the rate constants, indicating that, independent of the salt concentration, the rate-limiting step of the catalysis is a chemical process rather than a physical one. The reaction also has positive entropy of activation. On the other hand, the rate-limiting step for substrate QR changes with increasing salt concentration from a physical to chemical step, while the negative activation entropy becomes positive. The rate increase with substrate ER is 50-fold with respect to substrate QR in the presence of 0.1 M NaCl and diminishes to 3.5-fold at 2.0 M NaCl concentration, as a consequence of a considerable rate increase at high salt concentration with substrate QR but not with substrate ER. The Km value is much lower for the substrate ER (0.8 microM) than for substrate QR (15 microM), indicating a more effective binding for substrate ER at 0.1 M NaCl. Unexpectedly, the strong binding appears to be achieved by the unionized form of Glu in P2', as follows from the remarkably different pH-rate profiles for substrates QR and ER. The effective binding elicited by the glutamic acid may be utilized in designing inhibitors for therapeutic purposes.
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Affiliation(s)
- Z Szeltner
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest H-1518, Hungary
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