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Chopra A, Bauman JD, Ruiz FX, Arnold E. Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. J Med Chem 2023; 66:6013-6024. [PMID: 37115705 PMCID: PMC10184123 DOI: 10.1021/acs.jmedchem.2c01681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
X-ray crystallographic fragment screening (XCFS) uses fragment-sized molecules (∼60 to 300 Da) to access binding sites on proteins that may be inaccessible to larger drug-like molecules (>300 Da). Previous studies have shown that fragments containing halogen atoms bind more often to proteins than non-halogenated fragments. Here, we designed the Halo Library containing 46 halogenated fragments (including the "universal fragment" 4-bromopyrazole), a majority of which have been reported to bind to or inhibit one or more targets. The library was screened against the crystals of HIV-1 reverse transcriptase with the drug rilpivirine, yielding an overall hit rate of 26%. Two new binding sites were discovered, and several hot spots were identified. This small library may thus provide a convenient tool for rapidly assessing the feasibility of a target for XCFS, mapping hot spots and cryptic sites, as well as finding fragment binders that can be useful for developing drug leads.
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Affiliation(s)
- Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Joseph D Bauman
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Francesc X Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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Martín-Alonso S, Kang D, Martínez Del Río J, Luczkowiak J, Frutos-Beltrán E, Zhang L, Cheng X, Liu X, Zhan P, Menéndez-Arias L. Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase. J Mol Biol 2022; 434:167507. [PMID: 35217069 DOI: 10.1016/j.jmb.2022.167507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
In retroviruses, strand displacement DNA-dependent DNA polymerization catalyzed by the viral reverse transcriptase (RT) is required to synthesize double-stranded proviral DNA. In addition, strand displacement during RNA-dependent DNA synthesis is critical to generate high-quality cDNA for use in molecular biology and biotechnology. In this work, we show that the loss of RNase H activity due to inactivating mutations in HIV-1 RT (e.g. D443N or E478Q) has no significant effect on strand displacement while copying DNA templates, but has a large impact on DNA polymerization in reactions carried out with RNA templates. Similar effects were observed with β-thujaplicinol and other RNase H active site inhibitors, including compounds with dual activity (i.e., characterized also as inhibitors of HIV-1 integrase and/or the RT DNA polymerase). Among them, dual inhibitors of HIV-1 RT DNA polymerase/RNase H activities, containing a 7-hydroxy-6-nitro-2H-chromen-2-one pharmacophore were found to be very potent and effective strand displacement inhibitors in RNA-dependent DNA polymerization reactions. These findings might be helpful in the development of transcriptomics technologies to obtain more uniform read coverages when copying long RNAs and for the construction of more representative libraries avoiding biases towards 5' and 3' ends, while providing valuable information for the development of novel antiretroviral agents.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Javier Martínez Del Río
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Joanna Luczkowiak
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Lina Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Xiqiang Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China.
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain.
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Martín-Alonso S, Álvarez M, Nevot M, Martínez MÁ, Menéndez-Arias L. Defective Strand-Displacement DNA Synthesis Due to Accumulation of Thymidine Analogue Resistance Mutations in HIV-2 Reverse Transcriptase. ACS Infect Dis 2020; 6:1140-1153. [PMID: 32129987 DOI: 10.1021/acsinfecdis.9b00512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Retroviral reverse transcriptases (RTs) have the ability to carry out strand displacement DNA synthesis in the absence of accessory proteins. Although studies with RTs and other DNA polymerases suggest that fingers subdomain residues participate in strand displacement, molecular determinants of this activity are still unknown. A mutant human immunodeficiency virus type 2 (HIV-2) RT (M41L/D67N/K70R/S215Y) with low strand displacement activity was identified after screening a panel of purified enzymes, including several antiretroviral drug-resistant HIV-1 and HIV-2 RTs. In HIV-1, resistance to zidovudine and other thymidine analogues is conferred by different combinations of M41L, D67N, K70R, L210W, T215F/Y, and K219E/Q (designated as thymidine analogue resistance-associated mutations (TAMs)). However, those changes are rarely selected in HIV-2. We show that the strand displacement activity of HIV-2ROD mutants M41L/S215Y and D67N/K70R was only slightly reduced compared to the wild-type RT. In contrast, mutants D67N/K70R/S215Y and M41L/D67N/K70R/S215Y were the most defective RTs in reactions carried out with nicked and gapped substrates. Moreover, these enzymes showed the lowest nucleotide incorporation rates in assays carried out with strand displacement substrates. Unlike in HIV-2, substitutions M41L/T215Y and D67N/K70R/T215Y/K219Q had no effect on the strand displacement activity of HIV-1BH10 RT. The strand displacement efficiencies of HIV-2ROD RTs were consistent with the lower replication capacity of HIV-2 strains bearing the four major TAMs in their RT. Our results highlight the role of the fingers subdomain in strand displacement. These findings might be important for the development of strand-displacement defective RTs.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biologı́a Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Cientı́ficas and Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Mar Álvarez
- Centro de Biologı́a Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Cientı́ficas and Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - María Nevot
- Laboratori de Retrovirologia, Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, 08916 Barcelona, Spain
| | - Miguel Á. Martínez
- Laboratori de Retrovirologia, Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, 08916 Barcelona, Spain
| | - Luis Menéndez-Arias
- Centro de Biologı́a Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Cientı́ficas and Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
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Luczkowiak J, Matamoros T, Menéndez-Arias L. Template-primer binding affinity and RNase H cleavage specificity contribute to the strand transfer efficiency of HIV-1 reverse transcriptase. J Biol Chem 2018; 293:13351-13363. [PMID: 29991591 DOI: 10.1074/jbc.ra118.004324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/29/2018] [Indexed: 01/31/2023] Open
Abstract
During reverse transcription of the HIV-1 genome, two strand-transfer events occur. Both events rely on the RNase H cleavage activity of reverse transcriptases (RTs) and template homology. Using a panel of mutants of HIV-1BH10 (group M/subtype B) and HIV-1ESP49 (group O) RTs and in vitro assays, we demonstrate that there is a strong correlation between RT minus-strand transfer efficiency and template-primer binding affinity. The highest strand transfer efficiencies were obtained with HIV-1ESP49 RT mutants containing the substitutions K358R/A359G/S360A, alone or in combination with V148I or T355A/Q357M. These HIV-1ESP49 RT mutants had been previously engineered to increase their DNA polymerase activity at high temperatures. Now, we found that RTs containing RNase H-inactivating mutations (D443N or E478Q) were devoid of strand transfer activity, whereas enzymes containing F61A or L92P had very low strand transfer activity. The strand transfer defect produced by L92P was attributed to a loss of template-primer binding affinity and, more specifically, to the higher dissociation rate constants (koff) shown by RTs bearing this substitution. Although L92P also deleteriously affected the RT's nontemplated nucleotide addition activity, neither nontemplated nucleotide addition activity nor the RT's clamp activities contributed to increased template switching when all tested mutant and WT RTs were considered. Interestingly, our results also revealed an association between efficient strand transfer and the generation of secondary cleavages in the donor RNA, consistent with the creation of invasion sites. Exposure of the elongated DNA at these sites facilitate acceptor (RNA or DNA) binding and promote template switching.
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Affiliation(s)
- Joanna Luczkowiak
- From the Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Tania Matamoros
- From the Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Luis Menéndez-Arias
- From the Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain
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Li C, Wu A, Peng Y, Wang J, Guo Y, Chen Z, Zhang H, Wang Y, Dong J, Wang L, Qin FXF, Cheng G, Deng T, Jiang T. Integrating computational modeling and functional assays to decipher the structure-function relationship of influenza virus PB1 protein. Sci Rep 2014; 4:7192. [PMID: 25424584 PMCID: PMC4244630 DOI: 10.1038/srep07192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/03/2014] [Indexed: 11/12/2022] Open
Abstract
The influenza virus PB1 protein is the core subunit of the heterotrimeric polymerase complex (PA, PB1 and PB2) in which PB1 is responsible for catalyzing RNA polymerization and binding to the viral RNA promoter. Among the three subunits, PB1 is the least known subunit so far in terms of its structural information. In this work, by integrating template-based structural modeling approach with all known sequence and functional information about the PB1 protein, we constructed a modeled structure of PB1. Based on this model, we performed mutagenesis analysis for the key residues that constitute the RNA template binding and catalytic (TBC) channel in an RNP reconstitution system. The results correlated well with the model and further identified new residues of PB1 that are critical for RNA synthesis. Moreover, we derived 5 peptides from the sequence of PB1 that form the TBC channel and 4 of them can inhibit the viral RNA polymerase activity. Interestingly, we found that one of them named PB1(491–515) can inhibit influenza virus replication by disrupting viral RNA promoter binding activity of polymerase. Therefore, this study has not only deepened our understanding of structure-function relationship of PB1, but also promoted the development of novel therapeutics against influenza virus.
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Affiliation(s)
- Chunfeng Li
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China
| | - Aiping Wu
- 1] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [2] Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Yousong Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha. 410082, China
| | - Jingfeng Wang
- Suzhou Institute of Systems Medicine, Suzhou. 215123, China
| | - Yang Guo
- MOH Key Laboratory of Systems Biology of Pahogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100730, China
| | - Zhigao Chen
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China
| | - Hong Zhang
- Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Yongqiang Wang
- Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Jiuhong Dong
- Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Lulan Wang
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China
| | - F Xiao-Feng Qin
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China
| | - Genhong Cheng
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [3] Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Tao Deng
- MOH Key Laboratory of Systems Biology of Pahogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100730, China
| | - Taijiao Jiang
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [3] Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
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Matamoros T, Barrioluengo V, Abia D, Menéndez-Arias L. Major groove binding track residues of the connection subdomain of human immunodeficiency virus type 1 reverse transcriptase enhance cDNA synthesis at high temperatures. Biochemistry 2013; 52:9318-28. [PMID: 24303887 DOI: 10.1021/bi401390x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
At high temperatures, RNA denaturation can improve the efficiency and specificity of reverse transcription. Refined structures and molecular models of HIV-1 reverse transcriptases (RTs) from phylogenetically distant clades (i.e., group M subtype B and group O) revealed a major interaction between the template-primer and the Arg³⁵⁸-Gly³⁵⁹-Ala³⁶⁰ triad in the large subunit of HIV-1M/B RT. However, fewer contacts were predicted for the equivalent Lys³⁵⁸-Ala³⁵⁹-Ser³⁶⁰ triad of HIV-1O RT and the nucleic acid. An engineered HIV-1O K358R/A359G/S360A RT showed increased cDNA synthesis efficiency above 68 °C, as determined by qualitative and quantitative reverse transcription polymerase chain reactions. In comparison with wild-type HIV-1O RT, the mutant enzyme showed higher thermal stability but retained wild-type RNase H activity. Mutations that increased the accuracy of HIV-1M/B RTs were tested in combination with the K358R/A359G/S360A triple mutation. Some of them (e.g., F61A, K65R, K65R/V75I, and V148I) had a negative effect on reverse transcription efficiency above 65 °C. RTs with improved DNA binding affinities also showed higher cDNA synthesis efficiencies at elevated temperatures. Two of the most thermostable RTs (i.e., mutants T69SSG/K358R/A359G/S360A and K358R/A359G/S360A/E478Q) showed moderately increased fidelity in forward mutation assays. Our results demonstrate that the triad of Arg³⁵⁸, Gly³⁵⁹, and Ala³⁶⁰ in the major groove binding track of HIV-1 RT is a major target for RT stabilization, and most relevant for improving reverse transcription efficiency at high temperatures.
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Affiliation(s)
- Tania Matamoros
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid , 28049 Madrid, Spain
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Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SFJ, Nowotny M. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 2013; 41:3874-87. [PMID: 23382176 PMCID: PMC3616737 DOI: 10.1093/nar/gkt053] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
A key step in proliferation of retroviruses is the conversion of their RNA genome to double-stranded DNA, a process catalysed by multifunctional reverse transcriptases (RTs). Dimeric and monomeric RTs have been described, the latter exemplified by the enzyme of Moloney murine leukaemia virus. However, structural information is lacking that describes the substrate binding mechanism for a monomeric RT. We report here the first crystal structure of a complex between an RNA/DNA hybrid substrate and polymerase-connection fragment of the single-subunit RT from xenotropic murine leukaemia virus-related virus, a close relative of Moloney murine leukaemia virus. A comparison with p66/p51 human immunodeficiency virus-1 RT shows that substrate binding around the polymerase active site is conserved but differs in the thumb and connection subdomains. Small-angle X-ray scattering was used to model full-length xenotropic murine leukaemia virus-related virus RT, demonstrating that its mobile RNase H domain becomes ordered in the presence of a substrate-a key difference between monomeric and dimeric RTs.
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Affiliation(s)
- Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Wojciech Potrzebowski
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Petr V. Konarev
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Jason W. Rausch
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marion K. Bona
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Dmitri I. Svergun
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Janusz M. Bujnicki
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Stuart F. J. Le Grice
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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Deshayes S, Divita G. Fluorescence technologies for monitoring interactions between biological molecules in vitro. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:109-43. [PMID: 23244790 DOI: 10.1016/b978-0-12-386932-6.00004-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last two centuries, the discovery and understanding of the principle of fluorescence have provided new means of characterizing physical/biological/chemical processes in a noninvasive manner. Fluorescence spectroscopy has become one of the most powerful and widely applied methods in the life sciences, from fundamental research to clinical applications. In vitro, fluorescence approaches offer the potential to sense in real-time extra and intracellular molecular interactions and enzymatic reactions, which constitutes a major advantage over other approaches to the study of biomolecular interactions. This technology has been used for the characterization of protein/protein, protein/nucleic acid, protein/substrate, and biomembrane/biomolecule interactions, which play crucial roles in the regulation of cellular pathways. This chapter reviews the different fluorescence strategies that have been developed for sensing molecular interactions in vitro at both steady- and pre-steady-state levels.
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Affiliation(s)
- Sebastien Deshayes
- Centre de Recherches de Biochimie Macromoléculaire, Department of Chemical Biology and Nanotechnology for Therapeutics, CRBM-CNRS, UMR-5237, UM1-UM2, University of Montpellier, 1919 Route de Mende, Montpellier, France
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Xie J, Zhang P, Li C, Huang Q, Zhou R, Peng T. Mechanistic insights into the roles of three linked single-stranded template binding residues of MMLV reverse transcriptase in misincorporation and mispair extension fidelity of DNA synthesis. Gene 2011; 479:47-56. [DOI: 10.1016/j.gene.2011.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 02/07/2011] [Accepted: 02/13/2011] [Indexed: 11/25/2022]
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Thermostable HIV-1 group O reverse transcriptase variants with the same fidelity as murine leukaemia virus reverse transcriptase. Biochem J 2011; 436:599-607. [DOI: 10.1042/bj20101852] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Wild-type HIV-1 group O RT (reverse transcriptase) shows increased thermostability in comparison with HIV-1 group M subtype B RT and MLV (murine leukaemia virus) RT. However, its utility in the amplification of RNA targets is limited by the reduced accuracy of lentiviral RTs compared with oncoretroviral RTs (i.e. MLV RT). The effects of the mutations K65R, R78A and K65R/V75I on the fidelity of HIV-1 group O RTs were studied using gel-based and M13mp2 lacZ forward-mutation fidelity assays. Forward-mutation assays demonstrated that mutant RTs K65R, R78A and K65R/V75I showed >9-fold increased accuracy in comparison with the wild-type enzyme and were approximately two times more faithful than the MLV RT. Compared with MLV RT, all of the tested HIV-1 group O RT variants showed decreased frameshift fidelity. However, K65R RT showed a higher tendency to introduce one-nucleotide deletions in comparison with other HIV-1 group O RT variants. R78A had a destabilizing effect on the RT, either in the presence or absence of V75I. At temperatures above 52 °C, K65R and K65R/V75I retained similar levels of DNA polymerase activity to the wild-type HIV-1 group O RT, but were more efficient than HIV-1 group M subtype B and MLV RTs. K65R, K65R/V75I and R78A RTs showed decreased misinsertion and mispair extension fidelity in comparison with the wild-type enzyme for most base pairs studied. These assays revealed that nucleotide selection is mainly governed by kpol (pol is polymerization) in the case of K65R, whereas both kpol and Kd affect nucleotide discrimination in the case of K65R/V75I.
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Garforth SJ, Domaoal RA, Lwatula C, Landau MJ, Meyer AJ, Anderson KS, Prasad VR. K65R and K65A substitutions in HIV-1 reverse transcriptase enhance polymerase fidelity by decreasing both dNTP misinsertion and mispaired primer extension efficiencies. J Mol Biol 2010; 401:33-44. [PMID: 20538005 DOI: 10.1016/j.jmb.2010.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 05/27/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022]
Abstract
Lys65 residue, in the fingers domain of human immunodeficiency virus reverse transcriptase (RT), interacts with incoming dNTP in a sequence-independent fashion. We showed previously that a 5-amino-acid deletion spanning Lys65 and a K65A substitution both enhanced the fidelity of dNTP insertion. We hypothesized that the Lys65 residue enhances dNTP misinsertion via interactions with the gamma-phosphate of the incoming dNTP. We now examine this hypothesis in pre-steady-state kinetic studies using wild-type human immunodeficiency virus-1 RT and two substitution mutants, K65A and K65R. K65R mutation did not greatly increase misinsertion fidelity, but K65A mutation led to higher incorporation fidelity. For a misinsertion to become a permanent error, it needs to be accompanied by the extension of the mispaired terminus thus formed. Both mutants and the wild-type enzyme discriminated against the mismatched primer at the catalytic step (k(pol)). Additionally, K65A and K65R mutants displayed a further decrease in mismatch extension efficiency, primarily at the level of dNTP binding. We employed hydroxyl radical footprinting to determine the position of the RT on the primer/template. The wild-type and Lys65-substituted enzymes occupied the same position at the primer terminus; the presence of a mismatched primer terminus caused all three enzymes to be displaced to a -2 position relative to the primer 3' end. In the context of an efficiently extended mismatched terminus, the presence of the next complementary nucleotide overcame the displacement, resulting in a complex resembling the matched terminus. The results are consistent with the observed reduction in k(pol) in mispaired primer extension being due to the position of the enzyme at a mismatched terminus. Our work shows the influence of the stabilizing interactions of Lys65 with the incoming dNTP on two different aspects of polymerase fidelity.
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Affiliation(s)
- Scott J Garforth
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Menéndez-Arias L. Mutation rates and intrinsic fidelity of retroviral reverse transcriptases. Viruses 2009; 1:1137-65. [PMID: 21994586 PMCID: PMC3185545 DOI: 10.3390/v1031137] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 12/03/2009] [Accepted: 12/03/2009] [Indexed: 11/27/2022] Open
Abstract
Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that affect the accuracy of the viral polymerase have been identified by in vitro analysis of the fidelity of DNA synthesis, by using enzymological (gel-based) and genetic assays (e.g., M13mp2 lacZ forward mutation assays). For several amino acid substitutions, these observations have been confirmed in cell culture using viral vectors. This review provides an update on studies leading to the identification of the major components of the fidelity center in retroviral RTs.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" [Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid], Campus de Cantoblanco, 28049 Madrid, Spain; E-Mail: ; Tel.: +34 91 196 4494
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Upadhyay AK, Talele TT, Pandey VN. Impact of template overhang-binding region of HIV-1 RT on the binding and orientation of the duplex region of the template-primer. Mol Cell Biochem 2009; 338:19-33. [PMID: 19921401 DOI: 10.1007/s11010-009-0316-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 10/29/2009] [Indexed: 11/26/2022]
Abstract
Fingers domain of HIV-1 RT is one of the constituents of the dNTP-binding pocket that is involved in binding of both dNTP and the template-primer. In the ternary complex of HIV-1 RT, two residues Trp-24 and Phe-61 located on the beta1 and beta3, respectively, are seen interacting with N + 1 to N + 3 nucleotides in the template overhang. We generated nonconservative and conservative mutant derivatives of these residues and examined their impact on the template-primer binding and polymerase function of the enzyme. We noted that W24A, F61A, and F61Y and the double mutant (W24A/F61A) were significantly affected in their ability to bind template-primer and also to catalyze the polymerase reaction while W24F remained unaffected. Using a specially designed template-primer with photoactivatable bromo-dU base in the duplex region at the penultimate position to the primer terminus, we demonstrated that F61A, W24A, F61Y as well as the double mutant were also affected in their cross-linking ability with the duplex region of the template-primer. We also isolated the E-TP covalent complexes of these mutants and examined their ability to catalyze single dNTP incorporation onto the immobilized primer terminus. The E-TP covalent complexes from W24F mutant displayed wild-type activity while those from W24A, F61A, F61Y, and the double mutant (W24A/F61A) were significantly impaired in their ability to catalyze dNTP incorporation onto the immobilized primer terminus. This unusual observation indicated that amino acid residues involved in the positioning of the template overhang may also influence the binding and orientation of the duplex region of the template-primer. Molecular modeling studies based on our biochemical results suggested that conformation of both W24 and F61 are interdependent on their interactions with each other, which together are required for proper positioning of the +1 template nucleotide in the binary and ternary complexes.
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Affiliation(s)
- Alok K Upadhyay
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA
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Rutvisuttinunt W, Meyer PR, Scott WA. Interactions between HIV-1 reverse transcriptase and the downstream template strand in stable complexes with primer-template. PLoS One 2008; 3:e3561. [PMID: 18974785 PMCID: PMC2570493 DOI: 10.1371/journal.pone.0003561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 10/09/2008] [Indexed: 11/18/2022] Open
Abstract
Background Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP•RT•P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet•RT•P/T complex). Methods and Results UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP•RT•P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJF. UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet•RT•P/T complex (i.e., in the pre-translocation position). Conclusions For +1 dNTP•RT•P/T and foscarnet•RT•P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Peter R. Meyer
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Walter A. Scott
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- * E-mail:
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Agopian A, Gros E, Aldrian-Herrada G, Bosquet N, Clayette P, Divita G. A new generation of peptide-based inhibitors targeting HIV-1 reverse transcriptase conformational flexibility. J Biol Chem 2008; 284:254-264. [PMID: 18952602 DOI: 10.1074/jbc.m802199200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biologically active form of human immunodeficiency virus (HIV) type 1 reverse transcriptase (RT) is a heterodimer. The formation of RT is a two-step mechanism, including a rapid protein-protein interaction "the dimerization step," followed by conformational changes "the maturation step," yielding the biologically active form of the enzyme. We have previously proposed that the heterodimeric organization of RT constitutes an interesting target for the design of new inhibitors. Here, we propose a new class of RT inhibitors that targets protein-protein interactions and conformational changes involved in the maturation of heterodimeric reverse transcriptase. Based on a screen of peptides derived from the thumb domain of this enzyme, we have identified a short peptide P(AW) that inhibits the maturation step and blocks viral replication at subnanomolar concentrations. P(AW) only binds dimeric RT and stabilizes it in an inactive/non-processive conformation. From a mechanistic point of view, P(AW) prevents proper binding of primer/template by affecting the structural dynamics of the thumb/fingers of p66 subunit. Taken together, these results demonstrate that HIV-1 RT maturation constitutes an attractive target for AIDS chemotherapeutics.
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Affiliation(s)
- Audrey Agopian
- Centre de Recherches de Biochimie Macromoláculaire, Department of Molecular Biophysics & Therapeutic, UMR-5237 CNRS-UM2-UM1, 1919 Route de Mende, Montpellier 34293 and the SPI-BIO Commissariat á l'ánergie Atomique, Pharmacologie des Rátrovirus, 18 Route du Panorama, BP6, Fontenay aux Roses 9226, France
| | - Edwige Gros
- Centre de Recherches de Biochimie Macromoláculaire, Department of Molecular Biophysics & Therapeutic, UMR-5237 CNRS-UM2-UM1, 1919 Route de Mende, Montpellier 34293 and the SPI-BIO Commissariat á l'ánergie Atomique, Pharmacologie des Rátrovirus, 18 Route du Panorama, BP6, Fontenay aux Roses 9226, France
| | - Gudrun Aldrian-Herrada
- Centre de Recherches de Biochimie Macromoláculaire, Department of Molecular Biophysics & Therapeutic, UMR-5237 CNRS-UM2-UM1, 1919 Route de Mende, Montpellier 34293 and the SPI-BIO Commissariat á l'ánergie Atomique, Pharmacologie des Rátrovirus, 18 Route du Panorama, BP6, Fontenay aux Roses 9226, France
| | - Nathalie Bosquet
- Centre de Recherches de Biochimie Macromoláculaire, Department of Molecular Biophysics & Therapeutic, UMR-5237 CNRS-UM2-UM1, 1919 Route de Mende, Montpellier 34293 and the SPI-BIO Commissariat á l'ánergie Atomique, Pharmacologie des Rátrovirus, 18 Route du Panorama, BP6, Fontenay aux Roses 9226, France
| | - Pascal Clayette
- Centre de Recherches de Biochimie Macromoláculaire, Department of Molecular Biophysics & Therapeutic, UMR-5237 CNRS-UM2-UM1, 1919 Route de Mende, Montpellier 34293 and the SPI-BIO Commissariat á l'ánergie Atomique, Pharmacologie des Rátrovirus, 18 Route du Panorama, BP6, Fontenay aux Roses 9226, France
| | - Gilles Divita
- Centre de Recherches de Biochimie Macromoláculaire, Department of Molecular Biophysics & Therapeutic, UMR-5237 CNRS-UM2-UM1, 1919 Route de Mende, Montpellier 34293 and the SPI-BIO Commissariat á l'ánergie Atomique, Pharmacologie des Rátrovirus, 18 Route du Panorama, BP6, Fontenay aux Roses 9226, France.
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