1
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Jernigan RL, Bahar I, Covell DG, Atilgan AR, Erman B, Flatow DT. Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step. J Biomol Struct Dyn 2016; 17 Suppl 1:49-55. [PMID: 22607406 DOI: 10.1080/07391102.2000.10506603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract By treating an enzyme as a coarse-grained uniform block of material, utilizing only the α-Carbon positions, the normal modes of motion can be obtained. For reverse transcriptase the slower of these motions are suggestive of being involved in the processing step, where the RNA or DNA strand is copied onto a new DNA strand at a polymerase site, and the RNA strand is subsequently cut up at the distant Ribonuclease H site. The slowest mode of motion involves hinge bending about a site midway between the polymerase and Ribonuclease H sites, suggesting that it can push or pull the RNA strand between these two sites. Pulling the nucleic acid strand would require tight binding to the RNase H site. The next slowest mode involves a hinge that opens and closes the protein like a clamp, which could facilitate the release of the nucleic acids for their step-wise progression. The third mode could rotate the substrate. An overall description of the step-wise processing step would involve close coordination among these steps. Results suggest that the smaller p51 subunit serves only as ballast to support the various modes of motion involving the different parts of the p66 subunit.
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Affiliation(s)
- R L Jernigan
- a Molecular Structure Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences , National Cancer Institute, National Institutes of Health , MSC 5677 , Bethesda , MD , 20892-5677
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2
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Leng J, Ho HP, Buzon MJ, Pereyra F, Walker BD, Yu XG, Chang EJ, Lichterfeld M. A cell-intrinsic inhibitor of HIV-1 reverse transcription in CD4(+) T cells from elite controllers. Cell Host Microbe 2015; 15:717-728. [PMID: 24922574 DOI: 10.1016/j.chom.2014.05.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/30/2014] [Accepted: 04/23/2014] [Indexed: 01/22/2023]
Abstract
HIV-1 reverse transcription represents the predominant target for pharmacological inhibition of viral replication, but cell-intrinsic mechanisms that can block HIV-1 reverse transcription in a clinically significant way are poorly defined. We find that effective HIV-1 reverse transcription depends on the phosphorylation of viral reverse transcriptase by host cyclin-dependent kinase (CDK) 2 at a highly conserved Threonine residue. CDK2-dependent phosphorylation increased the efficacy and stability of viral reverse transcriptase and enhanced viral fitness. Interestingly, p21, a cell-intrinsic CDK inhibitor that is upregulated in CD4(+) T cells from "elite controllers," potently inhibited CDK2-dependent phosphorylation of HIV-1 reverse transcriptase and significantly reduced the efficacy of viral reverse transcription. These data suggest that p21 can indirectly block HIV-1 reverse transcription by inhibiting host cofactors supporting HIV-1 replication and identify sites of viral vulnerability that are effectively targeted in persons with natural control of HIV-1 replication.
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Affiliation(s)
- Jin Leng
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Hsin-Pin Ho
- Department of Chemistry, York College and the Graduate Center, City University of New York, New York, NY, USA
| | - Maria J Buzon
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Florencia Pereyra
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Emmanuel J Chang
- Department of Chemistry, York College and the Graduate Center, City University of New York, New York, NY, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
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3
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Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R. Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase. Proteins 2015; 83:1526-38. [PMID: 26061827 DOI: 10.1002/prot.24843] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 05/14/2015] [Accepted: 06/03/2015] [Indexed: 02/06/2023]
Abstract
The mature form of reverse transcriptase (RT) is a heterodimer comprising the intact 66-kDa subunit (p66) and a smaller 51-kDa subunit (p51) that is generated by removal of most of the RNase H (RNH) domain from a p66 subunit by proteolytic cleavage between residues 440 and 441. Viral infectivity is eliminated by mutations such as F440A and E438N in the proteolytic cleavage sequence, while normal processing and virus infectivity are restored by a compensatory mutation, T477A, that is located more than 10 Å away from the processing site. The molecular basis for this compensatory effect has remained unclear. We therefore investigated structural characteristics of RNH mutants using computational and experimental approaches. Our Nuclear Magnetic Resonance and Differential Scanning Fluorimetry results show that both F440A and E438N mutations disrupt RNH folding. Addition of the T477A mutation restores correct folding of the RNH domain despite the presence of the F440A or E438N mutations. Molecular dynamics simulations suggest that the T477A mutation affects the processing site by altering relative orientations of secondary structure elements. Predictions of sequence tolerance suggest that phenylalanine and tyrosine are structurally preferred at residues 440 and 441, respectively, which are the P1 and P1' substrate residues known to require bulky side chains for substrate specificity. Interestingly, our study demonstrates that the processing site residues, which are critical for protease substrate specificity and must be exposed to the solvent for efficient processing, also function to maintain proper RNH folding in the p66/p51 heterodimer.
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Affiliation(s)
- Ryan L Slack
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260
| | - Justin Spiriti
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260
| | - Michael A Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260
| | - Daniel M Zuckerman
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260
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4
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Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJL, Parniak MA, Gronenborn AM, Ishima R. The p66 immature precursor of HIV-1 reverse transcriptase. Proteins 2014; 82:2343-52. [PMID: 24771554 DOI: 10.1002/prot.24594] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/04/2014] [Accepted: 04/22/2014] [Indexed: 01/07/2023]
Abstract
In contrast to the wealth of structural data available for the mature p66/p51 heterodimeric human immunodeficiency virus type 1 reverse transcriptase (RT), the structure of the homodimeric p66 precursor remains unknown. In all X-ray structures of mature RT, free or complexed, the processing site in the p66 subunit, for generating the p51 subunit, is sequestered into a β-strand within the folded ribonuclease H (RNH) domain and is not readily accessible to proteolysis, rendering it difficult to propose a simple and straightforward mechanism of the maturation step. Here, we investigated, by solution NMR, the conformation of the RT p66 homodimer. Our data demonstrate that the RNH and Thumb domains in the p66 homodimer are folded and possess conformations very similar to those in mature RT. This finding suggests that maturation models which invoke a complete or predominantly unfolded RNH domain are unlikely. The present study lays the foundation for further in-depth mechanistic investigations at the atomic level.
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Affiliation(s)
- Naima G Sharaf
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260
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5
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Lu G, Gong P. Crystal Structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface. PLoS Pathog 2013; 9:e1003549. [PMID: 23950717 PMCID: PMC3738499 DOI: 10.1371/journal.ppat.1003549] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 06/27/2013] [Indexed: 12/17/2022] Open
Abstract
The flavivirus NS5 harbors a methyltransferase (MTase) in its N-terminal ≈265 residues and an RNA-dependent RNA polymerase (RdRP) within the C-terminal part. One of the major interests and challenges in NS5 is to understand the interplay between RdRP and MTase as a unique natural fusion protein in viral genome replication and cap formation. Here, we report the first crystal structure of the full-length flavivirus NS5 from Japanese encephalitis virus. The structure completes the vision for polymerase motifs F and G, and depicts defined intra-molecular interactions between RdRP and MTase. Key hydrophobic residues in the RdRP-MTase interface are highly conserved in flaviviruses, indicating the biological relevance of the observed conformation. Our work paves the way for further dissection of the inter-regulations of the essential enzymatic activities of NS5 and exploration of possible other conformations of NS5 under different circumstances. Due to limited coding capacity, RNA viruses often generate proteins that contain more than one enzyme module to fulfill their rather complicated life cycle. Among those, the flavivirus nonstructural protein NS5 comprises an N-terminal methyltransferase (MTase) and a C-terminal RNA-dependent RNA polymerase (RdRP), playing key roles in processes including viral genome replication and capping. Although high-resolution crystal structures are available for MTase or RdRP alone, the intra-molecular interactions between the two modules remain elusive. By solving the crystal-structure of the full-length Japanese encephalitis virus NS5, we provide the first high-resolution readout of NS5 in its integrity, featuring an MTase-RdRP interface that is highly conserved in flaviviruses. Flaviviruses also include other important human pathogens such as dengue, West Nile, yellow fever, and tick-borne encephalitis viruses, currently lacking effective anti-viral drug. The conserved interface revealed by our structure thus may provide possibilities for the pharmaceutical community in the development of anti-flavivirus drug in a broad-spectrum manner.
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Affiliation(s)
- Guoliang Lu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuchang District, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Gong
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuchang District, Wuhan, Hubei, China
- * E-mail: ,
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6
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VAILIKHIT V, BUNSAWANSONG P, TECHASAKUL S, HANNONGBUA S. CONFORMATIONAL ANALYSIS OF NEVIRAPINE IN SOLUTIONS BASED ON NMR SPECTROSCOPY AND QUANTUM CHEMICAL CALCULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633606002702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The conformational analysis of HIV-1 Reverse Transcriptase Inhibitor, nevirapine, 11-cyclopropyl-5,-11dihydro-4-methyl-6H-dipyrido[3,2-b2′,3′-e][1,4]diazepin-6-one, was investigated using ab initio and density functional theory calculations. The fully optimized structures and rotational potential energies of the nitrogen and carbon bonds in the cyclopropyl ring (C15-N11-C17-C19, α) were examined in detail. Geometries obtained from all applied calculations show similarities to the complex structure with HIV-1 reverse transcriptase. To obtain more information on the structure, conformational minima of nevirapine, optimized at the B3LYP/6-31G** level, were calculated for the 1H, 13C, and 15N-NMR chemical shifts at the B3LYP/6-311++G** level using the GIAO approach in DMSO and chloroform IEFPCM solvation models. The calculated 1H, 13C-NMR chemical shifts agree well with the experimental data, which indicates that the geometry of nevirapine in solution is similar to that of the molecule in the inhibition complex. Solvation free energies (ΔG sol ) of nevirapine in DMSO and chloroform were also obtained.
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Affiliation(s)
- V. VAILIKHIT
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - P. BUNSAWANSONG
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - S. TECHASAKUL
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - S. HANNONGBUA
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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7
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Yan J, Wu H, Tom T, Brodsky O, Maegley K. Targeting Divalent Metal Ions at the Active Site of the HIV-1 RNase H Domain: NMR Studies on the Interactions of Divalent Metal Ions with RNase H and Its Inhibitors. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/ajac.2011.26073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Coté ML, Roth MJ. Murine leukemia virus reverse transcriptase: structural comparison with HIV-1 reverse transcriptase. Virus Res 2008; 134:186-202. [PMID: 18294720 DOI: 10.1016/j.virusres.2008.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 12/31/2007] [Accepted: 01/02/2008] [Indexed: 10/22/2022]
Abstract
Recent X-ray crystal structure determinations of Moloney murine leukemia virus reverse transcriptase (MoMLV RT) have allowed for more accurate structure/function comparisons to HIV-1 RT than were formerly possible. Previous biochemical studies of MoMLV RT in conjunction with knowledge of sequence homologies to HIV-1 RT and overall fold similarities to RTs in general, provided a foundation upon which to build. In addition, numerous crystal structures of the MoMLV RT fingers/palm subdomain had also shed light on one of the critical functions of the enzyme, specifically polymerization. Now in the advent of new structural information, more intricate examination of MoMLV RT in its entirety can be realized, and thus the comparisons with HIV-1 RT may be more critically elucidated. Here, we will review the similarities and differences between MoMLV RT and HIV-1 RT via structural analysis, and propose working models for the MoMLV RT based upon that information.
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Affiliation(s)
- Marie L Coté
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, United States
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9
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Yap TL, Xu T, Chen YL, Malet H, Egloff MP, Canard B, Vasudevan SG, Lescar J. Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. J Virol 2007; 81:4753-65. [PMID: 17301146 PMCID: PMC1900186 DOI: 10.1128/jvi.02283-06] [Citation(s) in RCA: 318] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dengue fever, a neglected emerging disease for which no vaccine or antiviral agents exist at present, is caused by dengue virus, a member of the Flavivirus genus, which includes several important human pathogens, such as yellow fever and West Nile viruses. The NS5 protein from dengue virus is bifunctional and contains 900 amino acids. The S-adenosyl methionine transferase activity resides within its N-terminal domain, and residues 270 to 900 form the RNA-dependent RNA polymerase (RdRp) catalytic domain. Viral replication begins with the synthesis of minus-strand RNA from the dengue virus positive-strand RNA genome, which is subsequently used as a template for synthesizing additional plus-strand RNA genomes. This essential function for the production of new viral particles is catalyzed by the NS5 RdRp. Here we present a high-throughput in vitro assay partly recapitulating this activity and the crystallographic structure of an enzymatically active fragment of the dengue virus RdRp refined at 1.85-A resolution. The NS5 nuclear localization sequences, previously thought to fold into a separate domain, form an integral part of the polymerase subdomains. The structure also reveals the presence of two zinc ion binding motifs. In the absence of a template strand, a chain-terminating nucleoside analogue binds to the priming loop site. These results should inform and accelerate the structure-based design of antiviral compounds against dengue virus.
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Affiliation(s)
- Thai Leong Yap
- Novartis Institute for Tropical Diseases, 05-01 Chromos, 10 Biopolis Road, Singapore 138670, Singapore
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10
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Ercanli T, Boyd DB. Exploration of the conformational space of a polymeric material that inhibits human immunodeficiency virus. J Chem Inf Model 2006; 46:1321-33. [PMID: 16711751 DOI: 10.1021/ci050339a] [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: 11/28/2022]
Abstract
Baertschi et al. (Antiviral Chem. Chemother. 1997, 8, 353-362) clarified the nature of a polymeric degradation product formed from the cephalosporin ceftazidime. Interest in the polymeric material arises from its ability to inhibit the RNase H and polymerase activities of HIV-1 reverse transcriptase (RT). To shed light on the structure of the polymeric material like that which forms from degradation of third-generation cephalosporins, we apply molecular modeling and other computational chemistry techniques. Aminothiazole methoxime (2-amino-4-thiazolyl-methoxyimino; ATMO) is the parent structure related to the isolated degradation product of ceftazidime. The MMFF94 force field and Monte Carlo multiple minimum method as implemented in MacroModel are used to generate low-energy conformers. We built up oligomeric models starting from the trimer to the 16-mer and performed distribution analyses on the dihedral angles from the Monte Carlo runs to analyze the three-dimensional shapes of the oligomers. Although the larger oligomers are too long for a complete search of conformational space, the low-energy conformers examined do not show secondary structure or repetitive conformations. Polymeric ATMO material may, therefore, exhibit only random coil conformations. Topological similarity of ATMO structures to other reported RT inhibitors is also examined.
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Affiliation(s)
- Tulay Ercanli
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202-3274, USA
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11
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Zhou Z, Madrid M, Evanseck JD, Madura JD. Effect of a Bound Non-Nucleoside RT Inhibitor on the Dynamics of Wild-Type and Mutant HIV-1 Reverse Transcriptase. J Am Chem Soc 2005; 127:17253-60. [PMID: 16332074 DOI: 10.1021/ja053973d] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 reverse transcriptase (RT) is an important target for drugs used in the treatment of AIDS. Drugs known as non-nucleoside RT inhibitors (NNRTI) appear to alter the structural and dynamical properties of RT which in turn inhibit RT's ability to transcribe. Molecular dynamics (MD), principal component analysis (PCA), and binding free energy simulations are employed to explore the dynamics of RT and its interaction with the bound NNRTI nevirapine, for both wild-type and mutant (V106A, Y181C, Y188C) RT. These three mutations commonly arise in the presence of nevirapine and result in resistance to the drug. We show that a bound NNRTI hinders the motion of almost all RT amino acids. The mutations, located in the non-nucleoside RT inhibitor binding pocket, partially restore RT flexibility. The binding affinities calculated by molecular mechanics/Poisson-Boltzmann surface accessibility (MM-PBSA) show that nevirapine interacts stronger with wild-type RT than with mutant RT. The mutations cause a loss of van der Waals interactions between the drug and the binding pocket. The results from this study suggest that a good inhibitor should efficiently enter and maximally occupy the binding pocket, thereby interacting effectively with the amino acids around the binding pocket.
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Affiliation(s)
- Zhigang Zhou
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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12
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Computer-aided design of potential anti-HIV-1 non-nucleoside reverse transcriptase inhibitors by contraction of β-ring in TIBO derivatives. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Ragno R, Frasca S, Manetti F, Brizzi A, Massa S. HIV-reverse transcriptase inhibition: inclusion of ligand-induced fit by cross-docking studies. J Med Chem 2005; 48:200-12. [PMID: 15634014 DOI: 10.1021/jm0493921] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) have, in addition to the nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs), a definitive role in the treatment of HIV-1 infections. Since the appearance of HEPT and TIBO, more than 30 structurally different classes of compounds have been reported as NNRTIs, which are specific inhibitors of HIV-1 replication, targeting the HIV-1 reverse transcriptase (RT). Nevirapine and delavirdine are the first formally licensed for clinical use, and others have been licensed afterward, while several are in preclinical or clinical development. The NNRTIs interact with a specific site of HIV-1 RT (nonnucleoside binding site, NNBS) that is close to, but distinct from, the NRTI binding site. In this work we report the application of the Autodock program assessing its usability through reproduction of 41 NNRTI experimental bound conformations. Moreover, cross-docking experiments on the wild-type and mutated RT forms were conducted to take into account the enzyme flexibility as a valuable tool for structure-based drug design (SBDD) studies and to gain insight on the mode of action of new anti-HIV agents active against both wild-type and resistant strains.
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Affiliation(s)
- Rino Ragno
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via A. Moro, I-53100 Siena, Italy.
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14
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Bartenschlager R, Frese M, Pietschmann T. Novel insights into hepatitis C virus replication and persistence. Adv Virus Res 2005; 63:71-180. [PMID: 15530561 DOI: 10.1016/s0065-3527(04)63002-8] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hepatitis C virus (HCV) is a small enveloped RNA virus that belongs to the family Flaviviridae. A hallmark of HCV is its high propensity to establish a persistent infection that in many cases leads to chronic liver disease. Molecular studies of the virus became possible with the first successful cloning of its genome in 1989. Since then, the genomic organization has been delineated, and viral proteins have been studied in some detail. In 1999, an efficient cell culture system became available that recapitulates the intracellular part of the HCV life cycle, thereby allowing detailed molecular studies of various aspects of viral RNA replication and persistence. This chapter attempts to summarize the current state of knowledge in these most actively worked on fields of HCV research.
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Affiliation(s)
- Ralf Bartenschlager
- Department of Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
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15
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Arnold JJ, Cameron CE. Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg2+. Biochemistry 2004; 43:5126-37. [PMID: 15122878 PMCID: PMC2426923 DOI: 10.1021/bi035212y] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have solved the complete kinetic mechanism for correct nucleotide incorporation catalyzed by the RNA-dependent RNA polymerase from poliovirus, 3D(pol). The phosphoryl-transfer step is flanked by two isomerization steps. The first conformational change may be related to reorientation of the triphosphate moiety of the bound nucleotide, and the second conformational change may be translocation of the enzyme into position for the next round of nucleotide incorporation. The observed rate constant for nucleotide incorporation by 3D(pol) (86 s(-1)) is dictated by the rate constants for both the first conformational change (300 s(-1)) and phosphoryl transfer (520 s(-1)). Changes in the stability of the "activated" ternary complex correlate best with changes in the observed rate constant for incorporation resulting from modification of the nucleotide. With the exception of UTP, the K(d) values for nucleotides are at least 10-fold lower than the cellular concentration of the corresponding nucleotide. Our data predict that transition mutations should occur at a frequency of 1/15000, transversion mutations should occur at a frequency of less than 1/150000, and incorporation of a 2'-deoxyribonucleotide with a correct base should occur at a frequency 1/7500. Together, these data support the conclusion that 3D(pol) is actually as faithful as an exonuclease-deficient, replicative DNA polymerase. We discuss the implications of this work on the development of RNA-dependent RNA polymerase inhibitors for use as antiviral agents.
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Affiliation(s)
- Jamie J Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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16
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Pata JD, Stirtan WG, Goldstein SW, Steitz TA. Structure of HIV-1 reverse transcriptase bound to an inhibitor active against mutant reverse transcriptases resistant to other nonnucleoside inhibitors. Proc Natl Acad Sci U S A 2004; 101:10548-53. [PMID: 15249669 PMCID: PMC489975 DOI: 10.1073/pnas.0404151101] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have determined the crystal structure of the HIV type 1 reverse transcriptase complexed with CP-94,707, a new nonnucleoside reverse transcriptase inhibitor (NNRTI), to 2.8-A resolution. In addition to inhibiting the wild-type enzyme, this compound inhibits mutant enzymes that are resistant to inhibition by nevirapine, efavirenz, and delaviridine. In contrast to other NNRTI complexes where tyrosines 181 and 188 are pointing toward the enzyme active site, the binding pocket in this complex has the tyrosines pointing the opposite direction, as in the unliganded protein structure, to accommodate CP-94,707. This conformation of the pocket has not been observed previously in NNRTI complexes and substantially alters the shape and surface features that are available for interactions with the inhibitor. One ring of CP-94,707 makes extensive stacking interactions with tryptophan 229, one of the few residues in the NNRTI-binding pocket that cannot readily mutate to give rise to drug resistance. In this conformation of the pocket, mutations of tyrosines 181 and 188 are less likely to disrupt inhibitor binding. Modeling the asparagine mutation of lysine 103 shows that a hydrogen bond between it and tyrosine 188 could form as readily in the CP-94,707 complex as it does in the apoenzyme structure, providing an explanation for the activity of this inhibitor against this clinically important mutant.
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Affiliation(s)
- Janice D Pata
- Department of Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA
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17
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Shen L, Shen J, Luo X, Cheng F, Xu Y, Chen K, Arnold E, Ding J, Jiang H. Steered molecular dynamics simulation on the binding of NNRTI to HIV-1 RT. Biophys J 2003; 84:3547-63. [PMID: 12770866 PMCID: PMC1302942 DOI: 10.1016/s0006-3495(03)75088-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
HIV-1 reverse transcriptase (RT) is the primary target for anti-AIDS chemotherapy. Nonnucleoside RT inhibitors (NNRTIs) are very potent and most promising anti-AIDS drugs that specifically inhibit HIV-1 RT. The binding and unbinding processes of alpha-APA, an NNRTI, have been studied using nanosecond conventional molecular dynamics and steered molecular dynamics simulations. The simulation results show that the unbinding process of alpha-APA consists of three phases based on the position of alpha-APA in relation to the entrance of the binding pocket. When alpha-APA is bound in the binding pocket, the hydrophobic interactions between HIV-1 RT and alpha-APA dominate the binding; however, the hydrophilic interactions (both direct and water-bridged hydrogen bonds) also contribute to the stabilizing forces. Whereas Tyr-181 makes significant hydrophobic interactions with alpha-APA, Tyr-188 forms a strong hydrogen bond with the acylamino group (N14) of alpha-APA. These two residues have very flexible side chains and appear to act as two "flexible clamps" discouraging alpha-APA to dissociate from the binding pocket. At the pocket entrance, two relatively inflexible residues, Val-179 and Leu-100, gauge the openness of the entrance and form the bottleneck of the inhibitor-unbinding pathway. Two special water molecules at the pocket entrance appear to play important roles in inhibitor recognition of binding and unbinding. These water molecules form water bridges between the polar groups of the inhibitor and the residues around the entrance, and between the polar groups of the inhibitor themselves. The water-bridged interactions not only induce the inhibitor to adopt an energetically favorable conformation so the inhibitor can pass through the pocket entrance, but also stabilize the binding of the inhibitor in the pocket to prevent the inhibitor's dissociation. The complementary steered molecular dynamics and conventional molecular dynamics simulation results strongly support the hypothesis that NNRTIs inhibit HIV-1 RT polymerization activity by enlarging the DNA-binding cleft and restricting the flexibility and mobility of the p66 thumb subdomain that are believed to be essential during DNA translocation and polymerization.
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Affiliation(s)
- Lingling Shen
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China
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18
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Keller PA, Birch C, Leach SP, Tyssen D, Griffith R. Novel pharmacophore-based methods reveal gossypol as a reverse transcriptase inhibitor. J Mol Graph Model 2003; 21:365-73. [PMID: 12543135 DOI: 10.1016/s1093-3263(02)00183-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In a program to identify new structural entities for the inhibition of the HIV-1 reverse transcriptase (RT) enzyme via database searching, a series of RT pharmacophores were developed. By utilising a novel filtering technique, the National Cancer Institute database of compounds was scanned producing 15 compounds to be screened for activity. A notable inclusion was a series of gossypol derivatives. The testing of a series of compounds revealed the parent compound gossypol to be an HIV-1 reverse transcriptase inhibitor. These results suggest that at least a part of its anti-HIV activity is due to gossypol targeting the non-nucleoside inhibitor binding pocket of RT.
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Affiliation(s)
- Paul A Keller
- Department of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia.
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19
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O'Farrell D, Trowbridge R, Rowlands D, Jäger J. Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation. J Mol Biol 2003; 326:1025-35. [PMID: 12589751 DOI: 10.1016/s0022-2836(02)01439-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Several crystal structures of the hepatitis C virus NS5B protein (genotype-1b, strain J4) complexed with metal ions, single-stranded RNA or nucleoside-triphosphates have been determined. These complexes illustrate how conserved amino acid side-chains, together with essential structural features within the active site, control nucleotide binding and likely mediate de-novo initiation. The incoming nucleotide interacts with several basic residues from an extension on the NS5B fingers domain, a beta-hairpin from the NS5B thumb domain and the C-terminal arm. The modular, bi-partite fingers domain carries a long binding groove which guides the template towards the catalytic site. The apo-polymerase structure provides unprecedented insights into potential non-nucleoside inhibitor binding sites located between palm and thumb near motif E, which is unique to RNA polymerases and reverse transcriptases.
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Affiliation(s)
- Damien O'Farrell
- Astbury Centre of Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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20
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Zhou Z, Madrid M, Madura JD. Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase. Proteins 2002; 49:529-42. [PMID: 12402361 DOI: 10.1002/prot.10233] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The docking of small molecules to proteins has played an important role in the understanding of drug/receptor interactions. An important drug/receptor interaction is between non-nucleoside inhibitors of HIV-1 RT and the non-nucleoside binding pocket. We report the results of docking calculations in which we have docked known and proposed non-nucleoside reverse transcriptase inhibitors to the type 1 virus. The proposed NNRTIs dock in a similar position and orientation as known inhibitors. In addition, we observe a linear correlation between the calculated interaction energy and EC50 for the inhibitors, suggesting that the docked structure orientation and the interaction energies are reasonable. Two hydrogen bonds between nevirapine and RT (3HVT and 1VRT) are observed and are reproduced across different docking schemes. Since we used two different HIV-1 RT crystal structures (3HVT and 1VRT), which are at different levels of resolution (2.9 and 2.2 A, respectively), we propose that structures with resolutions better than 3 A can be used to produce reasonable docking results.
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Affiliation(s)
- Zhigang Zhou
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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21
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Abstract
The discovery and development of more than a dozen drugs in the past 15 years for the treatment of AIDS offer an excellent example of progress in the field of rational drug design. At this time, the principal targets are reverse transcriptase and protease, enzymes encoded by the human immunodeficiency virus. The introduction of protease inhibitors, in particular, has drastically decreased the mortality and morbidity associated with AIDS. This review presents the methods used to develop such drugs and discusses the remaining problems, such as the rapid emergence of drug resistance.
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Affiliation(s)
- Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.
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22
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Shogren-Knaak MA, Alaimo PJ, Shokat KM. Recent advances in chemical approaches to the study of biological systems. Annu Rev Cell Dev Biol 2002; 17:405-33. [PMID: 11687495 DOI: 10.1146/annurev.cellbio.17.1.405] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A number of novel chemical methods for studying biological systems have recently been developed that provide a means of addressing biological questions not easily studied with other techniques. In this review, examples that highlight the development and use of such chemical approaches are discussed. Specifically, strategies for modulating protein activity or protein-protein interactions using small molecules are presented. In addition, methods for generating and utilizing novel biomolecules (proteins, oligonucleotides, oligosaccharides, and second messengers) are examined.
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Affiliation(s)
- M A Shogren-Knaak
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143-0450, USA
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23
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Hannongbua S, Prasithichokekul S, Pungpo P. Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculations. J Comput Aided Mol Des 2001; 15:997-1004. [PMID: 11989627 DOI: 10.1023/a:1014881723431] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The structure and the conformational behavior of the HIV-1 reverse transcriptase inhibitor, 11-cyclopropyl-5,11dihydro-4-methyl-6H-dipyrido[3,2-b2',3'-e][1,4]diazepin-6-one (nevirapine), is investigated by semiempirical (MNDO, AMI and PM3) method, ab initio at the HF/3-21G and HF/6-31G** levels and density functional theory at the B3LYP/6-31G** level. The fully optimized structure and rotational potential of the nitrogen and carbon bond in the cyclopropyl ring were examined in detail. A similar geometrical minimum is obtained from all methods which shows an almost identical structure to the geometry of the molecule in the complex structure with HIV-1 reverse transcriptase. To get some information on the structure in solution, NMR chemical shift calculations were also performed by a density functional theory at the B3LYP/6-31G** level, using GIAO approximation. The calculated 1H-NMR and 13C-NMR spectra for the energy minimum geometry agree well with the experimental results, which indicated that the geometry of nevirapine in solution is very similar to that of the molecule in the inhibition complex. Furthermore, the obtained results are compared to the conformational studies of other non-nucleoside reverse transcriptase inhibitors and reveal a common agreement of the non-nucleoside reverse transcriptase inhibitors. The specific butterfly-like shape and conformational flexibility within the side chain of the non-nucleoside reverse transcriptase inhibitors play an important role inducing conformational change of HIV-1 reverse transcriptase structure and are essential for the association at the inhibition pocket.
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Affiliation(s)
- S Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.
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24
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Lavigne M, Polomack L, Buc H. Structures of complexes formed by HIV-1 reverse transcriptase at a termination site of DNA synthesis. J Biol Chem 2001; 276:31439-48. [PMID: 11402037 DOI: 10.1074/jbc.m102976200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study presents structural parameters associated with termination of human immunodeficiency virus, type 1 (HIV-1) reverse transcriptase (RT) at Ter2, the major termination site located in the center of the HIV-1 genome. DNA footprinting studies of various elongation complexes formed by RT around wild type and mutant Ter2 sites have revealed two major structural transformations of these complexes when the enzyme gets closer to Ter2. First, the interactions between RT and the DNA duplex are less extended, although the global affinity of the enzyme for this duplex is only decreased by 2-fold. Second, there is an atypical positioning of the RT RNase H domain on the DNA duplex. We interpret our data as indicating that the A(n)T(m) motif located upstream of Ter2 prevents a classical positioning of the enzyme on the double-stranded part of the DNA duplex at some precise positions of elongation downstream of this motif. Instead, novel species of binary and/or ternary complexes, characterized by atypical footprints, are formed. The new rate-limiting step of the reaction, characterized in the preceding paper (Lavigne, M., Polomack, L., and Buc, H. (2001) J. Biol. Chem. 276, 31429-31438), would be a transition leading from these new species to a catalytically competent ternary complex.
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Affiliation(s)
- M Lavigne
- Unité de Physicochimie des Macromolécules Biologiques, Institut Pasteur, CNRS URA 1773, 75724 Paris Cedex 15, France.
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25
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Földes-Papp Z, Angerer B, Thyberg P, Hinz M, Wennmalm S, Ankenbauer W, Seliger H, Holmgren A, Rigler R. Fluorescently labeled model DNA sequences for exonucleolytic sequencing. J Biotechnol 2001; 86:203-24. [PMID: 11257532 DOI: 10.1016/s0168-1656(00)00414-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We describe here the enzyme-catalyzed, low-density labeling of DNAs with fluorescent dyes. Firstly, for "natural" template DNAs, dNTPs were partially substituted in the labeling reactions by the respective fluorophore-bearing analogs. The DNAs were labeled by PCR using Taq DNA polymerase. The covalent incorporation of dye-dNTPs decreased in the following order: rhodamine-green-5-dUTP (Molecular Probes, the Netherlands), tetramethylrhodamine-4-dUTP (FluoroRed, Amersham Pharmacia Biotech), Cy5-dCTP (Amersham Pharmacia Biotech). Exonucleolytic degradation by the 3'-->5' exonuclease activity of T7 DNA polymerase (wild type) in the presence of excess reduced thioredoxin proceeded to complete breakdown of the labeled DNAs. The catalytic cleavage constants determined by fluorescence correlation spectroscopy were between 0.5 and 1.5 s(-1) at 16 degrees C, normalized for the covalently incorporated dye-nucleotides. Secondly, rhodamine-green-X-dUTP (Roche Diagnostics), tetramethylrhodamine-6-dUTP (Roche Diagnostics), and Cy5-dCTP were covalently incorporated into the antisense strand of "synthetic" 218-b DNA template constructs (master sequences) at well defined positions, starting from the primer binding site, by total substitution for the naturally occurring dNTPs. The 218-b DNA constructs were labeled by PCR with a thermostable 3'-->5' exonuclease deficient mutant of the Tgo DNA polymerase which we have selected. The advantage of the special, synthetic DNA constructs as compared to natural DNAs lies in the possibility of obtaining tailor-made nucleic acids, optimized for testing the performance of exonucleolytic sequencing. The number of incorporated fluorescent nucleotides determined by complete exonucleolytic degradation and fluorescence correlation spectroscopy were six out of six possible incorporations for rhodamine-green-X-dUTP and tetramethylrhodamine-6-dUTP, respectively. Their covalent and base-specific incorporations were confirmed by the novel analysis methodology of re-sequencing (i.e. mobility-shift gel electrophoresis, reversion-PCR and re-sequencing) first developed in the paper Földes-Papp et al. (2001) and in this paper. This methodology was then used by other groups within the whole sequencing project.
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Affiliation(s)
- Z Földes-Papp
- Department of Medical Biophysics, MBB, Karolinska Institute, S-17177 Stockholm, Sweden.
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26
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Kensch O, Restle T, Wöhrl BM, Goody RS, Steinhoff HJ. Temperature-dependent equilibrium between the open and closed conformation of the p66 subunit of HIV-1 reverse transcriptase revealed by site-directed spin labelling. J Mol Biol 2000; 301:1029-39. [PMID: 10966802 DOI: 10.1006/jmbi.2000.3998] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
X-ray crystallographic studies of human immunodeficiency virus type 1 reverse transcriptase complexed with or without substrates or inhibitors show that the heterodimeric enzyme adopts distinct conformations that differ in the orientation of the so-called thumb subdomain in the large subunit. Site-directed spin labelling of mutated residue positions W24C and K287C is applied here to determine the distances between the fingers and thumb subdomains of liganded and unliganded RT in solution. The inter-spin distances of a DNA/DNA and a pseudoknot RNA complexed reverse transcriptase in solution was found to agree with the respective crystal data of the open and closed conformations. For the unliganded reverse transcriptase a temperature-dependent equilibrium between these two states was observed. The fraction of the closed conformation decreased from 95% at 313 K to 65% at 273 K. The spectral separation between the two structures was facilitated by the use of a perdeuterated ([15)N]nitroxide methane-thiosulfonate spin label.
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Affiliation(s)
- O Kensch
- Max-Planck-Institut für molekulare Physiologie Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
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27
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Keller PA, Leach SP, Luu TT, Titmuss SJ, Griffith R. Development of computational and graphical tools for analysis of movement and flexibility in large molecules. J Mol Graph Model 2000; 18:235-41, 299. [PMID: 11021539 DOI: 10.1016/s1093-3263(00)00028-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
We developed a computer program for the calculation and display of the difference distance matrices (DDMs) of macromolecules that has the ability to compare multiple structures simultaneously. To demonstrate its use, a data set of atoms for superimposition of the HIV-1 reverse transcriptase enzyme was defined using the coordinates for the 21 available crystal structures of this enzyme and its complexes. The DDM technique for superimposition data set generation allows selection of atoms that are invariant in all structures, is free from user bias, and represents the most accurate and precise method of producing such subsets. Comparison of this technique was made against other published methods of generating superimposition data sets, and it was found that significant differences in magnitude and trends of atom movements are observed depending on which data set was used.
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Affiliation(s)
- P A Keller
- Department of Chemistry, University of Wollongong, Australia.
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28
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Huang H, Harrison SC, Verdine GL. Trapping of a catalytic HIV reverse transcriptase*template:primer complex through a disulfide bond. CHEMISTRY & BIOLOGY 2000; 7:355-64. [PMID: 10801473 DOI: 10.1016/s1074-5521(00)00113-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND HIV-1 reverse transcriptase (RT) is a major target for the treatment of acquired immunodeficiency syndrome (AIDS). Resistance mutations in RT compromise treatment, however. Efforts to understand the enzymatic mechanism of RT and the basis for mutational resistance to anti-RT drugs have been hampered by the failure to crystallize a catalytically informative RT-substrate complex. RESULTS We present here experiments that allow us to understand the reason for the failure to crystallize such a complex. Based on this understanding, we have devised a new approach for using a combinatorial disulfide cross-linking strategy to trap a catalytic RT*template:primer*dNTP ternary complex, thereby enabling the growth of co-crystals suitable for high-resolution structural analysis. The crystals contain a fully assembled active site poised for catalysis. The cross-link itself appears to be conformationally mobile, and the surrounding region is undistorted, suggesting that the cross-link is a structurally passive device that merely acts to prevent dissociation of the catalytic complex. CONCLUSIONS The new strategy discussed here has resulted in the crystallization and structure determination of a catalytically relevant RT*template:primer*dNTP complex. The structure has allowed us to analyze possible causes of drug resistance at the molecular level. This information will assist efforts to develop new classes of nucleoside analog inhibitors, which might help circumvent current resistance profiles. The covalent trapping strategy described here may be useful with other protein-DNA complexes that have been refractory to structural analysis.
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Affiliation(s)
- H Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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29
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Titmuss SJ, Keller PA, Griffith R. Docking experiments in the flexible non-nucleoside inhibitor binding pocket of HIV-1 reverse transcriptase. Bioorg Med Chem 1999; 7:1163-70. [PMID: 10428388 DOI: 10.1016/s0968-0896(99)00012-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Docking experiments were undertaken using a number of published crystal structures of HIV-1 reverse transcriptase complexes with various non-nucleoside inhibitors. The docking method was validated by successfully docking each ligand, in the conformation found in the crystal structure of the complex with the enzyme, back into its binding pocket in the right orientation and position. Each ligand was then subjected to conformational searching and a database of unique low-energy conformations of all ligands established. Docking this database into each of the reverse transcriptase binding pockets showed that all inhibitors could be fitted into each different pocket, without alteration of the pocket geometry. This contradicts findings from earlier docking investigations and implies that the conformation of the binding pocket in each different complex is conserved sufficiently to allow particular uniform ligand binding modes. The inhibitor conformations selected by this docking process are mostly the same as the one the ligand adopts in its own pocket and the selected conformations and orientations exhibit an impressive degree of similarity in the arrangement of their steric and electronic features. A correlation has also been observed between inhibitor flexibility and tightness of fit into the pockets with the more flexible inhibitors achieving a tighter fit and thus fewer favourable orientations upon docking.
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Affiliation(s)
- S J Titmuss
- Department of Chemistry, University of Wollongong, NSW, Australia
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30
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Madrid M, Jacobo-Molina A, Ding J, Arnold E. Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990515)35:3<332::aid-prot7>3.0.co;2-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Hopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B. Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc Natl Acad Sci U S A 1999; 96:3600-5. [PMID: 10097083 PMCID: PMC22340 DOI: 10.1073/pnas.96.7.3600] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA-protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this "closed" conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.
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Affiliation(s)
- K P Hopfner
- Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany.
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32
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Isel C, Westhof E, Massire C, Le Grice SF, Ehresmann B, Ehresmann C, Marquet R. Structural basis for the specificity of the initiation of HIV-1 reverse transcription. EMBO J 1999; 18:1038-48. [PMID: 10022845 PMCID: PMC1171195 DOI: 10.1093/emboj/18.4.1038] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition of the viral genome, tRNA3Lys, which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between HIV-1 RNA and tRNA3Lys, but remains poorly understood at the three-dimensional level. We used chemical probing to gain insight into the three-dimensional structure of the viral RNA-tRNA3Lys complex, and enzymatic footprinting to delineate regions interacting with RT. These and previous experimental data were used to derive a three-dimensional model of the initiation complex. The viral RNA and tRNA3Lys form a compact structure in which the two RNAs fold into distinct structural domains. The extended interactions between these molecules are not directly recognized by RT. Rather, they favor RT binding by preventing steric clashes between the nucleic acids and the polymerase and inducing a viral RNA-tRNA3Lys conformation which fits perfectly into the nucleic acid binding cleft of RT. Recognition of the 3' end of tRNA3Lys and of the first template nucleotides by RT is favored by a kink in the template strand promoted by the short junctions present in the previously established secondary structure.
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Affiliation(s)
- C Isel
- Unité Propre de Recherche No. 9002 du Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg Cedex, France
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33
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Abstract
Underpinned by a database of more than a dozen different crystal structures, an increasingly complete and coherent picture of polymerase structure and function is emerging. Recently determined structures of DNA and RNA polymerases have revealed some of the molecular features and structural changes governing catalysis, oligomerization, processivity and fidelity. Despite having minimal similarities in sequence and protein topology, the polymerases all display a functionally analogous set of subdomains that bind the primer, template and nucleotide substrates in similar though not identical fashions. The two-metal-ion mechanism for nucleotide incorporation, however, is shared even by nonhomologous polymerases.
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Affiliation(s)
- J Jäger
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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35
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Bahar I, Erman B, Jernigan RL, Atilgan AR, Covell DG. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J Mol Biol 1999; 285:1023-37. [PMID: 9887265 DOI: 10.1006/jmbi.1998.2371] [Citation(s) in RCA: 183] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to study the inferences of structure for mechanism, the collective motions of the retroviral reverse transcriptase HIV-1 RT (RT) are examined using the Gaussian network model (GNM) of proteins. This model is particularly suitable for elucidating the global dynamic characteristics of large proteins such as the presently investigated heterodimeric RT comprising a total of 982 residues. Local packing density and coordination order of amino acid residues is inspected by the GNM to determine the type and range of motions, both at the residue level and on a global scale, such as the correlated movements of entire subdomains. Of the two subunits, p66 and p51, forming the RT, only p66 has a DNA-binding cleft and a functional polymerase active site. This difference in the structure of the two subunits is shown here to be reflected in their dynamic characteristics: only p66 has the potential to undergo large-scale cooperative motions in the heterodimer, while p51 is essentially rigid. Taken together, the global motion of the RT heterodimer is comprised of movements of the p66 thumb subdomain perpendicular to those of the p66 fingers, accompanied by anticorrelated fluctuations of the RNase H domain and p51 thumb, thus providing information about the details of one processivity mechanism. A few clusters of residues, generally distant in sequence but close in space, are identified in the p66 palm and connection subdomains, which form the hinge-bending regions that control the highly concerted motion of the subdomains. These regions include the catalytically active site and the non-nucleoside inhibitor binding pocket of p66 polymerase, as well as sites whose mutations have been shown to impair enzyme activity. It is easily conceivable that this hinge region, indicated by GNM analysis to play a critical role in modulating the global motion, is locked into an inactive conformation upon binding of an inhibitor. Comparative analysis of the dynamic characteristics of the unliganded and liganded dimers indicates severe repression of the mobility of the p66 thumb in RT's global mode, upon binding of non-nucleoside inhibitors.
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Affiliation(s)
- I Bahar
- National Institutes of Health, Bethesda, MD, 20892-5677, USA
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36
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Smith RH, Jorgensen WL, Tirado-Rives J, Lamb ML, Janssen PA, Michejda CJ, Kroeger Smith MB. Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method. J Med Chem 1998; 41:5272-86. [PMID: 9857095 DOI: 10.1021/jm9804174] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Monte Carlo (MC) simulations in combination with a linear response approach were used to estimate the free energies of binding for a series of 12 TIBO nonnucleoside inhibitors of HIV-1 reverse transcriptase. Separate correlations were made for the R6 and S6 absolute conformations of the inhibitors, as well as for the analogous N6-monoprotonated species. Models based upon the neutral unbound inhibitors produced overall better fits to experimental values than did those using the protonated unbound inhibitors, with only slight differences between the neutral R6 and S6 cases. The best results were obtained with a three-parameter linear response equation containing van der Waals (alpha), electrostatic (beta), and solvent accessible surface area (SASA, gamma) terms. The averaged (R6 and S6) rms error was approximately 0.88 kcal/mol for the observed range of 4.06 kcal/mol in inhibitor activities. The averaged values of alpha, beta, and gamma were -0.150, 0.114, and 0. 0286, respectively. Omission of the alpha term gave beta 0.152 and gamma 0.022 with a rms of 0.92. The unweighted van der Waals components were found to be highly attractive but failed to correlate well across the series of inhibitors. Contrastingly, while the electrostatic components are all repulsive, they show a direct correlation with inhibitor activity as measured by DeltaGbinding. The role of gamma is primarily to produce an overall negative binding energy, and it can effectively be replaced with a negative constant. During the MC simulations of the unbound solvated inhibitors, the R6 and S6 absolute conformations do not interconvert due to the formation of a favorable hydrogen bond to solvent. In the complex, however, interconversion of these conformations of the inhibitor is observed during the course of the simulations, a phenomenon which is apparently not observed in the crystalline state of the complex. Hydrogen bonding of the inhibitor to the backbone NH of K101 and the lack of such an interaction with the C=O of K101 or with solvent correlate with enhanced activity, as does the ability to assume a number of different orientations of the inhibitor dimethylallyl moiety with respect to residues Y181 and Y188 while retaining contact with W229. Overall, the use of a combination of MC simulation with a linear response method shows promise as a relatively rapid means of estimating inhibitor activities. This approach should be useful in the preliminary evaluation of potential modifications to known inhibitors to enhance activity.
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Affiliation(s)
- R H Smith
- Department of Chemistry, Western Maryland College, Westminster, Maryland 21157, USA
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37
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Huang H, Chopra R, Verdine GL, Harrison SC. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 1998; 282:1669-75. [PMID: 9831551 DOI: 10.1126/science.282.5394.1669] [Citation(s) in RCA: 1137] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A combinatorial disulfide cross-linking strategy was used to prepare a stalled complex of human immunodeficiency virus-type 1 (HIV-1) reverse transcriptase with a DNA template:primer and a deoxynucleoside triphosphate (dNTP), and the crystal structure of the complex was determined at a resolution of 3.2 angstroms. The presence of a dideoxynucleotide at the 3'-primer terminus allows capture of a state in which the substrates are poised for attack on the dNTP. Conformational changes that accompany formation of the catalytic complex produce distinct clusters of the residues that are altered in viruses resistant to nucleoside analog drugs. The positioning of these residues in the neighborhood of the dNTP helps to resolve some long-standing puzzles about the molecular basis of resistance. The resistance mutations are likely to influence binding or reactivity of the inhibitors, relative to normal dNTPs, and the clustering of the mutations correlates with the chemical structure of the drug.
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Affiliation(s)
- H Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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38
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Ren J, Esnouf RM, Hopkins AL, Jones EY, Kirby I, Keeling J, Ross CK, Larder BA, Stuart DI, Stammers DK. 3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes. Proc Natl Acad Sci U S A 1998; 95:9518-23. [PMID: 9689112 PMCID: PMC21370 DOI: 10.1073/pnas.95.16.9518] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/1998] [Accepted: 05/27/1998] [Indexed: 02/08/2023] Open
Abstract
HIV reverse transcriptase (RT) is one of the main targets for the action of anti-AIDS drugs. Many of these drugs [e.g., 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxyinosine (ddI)] are analogues of the nucleoside substrates used by the HIV RT. One of the main problems in anti-HIV therapy is the selection of a mutant virus with reduced drug sensitivity. Drug resistance in HIV is generated for nucleoside analogue inhibitors by mutations in HIV RT. However, most of these mutations are situated some distance from the polymerase active site, giving rise to questions concerning the mechanism of resistance. To understand the possible structural bases for this, the crystal structures of AZT- and ddI-resistant RTs have been determined. For the ddI-resistant RT with a mutation at residue 74, no significant conformational changes were observed for the p66 subunit. In contrast, for the AZT-resistant RT (RTMC) bearing four mutations, two of these (at 215 and 219) give rise to a conformational change that propagates to the active site aspartate residues. Thus, these drug resistance mutations produce an effect at the RT polymerase site mediated simply by the protein. It is likely that such long-range effects could represent a common mechanism for generating drug resistance in other systems.
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Affiliation(s)
- J Ren
- Laboratory of Molecular Biophysics, Rex Richards Building, South Parks Road, University of Oxford, Oxford OX1 3QU, United Kingdom
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39
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Jaeger J, Restle T, Steitz TA. The structure of HIV-1 reverse transcriptase complexed with an RNA pseudoknot inhibitor. EMBO J 1998; 17:4535-42. [PMID: 9687519 PMCID: PMC1170784 DOI: 10.1093/emboj/17.15.4535] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Small RNA pseudoknots, selected to bind human immunodeficiency virus type 1 (HIV-1) reverse transcriptase tightly, are potent inhibitors of reverse transcriptase. The co-crystal structure of reverse transcriptase complexed with a 33 nucleotide RNA pseudoknot has been determined by fitting the ligand into a high quality, 4-fold averaged 4.8 A resolution electron density map. The RNA is kinked between stems S1 and S2, thereby optimizing its contacts with subunits of the heterodimer. Its binding site extends along the cleft that lies between the polymerase and RNase H active sites, partially overlaps with that observed for duplex DNA and presumably overlaps some portion of the tRNA site. Stem S2 and loop L1 stabilize the 'closed' conformation of the polymerase through extensive electrostatic interactions with several basic residues in helix I of the p66 thumb and in the p66 fingers domain. Presumably, this RNA ligand inhibits reverse transcriptase by binding to a site that partly overlaps the primer-template binding site.
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Affiliation(s)
- J Jaeger
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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40
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Sun D, Jessen S, Liu C, Liu X, Najmudin S, Georgiadis MM. Cloning, expression, and purification of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase: crystallization of nucleic acid complexes. Protein Sci 1998; 7:1575-82. [PMID: 9684890 PMCID: PMC2144058 DOI: 10.1002/pro.5560070711] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reverse transcriptase is an essential retroviral enzyme that uses RNA- and DNA-directed DNA polymerase activities as well as an RNaseH activity to synthesize a double-stranded DNA copy of the single-stranded RNA genome. In an effort to obtain high-resolution structural information regarding the polymerase active site of reverse transcriptase, we have pursued studies on a catalytic fragment from Moloney murine leukemia virus reverse transcriptase. DNA encoding the catalytic fragment, defined originally by limited proteolytic digestion, has been cloned, and the protein has been expressed and purified from Escherichia coli. The fragment obtained by limited proteolytic digestion and the bacterially expressed fragnment retain polymerase activity. Crystallization studies involving nucleic acid complexes with a catalytic fragment from both sources are reported, including variables screened to improve crystals and cryocooling. Three crystal forms of catalytic fragment-nucleic acid complexes have been characterized, which all contain at least two protein molecules in the asymmetric unit. As isolated, the catalytic fragment is monomeric. This analysis indicates that the enzyme dimerizes in the presence of nucleic acid.
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Affiliation(s)
- D Sun
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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41
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Brautigam CA, Steitz TA. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr Opin Struct Biol 1998; 8:54-63. [PMID: 9519297 DOI: 10.1016/s0959-440x(98)80010-9] [Citation(s) in RCA: 314] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
New levels in the understanding of DNA replication have been achieved from recent crystal structure determinations of several DNA polymerases and their substrate complexes. The structure of an alpha family DNA polymerase from bacteriophage RB69 shows some similarities, but also considerable differences in structure and organization from the pol I family DNA polymerases. Also, the functions of three polymerase domains and their conserved residues have been clarified by studying structures of pol I family DNA polymerases complexed to their substrates. These structures also confirm that an identical two-metal ion catalytic mechanism proposed previously is used by both the nonhomologous pol I and pol beta family DNA polymerases.
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Affiliation(s)
- C A Brautigam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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42
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Jeruzalmi D, Steitz TA. Use of organic cosmotropic solutes to crystallize flexible proteins: application to T7 RNA polymerase and its complex with the inhibitor T7 lysozyme. J Mol Biol 1997; 274:748-56. [PMID: 9405156 DOI: 10.1006/jmbi.1997.1366] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have crystallized, using several approaches that may be of general interest, T7 RNA polymerase (T7RP) and the T7 RNA polymerase-T7 lysozyme complex (T7RPL) in forms suitable for structure determination by X-ray crystallography. A series of polyhydric alcohols, sugars, amino and methylamino acids, compounds known to stabilize protein structure, were found to be critical for both crystallization and subsequent improvement of the crystal's diffraction resolution. Moreover, optimal crystallogenesis was achieved through an unconventional "reverse" vapor diffusion sitting drop method that is suitable for proteins that are insoluble at low ionic strength.T7RP has been crystallized in an orthorhombic form (I), space group P222, with cell parameters a=220 A, b=205 A, c=67 A and a monoclinic form (II), space group P21, with cell parameters a=229 A, b=205 A, c=70 A, beta=106 degrees. Crystal form I diffracts X-rays to 3.5 A and form II to 6.0 A. Three and six copies of the polymerase are predicted to be in the asymmetric unit forms I and II, respectively. Three monoclinic crystal forms of the T7RPL complex have been obtained in space group C2. Form I has cell parameters a=320 A, b=93 A, c=229 A, beta=129 degrees, form II has parameters a=293 A, b=93 A, c=68 A, beta=93 degrees, and form III has parameters a=270 A, b=93 A, c=63 A, beta=103 degrees. Crystal form I diffracts synchrotron wiggler radiation to 3.2 A and form III to 2.8 A. Calculations of crystal density imply three or four copies of the complex in form I and one copy in the asymmetric unit of forms II and III.
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Affiliation(s)
- D Jeruzalmi
- Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA
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43
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Janin YL, Aubertin AM, Chiaroni A, Riche C, Monneret C, Bisagni E, Grierson DS. Imidazo[1,5-g][1,4]diazepines, TIBO analogues lacking the phenyl ring: synthesis and evaluation as anti-HIV agents. Tetrahedron 1996. [DOI: 10.1016/s0040-4020(96)00952-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Hsiou Y, Ding J, Das K, Clark AD, Hughes SH, Arnold E. Structure of unliganded HIV-1 reverse transcriptase at 2.7 A resolution: implications of conformational changes for polymerization and inhibition mechanisms. Structure 1996; 4:853-60. [PMID: 8805568 DOI: 10.1016/s0969-2126(96)00091-3] [Citation(s) in RCA: 232] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND HIV-1 reverse transcriptase (RT) is a major target for anti-HIV drugs. A considerable amount of information about the structure of RT is available, both unliganded and in complex with template-primer or non-nucleoside RT inhibitors (NNRTIs). But significant conformational differences in the p66 polymerase domain among the unliganded structures have complicated the interpretation of these data, leading to different proposals for the mechanisms of polymerization and inhibition. RESULTS We report the structure of an unliganded RT at 2.7 A resolution, crystallized in space group C2 with a crystal packing similar to that of the RT-NNRTI complexes. The p66 thumb subdomain is folded into the DNA-binding cleft. Comparison of the unliganded RT structures with the DNA-bound RT and the NNRTI-bound RT structures reveals that the p66 thumb subdomain can exhibit two different upright conformations. In the DNA-bound RT, the p66 thumb subdomain adopts an upright position that can be described as resulting from a rigid-body rotation of the p66 thumb along the "thumb's knuckle' located near residues Trp239 (in strand beta 14) and Val317 (in beta 15) compared with the thumb position in the unliganded RT structure. NNRTI binding induces an additional hinge movement of the p66 thumb near the thumb's knuckle, causing the p66 thumb to adopt a configuration that is even more extended than in the DNA-bound RT structure. CONCLUSIONS The p66 thumb subdomain is extremely flexible. NNRTI binding induces both short-range and long-range structural distortions in several domains of RT, which are expected to alter the position and conformation of the template-primer. These changes may account for the inhibition of polymerization and the alteration of the cleavage specificity of RNase H by NNRTI binding.
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Affiliation(s)
- Y Hsiou
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
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45
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Rejto PA, Freer ST. Protein conformational substates from X-ray crystallography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1996; 66:167-96. [PMID: 9175428 DOI: 10.1016/s0079-6107(97)85629-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- P A Rejto
- Agouron Pharmaceuticals Inc., San Diego, CA 92121-1121, USA
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46
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Kroeger Smith MB, Rouzer CA, Taneyhill LA, Smith NA, Hughes SH, Boyer PL, Janssen PA, Moereels H, Koymans L, Arnold E. Molecular modeling studies of HIV-1 reverse transcriptase nonnucleoside inhibitors: total energy of complexation as a predictor of drug placement and activity. Protein Sci 1995; 4:2203-22. [PMID: 8535257 PMCID: PMC2142988 DOI: 10.1002/pro.5560041026] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Computer modeling studies have been carried out on three nonnucleoside inhibitors complexed with human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), using crystal coordinate data from a subset of the protein surrounding the binding pocket region. Results from the minimizations of solvated complexes of 2-cyclopropyl-4-methyl-5,11-dihydro-5H-dipyrido[3,2-b :2',3'-e][1,4] diazepin-6-one (nevirapine), alpha-anilino-2, 6-dibromophenylacetamide (alpha-APA), and 8-chloro-tetrahydro-imidazo(4,5,1-jk)(1,4)-benzodiazepin-2(1H)-thi one (TIBO) show that all three inhibitors maintain a very similar conformational shape, roughly overlay each other in the binding pocket, and appear to function as pi-electron donors to aromatic side-chain residues surrounding the pocket. However, side-chain residues adapt to each bound inhibitor in a highly specific manner, closing down around the surface of the drug to make tight van der Waals contacts. Consequently, the results from the calculated minimizations reveal that only when the inhibitors are modeled in a site constructed from coordinate data obtained from their particular RT complex can the calculated binding energies be relied upon to predict the correct orientation of the drug in the pocket. In the correct site, these binding energies correlate with EC50 values determined for all three inhibitors in our laboratory. Analysis of the components of the binding energy reveals that, for all three inhibitors, solvation of the drug is endothermic, but solvation of the protein is exothermic, and the sum favors complex formation. In general, the protein is energetically more stable and the drug less stable in their complexes as compared to the reactant conformations. For all three inhibitors, interaction with the protein in the complex is highly favorable. Interactions of the inhibitors with individual residues correlate with crystallographic and site-specific mutational data. pi-Stacking interactions are important in binding and correlate with drug HOMO RHF/6-31G* energies. Modeling results are discussed with respect to the mechanism of complex formation and the design of nonnucleoside inhibitors that will be more effective against mutants of HIV-1 RT that are resistant to the currently available drugs.
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Affiliation(s)
- M B Kroeger Smith
- ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, Maryland 21702, USA
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47
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Georgiadis MM, Jessen SM, Ogata CM, Telesnitsky A, Goff SP, Hendrickson WA. Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase. Structure 1995; 3:879-92. [PMID: 8535782 DOI: 10.1016/s0969-2126(01)00223-4] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Although the overall organization of HIV-1 RT is known from previously reported crystal structures, no structure of a complex including a metal ion, which is essential for its catalytic activity, has been reported. RESULTS Here we describe the structures at 1.8 Angstrum resolution of a catalytically active fragment of RT from Moloney murine leukemia virus (MMLV) and at 2.6 Angstrum of a complex of this fragment with Mn2+ coordinated in the polymerase active site. On the basis of similarities with HIV-1 RT and rat DNA polymerase beta, we have modeled template/primer and deoxyribonucleoside 5'-triphosphate substrates into the MMLV RT structure. CONCLUSIONS Our model, in the context of the disposition of evolutionarily conserved residues seen here at high resolution, provides new insights into the mechanisms of catalysis, fidelity, processivity and discrimination between deoxyribose and ribose nucleotides.
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Affiliation(s)
- M M Georgiadis
- Waksman Institute, Rutgers University, Piscataway, NJ 08855, USA
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48
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Ding J, Das K, Moereels H, Koymans L, Andries K, Janssen PA, Hughes SH, Arnold E. Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors. NATURE STRUCTURAL BIOLOGY 1995; 2:407-15. [PMID: 7545077 DOI: 10.1038/nsb0595-407] [Citation(s) in RCA: 252] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report the structure of HIV-1 reverse transcriptase (RT) complexed with the nonnucleoside inhibitor TIBO R 86183 at 3.0 A resolution. Comparing this structure with those of complexes of HIV-1 RT/alpha-APA R 95845 and HIV-1 RT/nevirapine provides a basis for understanding the nature of nonnucleoside inhibitor binding, the structure of the binding site and the interactions between the bound inhibitors and surrounding amino acid residues as well as for understanding mechanisms of inhibition by and resistance to nonnucleoside inhibitors. All three inhibitors considered assume a similar butterfly-like shape and bind to HIV-1 RT in a very similar way. Important differences occur in the conformation of amino acid residues that form the binding pocket.
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Affiliation(s)
- J Ding
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, New Jersey 08854-5638, USA
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49
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Ding J, Das K, Tantillo C, Zhang W, Clark AD, Jessen S, Lu X, Hsiou Y, Jacobo-Molina A, Andries K. Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution. Structure 1995; 3:365-79. [PMID: 7542140 DOI: 10.1016/s0969-2126(01)00168-x] [Citation(s) in RCA: 185] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that copies the RNA genome of HIV-1 into DNA. It is a heterodimer composed of a 66 kDa (p66) and a 51 kDa (p51) subunit. HIV-1 RT is a crucial target for structure-based drug design, and potent inhibitors have been identified, whose efficacy, however, is limited by drug resistance. RESULTS The crystal structure of HIV-1 RT in complex with the non-nucleoside inhibitor alpha-anilinophenyl-acetamide (alpha-APA) R95845 has been determined at 2.8 A resolution. The inhibitor binds in a hydrophobic pocket near the polymerase active site. The pocket contains five aromatic amino acid residues and the interactions of the side chains of these residues with the aromatic rings of non-nucleoside inhibitors appear to be important for inhibitor binding. Most of the amino acid residues where mutations have been correlated with high levels of resistance to non-nucleoside inhibitors of HIV-1 RT are located close to alpha-APA. The overall fold of HIV-1 RT in complex with alpha-APA is similar to that found when in complex with nevirapine, another non-nucleoside inhibitor, but there are significant conformational changes relative to an HIV-1 RT/DNA/Fab complex. CONCLUSIONS The non-nucleoside inhibitor-binding pocket has a flexible structure whose mobility may be required for effective polymerization, and may be part of a hinge that permits relative movements of two subdomains of the p66 subunit denoted the 'palm' and 'thumb'. An understanding of the structure of the inhibitor-binding pocket, of the interactions between HIV-1 RT and alpha-APA, and of the locations of mutations that confer resistance to inhibitors provides a basis for structure-based design of chemotherapeutic agents for the treatment of AIDS.
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Affiliation(s)
- J Ding
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ 08854-5638, USA
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50
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Arnold E, Ding J, Hughes SH, Hostomsky Z. Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates. Curr Opin Struct Biol 1995; 5:27-38. [PMID: 7539708 DOI: 10.1016/0959-440x(95)80006-m] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DNA and RNA polymerases are enzymes that are primarily responsible for copying genetic material in all living systems. The four polymerases whose structures have been determined by X-ray crystallographic methods have significant similarities at the polymerase active site that are indicative of common requirements for polynucleotide synthesis. Structural studies of complexes of the Klenow fragment of Escherichia coli DNA polymerase I, HIV type 1 reverse transcriptase, and rat DNA polymerase beta with DNA are leading to generalized models for catalysis.
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Affiliation(s)
- E Arnold
- Center for Advanced Biotechnology and Medicine and Rutgers University Chemistry Department, Piscataway, NJ 08854-5638, USA
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