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James L Keck - One of the best experts on this subject based on the ideXlab platform.
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structural and functional studies of h seropedicae reca protein insights into the Polymerization of reca protein as nucleoprotein filament
PLOS ONE, 2016Co-Authors: Wellington Claiton Leite, Carolina W Galvao, Rafael Mazer Etto, Sindhu Chittenipattu, Tyler Stanage, M.berenice R Steffens, Sérgio Da Costa Saab, Jorge Iulek, James L KeckAbstract:The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 A resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal Polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular Mechanisms of Polymerization of bacterial RecA as a helical nucleoprotein filament.
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Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament
PLOS ONE, 2016Co-Authors: Wellington Claiton Leite, Carolina W Galvao, Rafael Mazer Etto, Tyler Stanage, Sindhu Chitteni-pattu, M.berenice R Steffens, Sérgio Da Costa Saab, Jorge Iulek, James L KeckAbstract:The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 A resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal Polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular Mechanisms of Polymerization of bacterial RecA as a helical nucleoprotein filament.
Edward Arnold - One of the best experts on this subject based on the ideXlab platform.
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structure and function of hiv 1 reverse transcriptase molecular Mechanisms of Polymerization and inhibition
Journal of Molecular Biology, 2009Co-Authors: Stefan G Sarafianos, Bruno Marchand, Kalyan Das, Daniel M Himmel, Michael A Parniak, Stephen H Hughes, Edward ArnoldAbstract:The rapid replication of HIV-1 and the errors made during viral replication cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. In the absence of an effective vaccine, drugs are the only useful treatment. Anti-HIV drugs work; so far drug therapy has saved more than three million years of life. Unfortunately, HIV-1 develops resistance to all of the available drugs. Although a number of useful anti-HIV drugs have been approved for use in patients, the problems associated with drug toxicity and the development of resistance means that the search for new drugs is an ongoing process. The three viral enzymes, reverse transcriptase (RT), integrase (IN), and protease (PR) are all good drug targets. Two distinct types of RT inhibitors, both of which block the polymerase activity of RT, have been approved to treat HIV-1 infections, nucleoside analogs (NRTIs) and nonnucleosides (NNRTIs), and there are promising leads for compounds that either block the RNase H activity or block the polymerase in other ways. A better understanding of the structure and function(s) of RT and of the mechanism(s) of inhibition can be used to generate better drugs; in particular, drugs that are effective against the current drug-resistant strains of HIV-1.
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structure of unliganded hiv 1 reverse transcriptase at 2 7 a resolution implications of conformational changes for Polymerization and inhibition Mechanisms
Structure, 1996Co-Authors: Y Hsiou, Kalyan Das, Stephen H Hughes, Jianping Ding, Arthur D Clark, Edward ArnoldAbstract: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 β 14) and Val317 (in β 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. Conclusion 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.
Stanislaw Penczek - One of the best experts on this subject based on the ideXlab platform.
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Glossary of terms related to kinetics, thermodynamics, and Mechanisms of Polymerization (IUPAC Recommendations 2008)
Pure and Applied Chemistry, 2008Co-Authors: Stanislaw Penczek, Graeme MoadAbstract:This document presents recommended definitions of basic terms related to Polymerization processes. Recent developments relating to the kinetics, thermodynamics, and Mechanisms of Polymerization have necessitated the introduction of new terms and some revision or augmentation of terms previously defined in the Compendium of Chemical Terminology (the "Gold Book") or the IUPAC "Glossary of Basic Terms in Polymer Science".
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glossary of terms related to kinetics thermodynamics and Mechanisms of Polymerization
Pure and Applied Chemistry, 2008Co-Authors: Stanislaw Penczek, Graeme Moad, Marc Baron, K Hatada, Michael Hess, A D Jenkins, Richard J Jones, J Kahovec, Pavel Kratochvil, Przemyslaw KubisaAbstract:Abstract : This document presents recommended definitions of basic terms relatedto Polymerization processes. Recent developments relating to the kinetics, thermo-dynamics, and Mechanisms of Polymerization have necessitated the introductionof new terms and some revision or augmentation of terms previously defined in the Compendium of Chemical Terminology (the “Gold Book”) or the IUPAC“Glossary of Basic Terms in Polymer Science”. Keywords : kinetics; Polymerization; Mechanisms; glossary; thermodynamics;IUPAC Polymer Division. INTRODUCTION This document presents recommended definitions of basic terms related to Polymerization processes,principally to the kinetics, thermodynamics, and Mechanisms of Polymerization. Polymerizationprocesses have specific features which dictate that the definitions of terms presented here differ, in someinstances, from the general definitions provided in the Compendium of Chemical Terminology (the“Gold Book”) [1]. Some terms defined in the present document were also included in previous IUPACrecommendations, particularly in the “Glossary of Basic Terms in Polymer Science” (the “Glossary”)[2] and the “Basic Classification and Definitions of Polymerization Reactions”[3]. In most cases, thepreviously given definitions have been retained but, in a few cases, the development of the field has re-quired changes. Those definitions from the Gold Book and the Glossary that have been changed are pro-vided in appendices to the present document.The terms defined in this document are presented in alphabetical order. Italic typeface is used forcross-references to terms defined elsewhere in the document.
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Terminology of kinetics, thermodynamics, and Mechanisms of Polymerization
Journal of Polymer Science Part A: Polymer Chemistry, 2002Co-Authors: Stanislaw PenczekAbstract:This article, after a short introduction, written by a coordinator of the International Union of Pure and Applied Chemistry (IUPAC) Project devoted to the Terminology of the Kinetics, Thermodynamics, and Mechanisms of Polymerization presents the Provisional Document prepared by the IUPAC Macromolecular Division (Commission Nomenclature). It contains 95 entries, from “activated monomer Polymerization” to “zwitterionic Polymerization.” © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1665–1676, 2002
Wellington Claiton Leite - One of the best experts on this subject based on the ideXlab platform.
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structural and functional studies of h seropedicae reca protein insights into the Polymerization of reca protein as nucleoprotein filament
PLOS ONE, 2016Co-Authors: Wellington Claiton Leite, Carolina W Galvao, Rafael Mazer Etto, Sindhu Chittenipattu, Tyler Stanage, M.berenice R Steffens, Sérgio Da Costa Saab, Jorge Iulek, James L KeckAbstract:The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 A resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal Polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular Mechanisms of Polymerization of bacterial RecA as a helical nucleoprotein filament.
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Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament
PLOS ONE, 2016Co-Authors: Wellington Claiton Leite, Carolina W Galvao, Rafael Mazer Etto, Tyler Stanage, Sindhu Chitteni-pattu, M.berenice R Steffens, Sérgio Da Costa Saab, Jorge Iulek, James L KeckAbstract:The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 A resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal Polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular Mechanisms of Polymerization of bacterial RecA as a helical nucleoprotein filament.
Graeme Moad - One of the best experts on this subject based on the ideXlab platform.
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glossary of terms related to kinetics thermodynamics and Mechanisms of Polymerization
Pure and Applied Chemistry, 2008Co-Authors: Stanislaw Penczek, Graeme Moad, Marc Baron, K Hatada, Michael Hess, A D Jenkins, Richard J Jones, J Kahovec, Pavel Kratochvil, Przemyslaw KubisaAbstract:Abstract : This document presents recommended definitions of basic terms relatedto Polymerization processes. Recent developments relating to the kinetics, thermo-dynamics, and Mechanisms of Polymerization have necessitated the introductionof new terms and some revision or augmentation of terms previously defined in the Compendium of Chemical Terminology (the “Gold Book”) or the IUPAC“Glossary of Basic Terms in Polymer Science”. Keywords : kinetics; Polymerization; Mechanisms; glossary; thermodynamics;IUPAC Polymer Division. INTRODUCTION This document presents recommended definitions of basic terms related to Polymerization processes,principally to the kinetics, thermodynamics, and Mechanisms of Polymerization. Polymerizationprocesses have specific features which dictate that the definitions of terms presented here differ, in someinstances, from the general definitions provided in the Compendium of Chemical Terminology (the“Gold Book”) [1]. Some terms defined in the present document were also included in previous IUPACrecommendations, particularly in the “Glossary of Basic Terms in Polymer Science” (the “Glossary”)[2] and the “Basic Classification and Definitions of Polymerization Reactions”[3]. In most cases, thepreviously given definitions have been retained but, in a few cases, the development of the field has re-quired changes. Those definitions from the Gold Book and the Glossary that have been changed are pro-vided in appendices to the present document.The terms defined in this document are presented in alphabetical order. Italic typeface is used forcross-references to terms defined elsewhere in the document.
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Glossary of terms related to kinetics, thermodynamics, and Mechanisms of Polymerization (IUPAC Recommendations 2008)
Pure and Applied Chemistry, 2008Co-Authors: Stanislaw Penczek, Graeme MoadAbstract:This document presents recommended definitions of basic terms related to Polymerization processes. Recent developments relating to the kinetics, thermodynamics, and Mechanisms of Polymerization have necessitated the introduction of new terms and some revision or augmentation of terms previously defined in the Compendium of Chemical Terminology (the "Gold Book") or the IUPAC "Glossary of Basic Terms in Polymer Science".