1
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Pedersen LC, Yi M, Pedersen LG, Kaminski AM. From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function. Drug Metab Dispos 2022; 50:1027-1041. [PMID: 35197313 PMCID: PMC10753775 DOI: 10.1124/dmd.121.000478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation of endogenous compounds such as steroids, neurotransmitters, hormones, and bile acids as well as xenobiotics including drugs, toxins, and environmental chemicals. The Golgi associated membrane-bound sulfotransferases are involved in post-translational modification of macromolecules from glycosaminoglycans to proteins. The sulfation of small molecules can have profound biologic effects on the functionality of the acceptor, including activation, deactivation, or enhanced metabolism and elimination. Sulfation of macromolecules has been shown to regulate a number of physiologic and pathophysiological pathways by enhancing binding affinity to regulatory proteins or binding partners. Over the last 25 years, crystal structures of these enzymes have provided a wealth of information on the mechanisms of this process and the specificity of these enzymes. This review will focus on the general commonalities of the sulfotransferases, from enzyme structure to catalytic mechanism as well as providing examples into how structural information is being used to either design drugs that inhibit sulfotransferases or to modify the enzymes to improve drug synthesis. SIGNIFICANCE STATEMENT: This manuscript honors Dr. Masahiko Negishi's contribution to the understanding of sulfotransferase mechanism, specificity, and roles in biology by analyzing the crystal structures that have been solved over the last 25 years.
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Affiliation(s)
- Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - MyeongJin Yi
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Lee G Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Andrea M Kaminski
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
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2
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Markova M, von Neumann-Cosel P, Larsen AC, Bassauer S, Görgen A, Guttormsen M, Bello Garrote FL, Berg HC, Bjørøen MM, Dahl-Jacobsen T, Eriksen TK, Gjestvang D, Isaak J, Mbabane M, Paulsen W, Pedersen LG, Pettersen NIJ, Richter A, Sahin E, Scholz P, Siem S, Tveten GM, Valsdottir VM, Wiedeking M, Zeiser F. Comprehensive Test of the Brink-Axel Hypothesis in the Energy Region of the Pygmy Dipole Resonance. Phys Rev Lett 2021; 127:182501. [PMID: 34767384 DOI: 10.1103/physrevlett.127.182501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
The validity of the Brink-Axel hypothesis, which is especially important for numerous astrophysical calculations, is addressed for ^{116,120,124}Sn below the neutron separation energy by means of three independent experimental methods. The γ-ray strength functions (GSFs) extracted from primary γ-decay spectra following charged-particle reactions with the Oslo method and with the shape method demonstrate excellent agreement with those deduced from forward-angle inelastic proton scattering at relativistic beam energies. In addition, the GSFs are shown to be independent of excitation energies and spins of the initial and final states. The results provide a critical test of the generalized Brink-Axel hypothesis in heavy nuclei, demonstrating its applicability in the energy region of the pygmy dipole resonance.
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Affiliation(s)
- M Markova
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - P von Neumann-Cosel
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - A C Larsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - S Bassauer
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - A Görgen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - M Guttormsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | | | - H C Berg
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - M M Bjørøen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - T Dahl-Jacobsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - T K Eriksen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - D Gjestvang
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - J Isaak
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - M Mbabane
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - W Paulsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - L G Pedersen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - N I J Pettersen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - A Richter
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - E Sahin
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - P Scholz
- Institut für Kernphysik, Universität zu Köln, D-50937 Köln, Germany
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
| | - S Siem
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - G M Tveten
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - V M Valsdottir
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - M Wiedeking
- Department of Subatomic Physics, iThemba LABS, Somerset West 7129, South Africa
- School of Physics, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - F Zeiser
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
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3
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Butler PA, Gaffney LP, Spagnoletti P, Konki J, Scheck M, Smith JF, Abrahams K, Bowry M, Cederkäll J, Chupp T, de Angelis G, De Witte H, Garrett PE, Goldkuhle A, Henrich C, Illana A, Johnston K, Joss DT, Keatings JM, Kelly NA, Komorowska M, Kröll T, Lozano M, Singh BSN, O'Donnell D, Ojala J, Page RD, Pedersen LG, Raison C, Reiter P, Rodriguez JA, Rosiak D, Rothe S, Shneidman TM, Siebeck B, Seidlitz M, Sinclair J, Stryjczyk M, Van Duppen P, Vinals S, Virtanen V, Warr N, Wrzosek-Lipska K, Zielinska M. Publisher Correction: The observation of vibrating pear-shapes in radon nuclei. Nat Commun 2020; 11:5185. [PMID: 33037232 PMCID: PMC7547707 DOI: 10.1038/s41467-020-19081-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- P A Butler
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK.
| | - L P Gaffney
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK.,CERN, Geneva, 23 CH-1211, Switzerland
| | - P Spagnoletti
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J Konki
- CERN, Geneva, 23 CH-1211, Switzerland
| | - M Scheck
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J F Smith
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - K Abrahams
- Department of Physics & Astronomy, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa
| | - M Bowry
- TRIUMF, Vancouver, V6T 2A3, BC, Canada
| | - J Cederkäll
- Physics Department, Lund University, Box 118, Lund, SE-221 00, Sweden
| | - T Chupp
- Department of Physics, University of Michigan, Ann Arbor, 48104 MI, USA
| | - G de Angelis
- INFN Laboratori Nazionali di Legnaro, Legnaro, 35020 PD, Italy
| | - H De Witte
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - P E Garrett
- Department of Physics, University of Guelph, Guelph, N1G 2W1, Ontario, Canada
| | - A Goldkuhle
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - C Henrich
- Institut für Kernphysik, Technische Universität Darmstadt, Darmstadt, 64289, Germany
| | - A Illana
- INFN Laboratori Nazionali di Legnaro, Legnaro, 35020 PD, Italy
| | | | - D T Joss
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK
| | - J M Keatings
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - N A Kelly
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - M Komorowska
- Heavy Ion Laboratory, University of Warsaw, Warsaw, PL-02-093, Poland
| | - T Kröll
- Institut für Kernphysik, Technische Universität Darmstadt, Darmstadt, 64289, Germany
| | - M Lozano
- CERN, Geneva, 23 CH-1211, Switzerland
| | - B S Nara Singh
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - D O'Donnell
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J Ojala
- Department of Physics, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, FIN-40014, Finland.,Helsinki Institute of Physics, P.O. Box 64, Helsinki, FIN-00014, Finland
| | - R D Page
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK
| | - L G Pedersen
- Department of Physics, University of Oslo, P.O. Box 1048, Oslo, N-0316, Norway
| | - C Raison
- Department of Physics, University of York, York, YO10 5DD, UK
| | - P Reiter
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | | | - D Rosiak
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - S Rothe
- CERN, Geneva, 23 CH-1211, Switzerland
| | | | - B Siebeck
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - M Seidlitz
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - J Sinclair
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - M Stryjczyk
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - P Van Duppen
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - S Vinals
- Consejo Superior De Investigaciones Científicas, Madrid, S 28040, Spain
| | - V Virtanen
- Department of Physics, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, FIN-40014, Finland.,Helsinki Institute of Physics, P.O. Box 64, Helsinki, FIN-00014, Finland
| | - N Warr
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - K Wrzosek-Lipska
- Heavy Ion Laboratory, University of Warsaw, Warsaw, PL-02-093, Poland
| | - M Zielinska
- IRFU CEA, Université Paris-Saclay, Gif-sur-Yvette, F-91191, France
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4
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Butler PA, Gaffney LP, Spagnoletti P, Konki J, Scheck M, Smith JF, Abrahams K, Bowry M, Cederkäll J, Chupp T, de Angelis G, De Witte H, Garrett PE, Goldkuhle A, Henrich C, Illana A, Johnston K, Joss DT, Keatings JM, Kelly NA, Komorowska M, Kröll T, Lozano M, Singh BSN, O'Donnell D, Ojala J, Page RD, Pedersen LG, Raison C, Reiter P, Rodriguez JA, Rosiak D, Rothe S, Shneidman TM, Siebeck B, Seidlitz M, Sinclair J, Stryjczyk M, Van Duppen P, Vinals S, Virtanen V, Warr N, Wrzosek-Lipska K, Zielinska M. Addendum: The observation of vibrating pear-shapes in radon nuclei. Nat Commun 2020; 11:3560. [PMID: 32661232 PMCID: PMC7359340 DOI: 10.1038/s41467-020-17309-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- P A Butler
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK.
| | - L P Gaffney
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK.,CERN, Geneva, 23 CH-1211, Switzerland
| | - P Spagnoletti
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J Konki
- CERN, Geneva, 23 CH-1211, Switzerland
| | - M Scheck
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J F Smith
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - K Abrahams
- Department of Physics & Astronomy, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa
| | - M Bowry
- TRIUMF, Vancouver, V6T 2A3, BC, Canada
| | - J Cederkäll
- Physics Department, Lund University, Box 118, Lund, SE-221 00, Sweden
| | - T Chupp
- Department of Physics, University of Michigan, Ann Arbor, 48104, MI, USA
| | - G de Angelis
- INFN Laboratori Nazionali di Legnaro, Legnaro, 35020 PD, Italy
| | - H De Witte
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - P E Garrett
- Department of Physics, University of Guelph, Guelph, N1G 2W1, Ontario, Canada
| | - A Goldkuhle
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - C Henrich
- Institut für Kernphysik, Technische Universität Darmstadt, Darmstadt, 64289, Germany
| | - A Illana
- INFN Laboratori Nazionali di Legnaro, Legnaro, 35020 PD, Italy
| | | | - D T Joss
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK
| | - J M Keatings
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - N A Kelly
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - M Komorowska
- Heavy Ion Laboratory, University of Warsaw, Warsaw, PL-02-093, Poland
| | - T Kröll
- Institut für Kernphysik, Technische Universität Darmstadt, Darmstadt, 64289, Germany
| | - M Lozano
- CERN, Geneva, 23 CH-1211, Switzerland
| | - B S Nara Singh
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - D O'Donnell
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J Ojala
- Department of Physics, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, FIN-40014, Finland.,Helsinki Institute of Physics, P.O. Box 64, Helsinki, FIN-00014, Finland
| | - R D Page
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK
| | - L G Pedersen
- Department of Physics, University of Oslo, P.O. Box 1048, Oslo, N-0316, Norway
| | - C Raison
- Department of Physics, University of York, York, YO10 5DD, UK
| | - P Reiter
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | | | - D Rosiak
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - S Rothe
- CERN, Geneva, 23 CH-1211, Switzerland
| | | | - B Siebeck
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - M Seidlitz
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - J Sinclair
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - M Stryjczyk
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - P Van Duppen
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - S Vinals
- Consejo Superior De Investigaciones Científicas, Madrid, S 28040, Spain
| | - V Virtanen
- Department of Physics, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, FIN-40014, Finland.,Helsinki Institute of Physics, P.O. Box 64, Helsinki, FIN-00014, Finland
| | - N Warr
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - K Wrzosek-Lipska
- Heavy Ion Laboratory, University of Warsaw, Warsaw, PL-02-093, Poland
| | - M Zielinska
- IRFU CEA, Université Paris-Saclay, Gif-sur-Yvette, F-91191, France
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5
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Perera L, Beard WA, Pedersen LG, Shock DD, Wilson SH. Preferential DNA Polymerase β Reverse Reaction with Imidodiphosphate. ACS Omega 2020; 5:15317-15324. [PMID: 32637805 PMCID: PMC7331038 DOI: 10.1021/acsomega.0c01345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
DNA replication and repair reactions involve the addition of a deoxynucleoside monophosphate onto a growing DNA strand with the loss of pyrophosphate. This chemical reaction is also reversible; the addition of pyrophosphate generates a deoxynucleoside triphosphate, thereby shortening the DNA by one nucleotide. The forward DNA synthesis and reverse pyrophosphorolysis reactions strictly require the presence of divalent metals, usually magnesium, at the reactive center as cofactors. The overall equilibrium enzymatic reaction strongly favors DNA synthesis over pyrophosphorolysis with natural substrates. The DNA polymerase β chemical reaction has been structurally and kinetically characterized, employing natural and chemically modified substrates. Substituting an imido-moiety (NH) for the bridging oxygen between Pβ and Pγ of dGTP dramatically decreased the overall enzymatic activity and resulted in a chemical equilibrium that strongly favors the reverse reaction (i.e., K ≪ 1). Using QM/MM calculations in conjunction with the utilization of parameters such as quantum mechanically derived atomic charges, we have examined the chemical foundation for the altered equilibrium with this central biological reaction. The calculations indicate that the rapid reverse reaction is likely due, in part, to the increased nucleophilicity of the reactive oxygen on the tautomeric form of imidodiphosphate.
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Affiliation(s)
- Lalith Perera
- Genome
Integrity and Structural Biology Laboratory, National Institute of
Environmental Health Sciences, National
Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
| | - William A. Beard
- Genome
Integrity and Structural Biology Laboratory, National Institute of
Environmental Health Sciences, National
Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
| | - Lee G. Pedersen
- Genome
Integrity and Structural Biology Laboratory, National Institute of
Environmental Health Sciences, National
Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
- Department
of Chemistry, University of North Carolina
at Chapel Hill, Campus
Box 3290, Chapel Hill, North
Carolina 27599-3290, United States
| | - David D. Shock
- Genome
Integrity and Structural Biology Laboratory, National Institute of
Environmental Health Sciences, National
Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
| | - Samuel H. Wilson
- Genome
Integrity and Structural Biology Laboratory, National Institute of
Environmental Health Sciences, National
Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
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6
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Butler PA, Gaffney LP, Spagnoletti P, Abrahams K, Bowry M, Cederkäll J, de Angelis G, De Witte H, Garrett PE, Goldkuhle A, Henrich C, Illana A, Johnston K, Joss DT, Keatings JM, Kelly NA, Komorowska M, Konki J, Kröll T, Lozano M, Nara Singh BS, O'Donnell D, Ojala J, Page RD, Pedersen LG, Raison C, Reiter P, Rodriguez JA, Rosiak D, Rothe S, Scheck M, Seidlitz M, Shneidman TM, Siebeck B, Sinclair J, Smith JF, Stryjczyk M, Van Duppen P, Vinals S, Virtanen V, Warr N, Wrzosek-Lipska K, Zielińska M. Evolution of Octupole Deformation in Radium Nuclei from Coulomb Excitation of Radioactive ^{222}Ra and ^{228}Ra Beams. Phys Rev Lett 2020; 124:042503. [PMID: 32058764 DOI: 10.1103/physrevlett.124.042503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 06/10/2023]
Abstract
There is sparse direct experimental evidence that atomic nuclei can exhibit stable "pear" shapes arising from strong octupole correlations. In order to investigate the nature of octupole collectivity in radium isotopes, electric octupole (E3) matrix elements have been determined for transitions in ^{222,228}Ra nuclei using the method of sub-barrier, multistep Coulomb excitation. Beams of the radioactive radium isotopes were provided by the HIE-ISOLDE facility at CERN. The observed pattern of E3 matrix elements for different nuclear transitions is explained by describing ^{222}Ra as pear shaped with stable octupole deformation, while ^{228}Ra behaves like an octupole vibrator.
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Affiliation(s)
- P A Butler
- University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - L P Gaffney
- University of Liverpool, Liverpool L69 7ZE, United Kingdom
- ISOLDE, CERN, 1211 Geneva 23, Switzerland
| | - P Spagnoletti
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | - K Abrahams
- University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - M Bowry
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
- TRIUMF, Vancouver V6T 2A3 BC, Canada
| | - J Cederkäll
- Lund University, Box 118, Lund SE-221 00, Sweden
| | - G de Angelis
- INFN Laboratori Nazionali di Legnaro, Legnaro 35020 PD, Italy
| | | | - P E Garrett
- University of Guelph, Guelph N1G 2W1 Ontario, Canada
| | - A Goldkuhle
- University of Cologne, Cologne 50937, Germany
| | - C Henrich
- Technische Universität Darmstadt, Darmstadt 64289, Germany
| | - A Illana
- INFN Laboratori Nazionali di Legnaro, Legnaro 35020 PD, Italy
| | - K Johnston
- ISOLDE, CERN, 1211 Geneva 23, Switzerland
| | - D T Joss
- University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - J M Keatings
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | - N A Kelly
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | - M Komorowska
- Heavy Ion Laboratory, University of Warsaw, Warsaw PL-02-093, Poland
| | - J Konki
- ISOLDE, CERN, 1211 Geneva 23, Switzerland
| | - T Kröll
- Technische Universität Darmstadt, Darmstadt 64289, Germany
| | - M Lozano
- ISOLDE, CERN, 1211 Geneva 23, Switzerland
| | - B S Nara Singh
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | - D O'Donnell
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | - J Ojala
- University of Jyvaskyla, P.O. Box 35, Jyvaskyla FIN-40014, Finland
- Helsinki Institute of Physics, P.O. Box 64, Helsinki FIN-00014, Finland
| | - R D Page
- University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - L G Pedersen
- University of Oslo, P.O. Box 1048, Oslo N-0316, Norway
| | - C Raison
- University of York, York YO10 5DD, United Kingdom
| | - P Reiter
- University of Cologne, Cologne 50937, Germany
| | | | - D Rosiak
- University of Cologne, Cologne 50937, Germany
| | - S Rothe
- ISOLDE, CERN, 1211 Geneva 23, Switzerland
| | - M Scheck
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | - M Seidlitz
- University of Cologne, Cologne 50937, Germany
| | - T M Shneidman
- Joint Institute for Nuclear Research, RU-141980 Dubna, Russian Federation
| | - B Siebeck
- University of Cologne, Cologne 50937, Germany
| | - J Sinclair
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | - J F Smith
- University of the West of Scotland, Paisley PA1 2BE, United Kingdom
| | | | | | - S Vinals
- Consejo Superior De Investigaciones Científicas, Madrid S28040, Spain
| | - V Virtanen
- University of Jyvaskyla, P.O. Box 35, Jyvaskyla FIN-40014, Finland
- Helsinki Institute of Physics, P.O. Box 64, Helsinki FIN-00014, Finland
| | - N Warr
- University of Cologne, Cologne 50937, Germany
| | - K Wrzosek-Lipska
- Heavy Ion Laboratory, University of Warsaw, Warsaw PL-02-093, Poland
| | - M Zielińska
- IRFU CEA, Université Paris-Saclay, Gif-sur-Yvette F-91191, France
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7
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Butler PA, Gaffney LP, Spagnoletti P, Konki J, Scheck M, Smith JF, Abrahams K, Bowry M, Cederkäll J, Chupp T, de Angelis G, De Witte H, Garrett PE, Goldkuhle A, Henrich C, Illana A, Johnston K, Joss DT, Keatings JM, Kelly NA, Komorowska M, Kröll T, Lozano M, Nara Singh BS, O'Donnell D, Ojala J, Page RD, Pedersen LG, Raison C, Reiter P, Rodriguez JA, Rosiak D, Rothe S, Shneidman TM, Siebeck B, Seidlitz M, Sinclair J, Stryjczyk M, Van Duppen P, Vinals S, Virtanen V, Warr N, Wrzosek-Lipska K, Zielinska M. The observation of vibrating pear-shapes in radon nuclei. Nat Commun 2019; 10:2473. [PMID: 31171788 PMCID: PMC6554308 DOI: 10.1038/s41467-019-10494-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/15/2019] [Indexed: 11/09/2022] Open
Abstract
There is a large body of evidence that atomic nuclei can undergo octupole distortion and assume the shape of a pear. This phenomenon is important for measurements of electric-dipole moments of atoms, which would indicate CP violation and hence probe physics beyond the Standard Model of particle physics. Isotopes of both radon and radium have been identified as candidates for such measurements. Here, we observed the low-lying quantum states in 224Rn and 226Rn by accelerating beams of these radioactive nuclei. We show that radon isotopes undergo octupole vibrations but do not possess static pear-shapes in their ground states. We conclude that radon atoms provide less favourable conditions for the enhancement of a measurable atomic electric-dipole moment.
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Affiliation(s)
- P A Butler
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK.
| | - L P Gaffney
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK.,CERN, Geneva 23, CH-1211, Switzerland
| | - P Spagnoletti
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J Konki
- CERN, Geneva 23, CH-1211, Switzerland
| | - M Scheck
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J F Smith
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - K Abrahams
- Department of Physics & Astronomy, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa
| | - M Bowry
- TRIUMF, Vancouver, V6T 2A3, BC, Canada
| | - J Cederkäll
- Physics Department, Lund University, Box 118, Lund, SE-221 00, Sweden
| | - T Chupp
- Department of Physics, University of Michigan, Ann Arbor, 48104, MI, USA
| | - G de Angelis
- INFN Laboratori Nazionali di Legnaro, Legnaro, 35020, PD, Italy
| | - H De Witte
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - P E Garrett
- Department of Physics, University of Guelph, Guelph, N1G 2W1, Ontario, Canada
| | - A Goldkuhle
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - C Henrich
- Institut für Kernphysik, Technische Universität Darmstadt, Darmstadt, 64289, Germany
| | - A Illana
- INFN Laboratori Nazionali di Legnaro, Legnaro, 35020, PD, Italy
| | | | - D T Joss
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK
| | - J M Keatings
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - N A Kelly
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - M Komorowska
- Heavy Ion Laboratory, University of Warsaw, Warsaw, PL-02-093, Poland
| | - T Kröll
- Institut für Kernphysik, Technische Universität Darmstadt, Darmstadt, 64289, Germany
| | - M Lozano
- CERN, Geneva 23, CH-1211, Switzerland
| | - B S Nara Singh
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - D O'Donnell
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - J Ojala
- Department of Physics, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, FIN-40014, Finland.,Helsinki Institute of Physics, P.O. Box 64, Helsinki, FIN-00014, Finland
| | - R D Page
- Oliver Lodge Laboratory, University of Liverpool, Liverpool, L69 7ZE, UK
| | - L G Pedersen
- Department of Physics, University of Oslo, P.O. Box 1048, Oslo, N-0316, Norway
| | - C Raison
- Department of Physics, University of York, York, YO10 5DD, UK
| | - P Reiter
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | | | - D Rosiak
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - S Rothe
- CERN, Geneva 23, CH-1211, Switzerland
| | | | - B Siebeck
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - M Seidlitz
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - J Sinclair
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - M Stryjczyk
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - P Van Duppen
- Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven, B-3001, Belgium
| | - S Vinals
- Consejo Superior De Investigaciones Científicas, Madrid, S 28040, Spain
| | - V Virtanen
- Department of Physics, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, FIN-40014, Finland.,Helsinki Institute of Physics, P.O. Box 64, Helsinki, FIN-00014, Finland
| | - N Warr
- Institute for Nuclear Physics, University of Cologne, Cologne, 50937, Germany
| | - K Wrzosek-Lipska
- Heavy Ion Laboratory, University of Warsaw, Warsaw, PL-02-093, Poland
| | - M Zielinska
- IRFU CEA, Université Paris-Saclay, Gif-sur-Yvette, F-91191, France
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8
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Kabis CW, Sarasua MM, Gottschalk KE, Bourne CD, Pedersen LG, Jackson CM, Hiskey RG, Koehler KA. A Kinetic Model Describing the Interaction of Bovine Prothrombin Fragment 1 with Calcium Ions. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1661228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryA kinetic model is derived for the interaction of bovine prothrombin fragment 1 with calcium ions. The model requires binding of a minimum of two calcium ions for induction of the observed biphasic fluorescence decrease as a function of time. The model is shown to be consistent with experimental kinetic and equilibrium data by fitting theoretical curves for the biphasic fluorescence change to the data through exact solution of the nonlinear differential rate equations derived from the model. The rate constants for the binding of these two required calcium ions are calculated from the solutions as best fit parameters. The thermodynamic equilibrium constants, K1 and K2, for the binding of these two calcium ions are calculated from ratios of the forward and reverse rate constants as 0.6 × 104 and 5.4 × 104, respectively. Thus, the model correctly predicts positively cooperative calcium ion binding for at least the two calcium ions required to induce fluorescence quenching.
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Affiliation(s)
- Charles W Kabis
- The Chemistry Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Martha M Sarasua
- The Chemistry Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- The School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Karen E Gottschalk
- The Chemistry Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- The School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolyn D Bourne
- The Chemistry Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lee G Pedersen
- The Chemistry Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Craig M Jackson
- The Department of Biological Chemistry, Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard G Hiskey
- The Chemistry Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Karl A Koehler
- The Biochemistry Department, Case Western Reserve University, School of Medicine, Cleveland, Ohio and Department of Surgery, Cleveland Metropolitan General Hospital, Cleveland, Ohio, USA
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9
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Perera L, Freudenthal BD, Beard WA, Pedersen LG, Wilson SH. Revealing the role of the product metal in DNA polymerase β catalysis. Nucleic Acids Res 2017; 45:2736-2745. [PMID: 28108654 PMCID: PMC5389463 DOI: 10.1093/nar/gkw1363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/28/2016] [Indexed: 11/14/2022] Open
Abstract
DNA polymerases catalyze a metal-dependent nucleotidyl transferase reaction during extension of a DNA strand using the complementary strand as a template. The reaction has long been considered to require two magnesium ions. Recently, a third active site magnesium ion was identified in some DNA polymerase product crystallographic structures, but its role is not known. Using quantum mechanical/ molecular mechanical calculations of polymerase β, we find that a third magnesium ion positioned near the newly identified product metal site does not alter the activation barrier for the chemical reaction indicating that it does not have a role in the forward reaction. This is consistent with time-lapse crystallographic structures following insertion of Sp-dCTPαS. Although sulfur substitution deters product metal binding, this has only a minimal effect on the rate of the forward reaction. Surprisingly, monovalent sodium or ammonium ions, positioned in the product metal site, lowered the activation barrier. These calculations highlight the impact that an active site water network can have on the energetics of the forward reaction and how metals or enzyme side chains may interact with the network to modulate the reaction barrier. These results also are discussed in the context of earlier findings indicating that magnesium at the product metal position blocks the reverse pyrophosphorolysis reaction.
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Affiliation(s)
- Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA
| | - Bret D Freudenthal
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA.,Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, 1080 HLSIC, Mailstop 3030, Kansas City, KS 66160-7421, USA
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA
| | - Lee G Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA.,Department of Chemistry, University of North Carolina at Chapel Hill, P.O. Box 3290, Chapel Hill, NC 27517, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA
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10
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11
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Abstract
The transfer of phosphate groups is an essential function of many intracellular biological enzymes. The transfer is in many cases facilitated by a protein scaffold involving two closely spaced magnesium "ions". It has long been a mystery how these "ions" can retain their closely spaced positions throughout enzymatic phosphate transfer: Coulomb's law would dictate large repulsive forces between these ions at the observed distances. Here we show, however, that the electron density can be borrowed from nearby electron-rich oxygens to populate a bonding molecular orbital that is largely localized between the magnesium "ions". The result is that the Mg-Mg core of these phosphate transfer enzymes is surprisingly similar to a metastable [Mg2]2+ ion in the gas phase, an ion that has been identified experimentally and studied with high-level quantum-mechanical calculations. This similarity is confirmed by comparative computations of the electron densities of [Mg2]2+ in the gas phase and the Mg-Mg core in the structures derived from QM/MM studies of high-resolution X-ray crystal structures. That there is a level of covalent bonding between the two Mg "ions" at the core of these enzymes is a novel concept that enables an improved vision of how these enzymes function at the molecular level. The concept is broader than magnesium-other biologically relevant metals (e.g., Mn and Zn) can also form similar stabilizing covalent Me-Me bonds in both organometallic and inorganic crystals.
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Affiliation(s)
- Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health , P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health , P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
| | - Lee G Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health , P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States.,Department of Chemistry, University of North Carolina at Chapel Hill , P.O. Box 3290, Chapel Hill, North Carolina 27517, United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health , P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, United States
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12
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Wu S, Shim JY, Lee CJ, Pedersen LG. Do the crystallographic forms of prethrombin-2 revert to a single form in solution? Biophys Chem 2015; 203-204:28-32. [PMID: 26025788 DOI: 10.1016/j.bpc.2015.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/12/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022]
Abstract
It has been earlier established (Pozzi et al. Biochemistry 50 (2011) 10195-10202) that prethrombin-2 crystallizes into two similar but distinct forms: a collapsed form and an alternative form. We employed long molecular dynamics (MD) simulations for these two forms to obtain solvent-equilibrated forms. We find that, at 200ns, the simulated solution collapsed form is quite similar to the X-ray crystal collapsed form, while the simulated solution alternative form deviates from the X-ray crystal alternative form as well as from the solution collapsed form. A detailed structural analysis suggests that the fluctuation of the 140s-loop, in cross-talk with the 220s-loop, may alter the conformation of the W215-E217 segment near the nascent thrombin active site. A rationale is provided for the manner in which interactions of prethrombin-2 with FVa may affect the equilibrium between the two forms of prethrombin-2.
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Affiliation(s)
- Sangwook Wu
- Department of Physics, Pukyong National University, Busan 608-737, Republic of Korea
| | - Joong-Youn Shim
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chang Jun Lee
- Department of Chemistry, Pohang University of Science and Technology, POSTECH, Pohang 790-784, Republic of Korea
| | - Lee G Pedersen
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.
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13
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Perera L, Beard WA, Pedersen LG, Wilson SH. Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization. Adv Protein Chem Struct Biol 2014; 97:83-113. [PMID: 25458356 PMCID: PMC5573153 DOI: 10.1016/bs.apcsb.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We review theoretical attempts to model the chemical insertion reactions of nucleoside triphosphates catalyzed by the nucleic acid polymerases using combined quantum mechanical/molecular mechanical methodology. Due to an existing excellent database of high-resolution X-ray crystal structures, the DNA polymerase β system serves as a useful template for discussion and comparison. The convergence of structures of high-quality complexes and continued developments of theoretical techniques suggest a bright future for understanding the global features of nucleic acid polymerization.
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Affiliation(s)
- Lalith Perera
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.
| | - William A Beard
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Lee G Pedersen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samuel H Wilson
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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14
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Wu S, Lee CJ, Pedersen LG. Analysis on long-range residue-residue communication using molecular dynamics. Proteins 2014; 82:2896-2901. [PMID: 24935629 DOI: 10.1002/prot.24629] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/03/2014] [Accepted: 06/08/2014] [Indexed: 11/08/2022]
Abstract
We investigated the possibility of inter-residue communication of side chains in barstar, an 89 residue protein, using mutual information theory. The normalized mutual information (NMI) of the dihedral angles of the side chains was obtained from all-atom molecular dynamics simulations. The accumulated NMI from an explicit solvent equilibrated trajectory (600 ns) with free backbone exhibits a parabola-shaped distribution over the inter-residue distances (0-36 Å): smaller at the end regimes but larger in the middle regime. This analysis, plus several other measures, does not find unusual long-range communication for free backbone in explicit solvent simulations.
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Affiliation(s)
- Sangwook Wu
- Department of Chemistry, University of North Carolina at Chapel Hill
| | - Chang Jun Lee
- Department of Chemistry, University of North Carolina at Chapel Hill
| | - Lee G Pedersen
- Department of Chemistry, University of North Carolina at Chapel Hill
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15
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Affiliation(s)
- S Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
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16
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Wu S, Beard WA, Pedersen LG, Wilson SH. Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site. Chem Rev 2013; 114:2759-74. [PMID: 24359247 DOI: 10.1021/cr3005179] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sangwook Wu
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
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17
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Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH. Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction. J Am Chem Soc 2013; 135:8078-88. [PMID: 23647366 DOI: 10.1021/ja403842j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA polymerase β (pol β) is a bifunctional enzyme widely studied for its roles in base excision DNA repair, where one key function is gap-filling DNA synthesis. In spite of significant progress in recent years, the atomic level mechanism of the DNA synthesis reaction has remained poorly understood. Based on crystal structures of pol β in complex with its substrates and theoretical considerations of amino acids and metals in the active site, we have proposed that a nearby carboxylate group of Asp256 enables the reaction by accepting a proton from the primer O3'group, thus activating O3'as the nucleophile in the reaction path. Here, we tested this proposal by altering the side chain of Asp256 to Glu and then exploring the impact of this conservative change on the reaction. The D256E enzyme is more than 1000-fold less active than the wild-type enzyme, and the crystal structures are subtly different in the active sites of the D256E and wild-type enzymes. Theoretical analysis of DNA synthesis by the D256E enzyme shows that the O3'proton still transfers to the nearby carboxylate of residue 256. However, the electrostatic stabilization and location of the O3' proton transfer during the reaction path are dramatically altered compared with wild-type. Surprisingly, this is due to repositioning of the Arg254 side chain in the Glu256 enzyme active site, such that Arg254 is not in position to stabilize the proton transfer from O3'. The theoretical results with the wild-type enzyme indicate an early charge reorganization associated with the O3' proton transfer, and this does not occur in the D256E enzyme. The charge reorganization is mediated by the catalytic magnesium ion in the active site.
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Affiliation(s)
- Vinod K Batra
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709-12233, USA
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18
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Lee CJ, Wu S, Bartolotti LJ, Pedersen LG. Molecular dynamic simulations of the binary complex of human tissue factor (TF(1-242) ) and factor VIIa (TF(1-242) /FVIIa) on a 4:1 POPC/POPS lipid bilayer. J Thromb Haemost 2012; 10:2402-5. [PMID: 22967237 PMCID: PMC3537916 DOI: 10.1111/j.1538-7836.2012.04920.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chang Jun Lee
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Sangwook Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Libero J. Bartolotti
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Lee G. Pedersen
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 USA
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19
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Wu S, Liu S, Sim S, Pedersen LG. Weakly Antiferromagentic Coupling Via Superexchange Interaction Between Mn(II)-Mn(II) Atoms: A QM/MM Study of the Active Site of Human Cytosolic X-Propyl Aminopeptidase P. J Phys Chem Lett 2012; 3:2293-2297. [PMID: 23145216 PMCID: PMC3491985 DOI: 10.1021/jz300768g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We investigate the dinuclear manganese, Mn(II)-Mn(II), active site of human cytosolic X-propyl aminopeptidase (XPNPEP1) employing the QM/MM method. The optimized structure supports two manganese atoms at the active site and excludes the possibility of a single Mn(II) atom or other combination of divalent metal ions: Ca(II), Fe(II), Mg(II). A broken symmetry solution verifies an antiferromagnetically coupled state between the Mn(II)-Mn(II) pair, which is the ground state. From the energy difference between the high spin state (HS) and the broken symmetry state (BS), we estimate the exchange coupling constant, J, to be 5.15 cm(-1). Also, we observe multiple bridges (p orbitals) from solvent and two carboxylate linking to the Mn(II)-Mn(II), which leads to the weakly antiferromagnetic interaction of d(5)-d(5) electrons through superexchange coupling.
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Affiliation(s)
- Sangwook Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-329
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420
| | - Sooyeon Sim
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-329
| | - Lee G. Pedersen
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-329
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20
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Abstract
An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l(max) on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from l(max) = 0 (atomic charges) to l(max) = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank l(max) are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ l(max). In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (l(max) = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used.
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Affiliation(s)
- Dennis M. Elking
- University of North Carolina, Department of Chemistry, Chapel Hill, NC 27599, USA
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Lee G. Pedersen
- University of North Carolina, Department of Chemistry, Chapel Hill, NC 27599, USA
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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21
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Lee CJ, Wu S, Pedersen LG. A revisit to the one-form kinetic model of prothrombinase: A comment on the rebuttal. Biophys Chem 2012. [DOI: 10.1016/j.bpc.2011.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Lee CJ, Wu S, Pedersen LG. A proposed ternary complex model of prothrombinase with prothrombin: protein-protein docking and molecular dynamics simulations. J Thromb Haemost 2011; 9:2123-6. [PMID: 21827606 DOI: 10.1111/j.1538-7836.2011.04463.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Elking DM, Perera L, Duke R, Darden T, Pedersen LG. A finite field method for calculating molecular polarizability tensors for arbitrary multipole rank. J Comput Chem 2011; 32:3283-95. [PMID: 21915883 DOI: 10.1002/jcc.21914] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 07/06/2011] [Accepted: 07/25/2011] [Indexed: 11/07/2022]
Abstract
A finite field method for calculating spherical tensor molecular polarizability tensors α(lm;l'm') = ∂Δ(lm)/∂ϕ(l'm')* by numerical derivatives of induced molecular multipole Δ(lm) with respect to gradients of electrostatic potential ϕ(l'm')* is described for arbitrary multipole ranks l and l'. Interconversion formulae for transforming multipole moments and polarizability tensors between spherical and traceless Cartesian tensor conventions are derived. As an example, molecular polarizability tensors up to the hexadecapole-hexadecapole level are calculated for water using the following ab initio methods: Hartree-Fock (HF), Becke three-parameter Lee-Yang-Parr exchange-correlation functional (B3LYP), Møller-Plesset perturbation theory up to second order (MP2), and Coupled Cluster theory with single and double excitations (CCSD). In addition, intermolecular electrostatic and polarization energies calculated by molecular multipoles and polarizability tensors are compared with ab initio reference values calculated by the Reduced Variation Space method for several randomly oriented small molecule dimers separated by a large distance. It is discussed how higher order molecular polarizability tensors can be used as a tool for testing and developing new polarization models for future force fields.
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Affiliation(s)
- Dennis M Elking
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, USA
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24
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25
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Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH. Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J Biol Chem 2011; 286:31650-60. [PMID: 21733843 DOI: 10.1074/jbc.m111.253401] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA polymerases can misinsert ribonucleotides that lead to genomic instability. DNA polymerase β discourages ribonucleotide insertion with the backbone carbonyl of Tyr-271; alanine substitution of Tyr-271, but not Phe-272, resulted in a >10-fold loss in discrimination. The Y271A mutant also inserted ribonucleotides more efficiently than wild type on a variety of ribonucleoside (rNMP)-containing DNA substrates. Substituting Mn(2+) for Mg(2+) decreased sugar discrimination for both wild-type and mutant enzymes primarily by increasing the affinity for rCTP. This facilitated crystallization of ternary substrate complexes of both the wild-type and Y271A mutant enzymes. Crystallographic structures of Y271A- and wild type-substrate complexes indicated that rCTP is well accommodated in the active site but that O2' of rCTP and the carbonyl oxygen of Tyr-271 or Ala-271 are unusually close (∼2.5 and 2.6 Å, respectively). Structure-based modeling indicates that the local energetic cost of positioning these closely spaced oxygens is ∼2.2 kcal/mol for the wild-type enzyme. Because the side chain of Tyr-271 also hydrogen bonds with the primer terminus, loss of this interaction affects its catalytic positioning. Our results support a model where DNA polymerase β utilizes two strategies, steric and geometric, with a single protein residue to deter ribonucleotide insertion.
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Affiliation(s)
- Nisha A Cavanaugh
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
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26
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Schorzman AN, Perera L, Cutalo-Patterson JM, Pedersen LC, Pedersen LG, Kunkel TA, Tomer KB. Modeling of the DNA-binding site of yeast Pms1 by mass spectrometry. DNA Repair (Amst) 2011; 10:454-65. [PMID: 21354867 PMCID: PMC3084373 DOI: 10.1016/j.dnarep.2011.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/07/2011] [Accepted: 01/24/2011] [Indexed: 11/26/2022]
Abstract
Mismatch repair (MMR) corrects replication errors that would otherwise lead to mutations and, potentially, various forms of cancer. Among several proteins required for eukaryotic MMR, MutLα is a heterodimer comprised of Mlh1 and Pms1. The two proteins dimerize along their C-terminal domains (CTDs), and the CTD of Pms1 houses a latent endonuclease that is required for MMR. The highly conserved N-terminal domains (NTDs) independently bind DNA and possess ATPase active sites. Here we use two protein footprinting techniques, limited proteolysis and oxidative surface mapping, coupled with mass spectrometry to identify amino acids involved along the DNA-binding surface of the Pms1-NTD. Limited proteolysis experiments elucidated several basic residues that were protected in the presence of DNA, while oxidative surface mapping revealed one residue that is uniquely protected from oxidation. Furthermore, additional amino acids distributed throughout the Pms1-NTD were protected from oxidation either in the presence of a non-hydrolyzable analog of ATP or DNA, indicating that each ligand stabilizes the protein in a similar conformation. Based on the recently published X-ray crystal structure of yeast Pms1-NTD, a model of the Pms1-NTD/DNA complex was generated using the mass spectrometric data as constraints. The proposed model defines the DNA-binding interface along a positively charged groove of the Pms1-NTD and complements prior mutagenesis studies of Escherichia coli and eukaryotic MutL.
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Affiliation(s)
- Allison N. Schorzman
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Jenny M. Cutalo-Patterson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Lee G. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Thomas A. Kunkel
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Kenneth B. Tomer
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
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Wu S, Liu S, Davis CH, Stafford DW, Kulman JD, Pedersen LG. A hetero-dimer model for concerted action of vitamin K carboxylase and vitamin K reductase in vitamin K cycle. J Theor Biol 2011; 279:143-9. [PMID: 21453708 DOI: 10.1016/j.jtbi.2011.03.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 03/23/2011] [Accepted: 03/23/2011] [Indexed: 10/18/2022]
Abstract
Vitamin K carboxylase (VKC) is believed to convert vitamin K, in the vitamin K cycle, to an alkoxide-epoxide form which then reacts with CO(2) and glutamate to generate γ-carboxyglutamic acid (Gla). Subsequently, vitamin K epoxide reductase (VKOR) is thought to convert the alkoxide-epoxide to a hydroquinone form. By recycling vitamin K, the two integral-membrane proteins, VKC and VKOR, maintain vitamin K levels and sustain the blood coagulation cascade. Unfortunately, NMR or X-ray crystal structures of the two proteins have not been characterized. Thus, our understanding of the vitamin K cycle is only partial at the molecular level. In this study, based on prior biochemical experiments on VKC and VKOR, we propose a hetero-dimeric form of VKC and VKOR that may explain the efficient oxidation and reduction of vitamin K during the vitamin K cycle.
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Affiliation(s)
- Sangwook Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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28
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Abstract
Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics. In many cases, a reasonable approximation to quantum mechanics is classical mechanics realized through Newton’s equations of motion. Dr. Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems. To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules, not just biological molecules. Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.
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Affiliation(s)
- Lee G Pedersen
- Lee G Pedersen, Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC 27599, United States
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29
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Elking DM, Perera L, Duke R, Darden T, Pedersen LG. Atomic forces for geometry-dependent point multipole and gaussian multipole models. J Comput Chem 2010; 31:2702-13. [PMID: 20839297 DOI: 10.1002/jcc.21563] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In this study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives partial derivative D(m'm)(l)/partial derivative Omega. The force equations can be applied to electrostatic models based on atomic point multipoles or gaussian multipole charge density. Hydrogen-bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models.
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Affiliation(s)
- Dennis M Elking
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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Wu S, Liu S, Davis CH, Stafford DW, Pedersen LG. Quantum Chemical Study of the Mechanism of Action of Vitamin K Carboxylase in Solvent. Int J Quantum Chem 2010; 110:2744-2751. [PMID: 21892230 PMCID: PMC3164839 DOI: 10.1002/qua.22740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We investigate the post-translational generation of Gla (γ-carboxy glutamic acid) from Glu (glutamic acid) by vitamin K carboxylase (VKC) in solvent. VKC is thought to convert vitamin K, in the vitamin K cycle, to an alkoxide-epoxide form, which then reacts with CO(2) to generate an essential ingredient in blood coagulation, γ-carboxyglutamic acid (Gla). The generation of Gla from Glu is found to be exergenic (-15 kcal/mol) in aqueous solution with the SM6 method. We also produced the free energy profile for this model biochemical process with other solvent methods (polarizable continuum model, dielectric polarizable continuum model) and different dielectric constants. The biological implications are discussed.
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Affiliation(s)
- Sangwook Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
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31
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Abstract
Biomolecular nucleophilic substitution reactions, S(N)2, are fundamental and commonplace in chemistry. It is the well-documented experimental finding in the literature that vicinal substitution with bulkier groups near the reaction center significantly slows the reaction due to steric hindrance, but theoretical understanding in the quantitative manner about factors dictating the S(N)2 reaction barrier height is still controversial. In this work, employing the new quantification approach that we recently proposed for the steric effect from the density functional theory framework, we investigate the relative contribution of three independent effects-steric, electrostatic, and quantum-to the S(N)2 barrier heights in gas phase for substituted methyl halide systems, R(1)R(2)R(3)CX, reacting with the fluorine anion, where R(1), R(2), and R(3) denote substituting groups and X = F or Cl. We found that in accordance with the experimental finding, for these systems, the steric effect dominates the transition state barrier, contributing positively to barrier heights, but this contribution is largely compensated by the negative, stabilizing contribution from the quantum effect due to the exchange-correlation interactions. Moreover, we find that it is the component from the electrostatic effect that is linearly correlated with the S(N)2 barrier height for the systems investigated in the present study. In addition, we compared our approach with the conventional method of energy decomposition in density functional theory as well as examined the steric effect from the wave function theory for these systems via natural bond orbital analysis.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina, 27599-3420, USA.
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32
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Lee CJ, Chandrasekaran V, Wu S, Duke RE, Pedersen LG. Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex. Thromb Res 2010; 125 Suppl 1:S7-S10. [PMID: 20156644 DOI: 10.1016/j.thromres.2010.01.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The putative structure of the Tissue Factor/Factor VIIa/Factor Xa (TF/FVIIa/FXa) ternary complex is reconsidered. Two independently derived docking models proposed in 2003 (one for our laboratory: CHeA and one from the Scripps laboratory: Ss) are dynamically equilibrated for over 10 ns in an electrically neutral solution using all-atom molecular dynamics. Although the dynamical models (CHeB and Se) differ in atomic detail, there are similarities in that TF is found to interact with the gamma-carboxyglutamic acid (Gla) and Epidermal Growth Factor-like 1 (EGF-1) domains of FXa, and FVIIa is found to interact with the Gla, EGF-2 and serine protease (SP) domains of FXa in both models. FVIIa does not interact with the FXa EGF-1 domain in Se and the EGF domains of FVIIa do not interact with FXa in the CHeB. Both models are consistent with experimentally suggested contacts between the SP domain of FVIIa with the EGF-2 and SP domains of FXa.
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Affiliation(s)
- Chang Jun Lee
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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33
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Abstract
Accurate predictions of molecular acidity using ab initio and density functional approaches are still a daunting task. Using electronic and reactivity properties, one can quantitatively estimate pKa values of acids. In a recent paper [S. B. Liu and L. G. Pedersen, J. Phys. Chem. A 113, 3648 (2009)], we employed the molecular electrostatic potential (MEP) on the nucleus and the sum of valence natural atomic orbital (NAO) energies for the purpose. In this work, we reformulate these relationships on the basis of conceptual density functional theory and compare the results with those from the thermodynamic cycle method. We show that MEP and NAO properties of the dissociating proton of an acid should satisfy the same relationships with experimental pKa data. We employ 27 main groups and first to third row transition metal-water complexes as illustrative examples to numerically verify the validity of these strong linear correlations. Results also show that the accuracy of our approach and that of the conventional method through the thermodynamic cycle are statistically similar.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA.
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34
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Abstract
An electrostatic model based on charge density is proposed as a model for future force fields. The model is composed of a nucleus and a single Slater-type contracted Gaussian multipole charge density on each atom. The Gaussian multipoles are fit to the electrostatic potential (ESP) calculated at the B3LYP/6-31G* and HF/aug-cc-pVTZ levels of theory and tested by comparing electrostatic dimer energies, inter-molecular density overlap integrals, and permanent molecular multipole moments with their respective ab initio values. For the case of water, the atomic Gaussian multipole moments Q(lm) are shown to be a smooth function of internal geometry (bond length and bond angle), which can be approximated by a truncated linear Taylor series. In addition, results are given when the Gaussian multipole charge density is applied to a model for exchange-repulsion energy based on the inter-molecular density overlap.
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Affiliation(s)
- Dennis M Elking
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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35
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Liu S, Pedersen LG. Estimation of molecular acidity via electrostatic potential at the nucleus and valence natural atomic orbitals. J Phys Chem A 2009; 113:3648-55. [PMID: 19317439 DOI: 10.1021/jp811250r] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An effective approach of estimating molecular pK(a) values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pK(a) values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pK(a) data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pK(a) values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA.
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36
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Wu S, Lee CJ, Pedersen LG. Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface. Phys Rev E Stat Nonlin Soft Matter Phys 2009; 79:041909. [PMID: 19518258 PMCID: PMC2746997 DOI: 10.1103/physreve.79.041909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Indexed: 05/27/2023]
Abstract
We test a hypothesis that the closed form of the C2 domain of coagulation factor V is more stable than the open form in an aqueous environment using a two-dimensional free-energy calculation with a simple dielectric solvent model. Our result shows that while the free-energy difference between two forms is small, favoring the closed form, a two-dimensional free-energy surface (FES) reveals that a transition state (1.53 kcal/mol) exists between the two conformations. By mapping the one-dimensional order parameter DeltaQ onto the two-dimensional FES, we search the conformational change path with the highest Boltzmann weighting factor between the closed and open form of the factor V C2 domain. The predicted transition path from the closed to open form is not that of simple side chain movements, but instead concerted movements of several loops. We also present a one-dimensional free-energy profile using a collective order parameter, which in a coarse manner locates the energy barriers found on the two-dimensional FES.
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Affiliation(s)
- Sangwook Wu
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
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37
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Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA. Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J Am Chem Soc 2009; 131:1550-6. [PMID: 19119875 DOI: 10.1021/ja8082818] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The 28 kDa epsilon subunit of Escherichia coli DNA polymerase III is the exonucleotidic proofreader responsible for editing polymerase insertion errors. Here, we study the mechanism by which epsilon carries out the exonuclease activity. We performed quantum mechanics/molecular mechanics calculations on the N-terminal domain containing the exonuclease activity. Both the free-epsilon and a complex epsilon bound to a theta homologue (HOT) were studied. For the epsilon-HOT complex Mg(2+) or Mn(2+) were investigated as the essential divalent metal cofactors, while only Mg(2+) was used for free-epsilon. In all calculations a water molecule bound to the catalytic metal acts as the nucleophile for hydrolysis of the phosphate bond. Initially, a direct proton transfer to H162 is observed. Subsequently, the nucleophilic attack takes place followed by a second proton transfer to E14. Our results show that the reaction catalyzed with Mn(2+) is faster than that with Mg(2+), in agreement with experiment. In addition, the epsilon-HOT complex shows a slightly lower energy barrier compared to free-epsilon. In all cases the catalytic metal is observed to be pentacoordinated. Charge and frontier orbital analyses suggest that charge transfer may stabilize the pentacoordination. Energy decomposition analysis to study the contribution of each residue to catalysis suggests that there are several important residues. Among these, H98, D103, D129, and D146 have been implicated in catalysis by mutagenesis studies. Some of these residues were found to be structurally conserved on human TREX1, the exonuclease domains from E. coli DNA-Pol I, and the DNA polymerase of bacteriophage RB69.
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Affiliation(s)
- G Andrés Cisneros
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
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38
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Chandrasekaran V, Lee CJ, Lin P, Duke RE, Pedersen LG. A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa). J Mol Model 2009; 15:897-911. [PMID: 19172319 DOI: 10.1007/s00894-008-0444-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 12/08/2008] [Indexed: 11/25/2022]
Abstract
Protein Z-dependent protease inhibitor (ZPI) and antithrombin III (AT3) are members of the serpin superfamily of protease inhibitors that inhibit factor Xa (FXa) and other proteases in the coagulation pathway. While experimental structural information is available for the interaction of AT3 with FXa, at present there is no structural data regarding the interaction of ZPI with FXa, and the precise role of this interaction in the blood coagulation pathway is poorly understood. In an effort to gain a structural understanding of this system, we have built a solvent equilibrated three-dimensional structural model of the Michaelis complex of human ZPI/FXa using homology modeling, protein-protein docking and molecular dynamics simulation methods. Preliminary analysis of interactions at the complex interface from our simulations suggests that the interactions of the reactive center loop (RCL) and the exosite surface of ZPI with FXa are similar to those observed from X-ray crystal structure-based simulations of AT3/FXa. However, detailed comparison of our modeled structure of ZPI/FXa with that of AT3/FXa points to differences in interaction specificity at the reactive center and in the stability of the inhibitory complex, due to the presence of a tyrosine residue at the P1 position in ZPI, instead of the P1 arginine residue in AT3. The modeled structure also shows specific structural differences between AT3 and ZPI in the heparin-binding and flexible N-terminal tail regions. Our structural model of ZPI/FXa is also compatible with available experimental information regarding the importance for the inhibitory action of certain basic residues in FXa.
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39
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Liu S, Govind N, Pedersen LG. Exploring the origin of the internal rotational barrier for molecules with one rotatable dihedral angle. J Chem Phys 2009; 129:094104. [PMID: 19044862 DOI: 10.1063/1.2976767] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Continuing our recent endeavor, we systematically investigate in this work the origin of internal rotational barriers for small molecules using the new energy partition scheme proposed recently by one of the authors [S. B. Liu, J. Chem. Phys. 126, 244103 (2007)], where the total electronic energy is decomposed into three independent components, steric, electrostatic, and fermionic quantum. Specifically, we focus in this work on six carbon, nitrogen, and oxygen containing hydrides, CH(3)CH(3), CH(3)NH(2), CH(3)OH, NH(2)NH(2), NH(2)OH, and H(2)O(2), with only one rotatable dihedral angle [angle]H-X-Y-H (X,Y=C,N,O). The relative contributions of the different energy components to the total energy difference as a function of the internal dihedral rotation will be considered. Both optimized-geometry (adiabatic) and fixed-geometry (vertical) differences are examined, as are the results from the conventional energy partition and natural bond orbital analysis. A wealth of strong linear relationships among the total energy difference and energy component differences for different systems have been observed but no universal relationship applicable to all systems for both cases has been discovered, indicating that even for simple systems such as these, there exists no omnipresent, unique interpretation on the nature and origin of the internal rotation barrier. Different energy components can be employed for different systems in the rationalization of the barrier height. Confirming that the two differences, adiabatic and vertical, are disparate in nature, we find that for the vertical case there is a unique linear relationship applicable to all the six molecules between the total energy difference and the sum of the kinetic and electrostatic energy differences. For the adiabatic case, it is the total potential energy difference that has been found to correlate well with the total energy difference except for ethane whose rotation barrier is dominated by the quantum effect.
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Affiliation(s)
- Shubin Liu
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina 27599-3455, USA
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40
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Chandrasekaran V, Lee CJ, Duke RE, Perera L, Pedersen LG. Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling. Protein Sci 2008; 17:1354-61. [PMID: 18493021 DOI: 10.1110/ps.034801.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Although protein Z (PZ) has a domain arrangement similar to the essential coagulation proteins FVII, FIX, FX, and protein C, its serine protease (SP)-like domain is incomplete and does not exhibit proteolytic activity. We have generated a trial sequence of putative activated protein Z (PZa) by identifying amino acid mutations in the SP-like domain that might reasonably resurrect the serine protease catalytic activity of PZ. The structure of the activated form was then modeled based on the proposed sequence using homology modeling and solvent-equilibrated molecular dynamics simulations. In silico docking of inhibitors of FVIIa and FXa to the putative active site of equilibrated PZa, along with structural comparison with its homologous proteins, suggest that the designed PZa can possibly act as a serine protease.
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Affiliation(s)
- Vasu Chandrasekaran
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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41
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Abstract
BACKGROUND The prothrombinase complex consists of factor Xa, FVa, calcium ions, and phospholipid membrane. The prothrombinase complex plays a key role in the blood coagulation process. OBJECTIVE To derive solvent-equilibrated models of human FVa and the prothrombinase complex. METHODS Several modeling techniques have been employed, including homology modeling, protein-protein docking, and molecular dynamics simulation methods, to build the structural models. RESULTS AND CONCLUSIONS We found, upon simulation, a possibly significant shift towards planarity of the five FVa domains. To estimate a prothrombinase structure, we docked an FXa model to the equilibrated FVa model using experimental data as docking filters. We found that simulation of the docked complex led to some changes in the protein-protein contacts, but not buried surface area, as compared to the initial docking model. Possible locations of prothrombin binding to prothrombinase are indicated.
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Affiliation(s)
- C J Lee
- Department of Chemistry, UNC-CH, Chapel Hill, NC, USA
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Davis CH, Deerfield D, Wymore T, Stafford DW, Pedersen LG. A quantum chemical study of the mechanism of action of Vitamin K epoxide reductase (VKOR). J Mol Graph Model 2007; 26:401-8. [PMID: 17182266 DOI: 10.1016/j.jmgm.2006.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 10/24/2006] [Indexed: 11/25/2022]
Abstract
A reaction path including transition states is generated for the Silverman mechanism [R.B. Silverman, Chemical model studies for the mechanism of Vitamin K epoxide reductase, J. Am. Chem. Soc. 103 (1981) 5939-5941] of action for Vitamin K epoxide reductase (VKOR) using quantum mechanical methods (B3LYP/6-311G**). VKOR, an essential enzyme in mammalian systems, acts to convert Vitamin K epoxide, formed by Vitamin K carboxylase, to its (initial) quinone form for cellular reuse. This study elaborates on a prior work that focused on the thermodynamics of VKOR [D.W. Deerfield II, C.H. Davis, T. Wymore, D.W. Stafford, L.G. Pedersen, Int. J. Quant. Chem. 106 (2006) 2944-2952]. The geometries of proposed model intermediates and transition states in the mechanism are energy optimized. We find that once a key disulfide bond is broken, the reaction proceeds largely downhill. An important step in the conversion of the epoxide back to the quinone form involves initial protonation of the epoxide oxygen. We find that the source of this proton is likely a free mercapto group rather than a water molecule. The results are consistent with the current view that the widely used drug Warfarin likely acts by blocking binding of Vitamin K at the VKOR active site and thereby effectively blocking the initiating step. These results will be useful for designing more complete QM/MM studies of the enzymatic pathway once three-dimensional structural data is determined and available for VKOR.
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Affiliation(s)
- Charles H Davis
- Department of Biochemistry and Biophysics, UNC-CH, Chapel Hill, NC 27599, United States
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Davis CH, Deerfield D, Wymore T, Stafford DW, Pedersen LG. A quantum chemical study of the mechanism of action of Vitamin K carboxylase (VKC). J Mol Graph Model 2007; 26:409-14. [PMID: 17182265 DOI: 10.1016/j.jmgm.2006.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 10/24/2006] [Indexed: 10/23/2022]
Abstract
A reaction path including transition states is generated for the Dowd mechanism [P. Dowd, R. Hershlne, S.W. Ham, S. Naganathan. Vitamin K and energy transduction: a base strength amplification mechanism. Science 269 (2005) 1684-1691] of action for Vitamin K carboxylase (VKC) using quantum chemical methods (B3LYP/6-311G**). VKC, an essential enzyme in mammalian systems, catalyzes the conversion of hydroquinone form of Vitamin K to the epoxide form in the presence of oxygen. An intermediate species of the oxidation of Vitamin K, an alkoxide, acts apparently to abstract the gamma hydrogen from specifically located glutamate residues. We are able to follow the Dowd proposed path to generate this alkoxide species. The geometries of the proposed model intermediates and transition states in the mechanism are energy optimized. We find that the most energetic step in the mechanism is the uni-deprotonation of the hydroquinone - once this occurs, there is only a small barrier of 3.5kcal/mol for the interaction of oxygen with the carbon to be attacked - and then the reaction proceeds downhill in free energy to form the critical alkoxide species. The results are consistent with the idea that the enzyme probably acts to facilitate the formation of the epoxide by reducing the energy required to deprotonate the hydroquinone form.
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Affiliation(s)
- Charles H Davis
- Department of Biochemistry and Biophysics, UNC-CH, Chapel Hill, 27599, United States
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Pedersen LG, Offenberg H, Moesgaard SG, Thomsen PD, Pedersen HD, Olsen LH. Transcription levels of endothelin-1 and endothelin receptors are associated with age and leaflet location in porcine mitral valves. ACTA ACUST UNITED AC 2007; 54:113-8. [PMID: 17381672 DOI: 10.1111/j.1439-0442.2007.00894.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aim of the study was to investigate the expression levels of endothelin-1 (ET-1) and ET(A) and ET(B) receptors (ET(A)-R and ET(B)-R) in porcine mitral valves and associate the transcription levels to age, leaflet location and deposition of mucopolysaccharides (MPS). Tissue samples from the chordal and inter-chordal insertion area of the anterior mitral valve leaflet from 11 sows (> or = 2 years of age) and 10 slaughter pigs (approximately 6 months old) were obtained and the relative gene expression levels of ET-1, ET(A)-R and ET(B)-R measured by semi-quantitative real-time PCR. A separate tissue sample was taken for histopathological grading of MPS deposition. The transcription levels of ET-1 (P < 0.0001) and ET(A)-R (P < 0.0004) were significantly higher in leaflets from the sows compared with slaughter pigs. The gene expression of ET(B)-R was not associated to age (P = 0.38), but increased in chordal insertion areas compared with inter-chordal areas (P = 0.01). The expression of ET-1 and ET(A)-R mRNA did not differ significantly between the two leaflet locations. The valve leaflets from sows had a significantly increased degree of MPS deposition compared with slaughter pigs upon histological examination (P = 0.04). In conclusion, an age-related valvular degeneration is observed in porcine mitral valve leaflets and ET-1 is suggested to be involved through action of both ET(A) and ET(B) receptors.
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Affiliation(s)
- L G Pedersen
- Department of Basic Animal and Veterinary Sciences, The Royal Vetinary and Agricultural University, Copenhagen, Denmark
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Moesgaard SG, Olsen LH, Aasted B, Viuff BM, Pedersen LG, Pedersen HD, Harrison AP. Direct measurements of nitric oxide release in relation to expression of endothelial nitric oxide synthase in isolated porcine mitral valves. ACTA ACUST UNITED AC 2007; 54:156-60. [PMID: 17381681 DOI: 10.1111/j.1439-0442.2007.00915.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aim of this study was to measure the direct release of nitric oxide (NO) from the porcine mitral valve using a NO microelectrode. Furthermore, the expression and localization of endothelial nitric oxide synthase (eNOS) in the mitral valve was studied using immunohistochemistry, Western blotting and RT-PCR. Results show that bradykinin increases NO release from mitral valves (DeltaBradykinin: 33.71 +/- 10.41 nm NO, P < 0.001, n = 10), whereas N-nitro-l-arginine methyl esther (l-NAME) decreases NO release when compared with basal level (Deltal-NAME: 82.69 +/- 15.66 nm NO, P < 0.005, n = 4). Both protein and mRNA expression of eNOS in mitral valves and in isolated valvular endothelial cells suggest that the NO release is mainly associated with the mitral valve endothelium. It is concluded that direct NO release from porcine mitral valves coincides with eNOS expression. This study documents useful techniques for investigations into the role of local NO release in mitral valve diseases.
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Affiliation(s)
- S G Moesgaard
- Department of Basic Animal and Veterinary Sciences, The Royal Vetinary and Agricultural University, Fredriksberg, Denmark.
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Davis CH, Ii DD, Stafford DW, Pedersen LG. Quantum chemical study of the mechanism of action of vitamin K carboxylase (VKC). IV. Intermediates and transition states. J Phys Chem A 2007; 111:7257-61. [PMID: 17503787 DOI: 10.1021/jp068564y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We studied proposed steps for the enzymatic formation of gamma-carboxyglutamic acid by density functional theory (DFT) quantum chemistry. Our results for one potentially feasible mechanism show that a vitamin K alkoxide intermediate can abstract a proton from glutamic acid at the gamma-carbon to form a carbanion and vitamin K epoxide. The hydrated carbanion can then react with CO2 to form gamma-carboxyglutamic acid. Computations at the B3LYP/6-311G** level were used to determine the intermediates and transition states for the overall process. The activation free energy for the gas-phase path is 22 kcal/mol, with the rate-limiting step for the reaction being the attack of the carbanion on CO2. Additional solvation studies, however, indicate that the formation of the carbanion step can be competitive with the CO2 attack step in high-dielectric systems. We relate these computations to the entire vitamin K cycle in the blood coagulation cascade, which is essential for viability of vertebrates.
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Affiliation(s)
- Charles H Davis
- Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Pedersen LG, Zhao J, Yang J, Thomsen PD, Gregersen H, Hasenkam JM, Smerup M, Pedersen HD, Olsen LH. Increased expression of endothelin B receptor in static stretch exposed porcine mitral valve leaflets. Res Vet Sci 2006; 82:232-8. [PMID: 17011002 DOI: 10.1016/j.rvsc.2006.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 07/22/2006] [Indexed: 10/24/2022]
Abstract
The aim of this study was to evaluate the effect of mechanical stretch on the expression of ET-1 and ET(A)- and ET(B)-receptors in porcine mitral valve leaflets. Leaflet segments from 10 porcine mitral valves were exposed to a static stretch load of 1.5 N for 3.5h in buffer at 37 degrees C together with matching control segments. Subsequently, the mRNA expression of ET-1, ET(A)-R and ET(B)-R was measured by real-time RT-PCR in the chordal insertion areas. The analyses showed an increased transcription of ET(B)-receptors in stretch-exposed leaflet segments compared to unstretched segments median 2.23 (quartiles 1.37 and 2.70) vs. median 1.56 (quartiles 1.38 and 2.17, P=0.03) whereas the mRNA expression of ET(A)-receptors (P=0.90) and ET-1 (P=0.51) remained unchanged. Stretch increased the expression of ET(B)-receptors in porcine mitral valve leaflets. The finding could lead to a better understanding of the pathogenesis of myxomatous mitral valve disease.
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Affiliation(s)
- L G Pedersen
- Department of Basic Animal and Veterinary Sciences, The Royal Veterinary and Agricultural University, 7 Groennegaardsvej, DK-1870 Frederiksberg, Copenhagen, Denmark.
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Lin P, Pedersen LC, Batra VK, Beard WA, Wilson SH, Pedersen LG. Energy analysis of chemistry for correct insertion by DNA polymerase beta. Proc Natl Acad Sci U S A 2006; 103:13294-9. [PMID: 16938895 PMCID: PMC1569157 DOI: 10.1073/pnas.0606006103] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-ray crystallographic structures of human DNA polymerase beta with nonhydrolyzable analogs containing all atoms in the active site required for catalysis provide a secure starting point for a theoretical analysis (quantum mechanics/molecular mechanics) of the mechanism of chemistry without biasing of modeling assumptions as required in previous studies. These structures provide the basis for a detailed quantum mechanics/molecular mechanics study of the path for the complete transfer of a monophosphate nucleoside donor to the sugar acceptor in the active site. The reaction is largely associative with the main energetic step preceded by proton transfer from the terminal primer deoxyribose O3' to Asp-256. The key residues that provide electrostatic stabilization of the transition state are identified and compared with those identified by mutational studies.
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Affiliation(s)
- Ping Lin
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599; and
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233
| | - Vinod K. Batra
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233
| | - Lee G. Pedersen
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599; and
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233
- To whom correspondence should be addressed. E-mail:
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