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Athanasiadis A, de Rosa M, de Sanctis D, Rosario AL, Archer M, Rich A, Carrondo MA. The structure of conformational junctions in DNA and genomic instability. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311096395] [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: 11/10/2022] Open
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2
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Bandeiras TM, Gorynia S, Vonrhein C, Donner P, Matias PM, Carrondo MA. Structural insights into a dodecameric machine – the RuvBL1/RuvBL2 complex. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311093329] [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: 11/10/2022] Open
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3
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Gonçalves AT, Marçal D, Carrondo MA, Enguita FJ. Crystallization and preliminary X-ray characterization of a glycerol dehydrogenase from the human pathogen Salmonella enterica serovar Typhimurium. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:698-701. [PMID: 19574643 PMCID: PMC2705638 DOI: 10.1107/s1744309109020296] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 05/27/2009] [Indexed: 11/10/2022]
Abstract
Glycerol dehydrogenase (GldA) encoded by the STM4108 gene (gldA) has been related to the synthesis of HilA, a major transcriptional regulator that is responsible for the expression of invasion genes in the human pathogen Salmonella enterica serovar Typhimurium. Single colourless crystals were obtained from a recombinant preparation of GldA overexpressed in Escherichia coli. They belonged to space group P222(1), with unit-cell parameters a = 127.0, b = 160.1, c = 665.2 A. The crystals contained a very large number of molecules in the asymmetric unit, probably 30-35. Diffraction data were collected to 3.5 A resolution using synchrotron radiation at the European Synchrotron Radiation Facility.
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Affiliation(s)
- A. T. Gonçalves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - D. Marçal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - M. A. Carrondo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - F. J. Enguita
- Cell Biology Unit, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
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Gonçalves AMD, Rêgo AT, Thomaz M, Enguita FJ, Carrondo MA. Expression, purification, crystallization and preliminary X-ray characterization of two crystal forms of stationary-phase survival E protein from Campylobacter jejuni. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:213-6. [PMID: 18323612 PMCID: PMC2374147 DOI: 10.1107/s1744309108003096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 01/28/2008] [Indexed: 11/10/2022]
Abstract
Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. The first form belongs to space group P2(1)2(1)2(1), with a tetramer in the asymmetric unit and unit-cell parameters a = 80.5, b = 119.0, c = 135.3 A. The second form belongs to space group C2, with unit-cell parameters a = 121.4, b = 47.1, c = 97.8 A, and contains a dimer in the asymmetric unit. Diffraction data have been collected from these crystal forms to 2.5 and 2.95 A resolution, respectively.
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Affiliation(s)
- A. M. D. Gonçalves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - A. T. Rêgo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - M. Thomaz
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2748-901 Oeiras, Portugal
| | - F. J. Enguita
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - M. A. Carrondo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
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Marçal D, Rego AT, Fogg MJ, Wilson KS, Carrondo MA, Enguita FJ. Crystallization and preliminary X-ray characterization of 1,3-propanediol dehydrogenase from the human pathogen Klebsiella pneumoniae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:249-51. [PMID: 17329826 PMCID: PMC2330189 DOI: 10.1107/s1744309107008834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 02/22/2007] [Indexed: 05/14/2023]
Abstract
1,3-Propanediol dehydrogenase (1,3-PD-DH), encoded by the dhaT gene, is a key enzyme in the dissimilation process for converting glycerol to 1,3-propanediol in the human pathogen Klebsiella pneumoniae. Single colourless crystals were obtained from a recombinant preparation of 1,3-propanediol dehydrogenase overexpressed in Escherichia coli. The crystals belong to space group P2(1), with unit-cell parameters a = 91.9, b = 226.6, c = 232.6 A, beta = 92.9 degrees. The crystals probably contain two decamers in the asymmetric unit, with a V(M) value of 3.07 A3 Da(-1) and an estimated solvent content of 59%. Diffraction data were collected to 2.7 A resolution using synchrotron radiation at the ID14-4 beamline of the European Synchrotron Radiation Facility.
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Affiliation(s)
- D. Marçal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - A. T. Rego
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - M. J. Fogg
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, England
| | - K. S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, England
| | - M. A. Carrondo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - F. J. Enguita
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
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6
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Fogg MJ, Alzari P, Bahar M, Bertini I, Betton JM, Burmeister WP, Cambillau C, Canard B, Carrondo MA, Coll M, Daenke S, Dym O, Egloff MP, Enguita FJ, Geerlof A, Haouz A, Jones TA, Ma Q, Manicka SN, Migliardi M, Nordlund P, Owens RJ, Peleg Y, Schneider G, Schnell R, Stuart DI, Tarbouriech N, Unge T, Wilkinson AJ, Wilmanns M, Wilson KS, Zimhony O, Grimes JM. Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens. Corrigendum. Acta Crystallogr D Biol Cryst 2006. [DOI: 10.1107/s0907444906044246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Aragão D, Marques AR, Frazão C, Enguita FJ, Carrondo MA, Fialho AM, Sá-Correia I, Mitchell EP. Cloning, expression, purification, crystallization and preliminary structure determination of glucose-1-phosphate uridylyltransferase (UgpG) from Sphingomonas elodea ATCC 31461 bound to glucose-1-phosphate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:930-4. [PMID: 16946483 PMCID: PMC2242879 DOI: 10.1107/s1744309106030107] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 08/01/2006] [Indexed: 05/11/2023]
Abstract
The cloning, expression, purification, crystallization and preliminary crystallographic analysis of glucose-1-phosphate uridylyltransferase (UgpG) from Sphingomonas elodea ATCC 31461 bound to glucose-1-phosphate are reported. Diffraction data sets were obtained from seven crystal forms in five different space groups, with highest resolutions ranging from 4.20 to 2.65 A. The phase problem was solved for a P2(1) crystal form using multiple isomorphous replacement with anomalous scattering from an osmium derivative and a SeMet derivative. The best native crystal in space group P2(1) has unit-cell parameters a = 105.5, b = 85.7, c = 151.8 A, beta = 105.2 degrees . Model building and refinement are currently under way.
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Affiliation(s)
- D. Aragão
- European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX, France
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, P-2781-901 Oeiras, Portugal
| | - A. R. Marques
- Biological Sciences Research Group, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - C. Frazão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, P-2781-901 Oeiras, Portugal
| | - F. J. Enguita
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, P-2781-901 Oeiras, Portugal
| | - M. A. Carrondo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, P-2781-901 Oeiras, Portugal
| | - A. M. Fialho
- Biological Sciences Research Group, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - I. Sá-Correia
- Biological Sciences Research Group, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - E. P. Mitchell
- European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX, France
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Carrondo MA. Structural insights into the RNA degradation mechanism. Acta Crystallogr A 2006. [DOI: 10.1107/s0108767306099843] [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: 11/10/2022] Open
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9
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Palma PN, Rodrigues ML, Archer M, Bonifácio MJ, Loureiro AI, Learmonth DA, Carrondo MA, Soares-da-Silva P. Comparative Study ofortho-andmeta-Nitrated Inhibitors of Catechol-O-methyltransferase: Interactions with the Active Site and Regioselectivity ofO-Methylation. Mol Pharmacol 2006; 70:143-53. [PMID: 16618795 DOI: 10.1124/mol.106.023119] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [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: 11/22/2022] Open
Abstract
In this work, we present a comparative case study of "ortho-" and "meta-nitrated" catecholic inhibitors of catechol-O-methyltransferase (COMT), with regard to their interaction with the catalytic site of the enzyme and the in vitro regioselective formation of their mono-O-methyl ether metabolites. In particular, the effects of altering the attachment position of the inhibitors' side-chain substituent, within the classic nitrocatechol pharmacophore, were investigated. For this purpose, we compared two simple regioisomeric nitrocatechol-type inhibitors of COMT, BIA 3-228 and BIA 8-176, which contain the benzoyl substituent attached at the meta and ortho positions, respectively, relative to the nitro group. The two compounds were slowly O-methylated by COMT in vitro, but the particular substitution pattern of each compound was shown to have a profound impact on the regioselectivity of their O-methylation. To provide a plausible interpretation of these results, a comprehensive analysis of the protein-inhibitor interactions and of the relative chemical susceptibility to O-methylation of the catechol hydroxyl groups was performed by means of docking simulations and ab initio molecular orbital calculations. The major structural and chemical factors that determine the enzyme regioselectivity of O-methylation were identified, and the X-ray structure of the complex of COMT with S-adenosyl-l-methionine and BIA 8-176 is herein disclosed. This is the first reported structure of the soluble form of COMT complexed with a nitrocatecholic inhibitor having a bulky substituent group in adjacent position (ortho) to the nitro group. Structural and dynamic aspects of this complex are analyzed and discussed, in the context of the present study.
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Affiliation(s)
- P N Palma
- Department of Research and Development, Bial., A. Av. da Siderurgia Nacional, 4745-457 S. Mamede do Coronado, Trofa, Portugal.
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Rodrigues ML, Bonifácio MJ, Soares-da-Silva P, Carrondo MA, Archer M. Crystallization and preliminary X-ray diffraction studies of a catechol-O-methyltransferase/inhibitor complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:118-20. [PMID: 16508109 PMCID: PMC1952394 DOI: 10.1107/s1744309104031197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Accepted: 11/26/2004] [Indexed: 05/06/2023]
Abstract
Inhibitors of the enzyme catechol-O-methyltransferase (COMT) are used as co-adjuvants in the therapy of Parkinson's disease. A recombinant form of the soluble cytosolic COMT from rat has been co-crystallized with a new potent inhibitor, BIA 8-176 [(3,4-dihydroxy-2-nitrophenyl)phenylmethanone], by the vapour-diffusion method using PEG 6K as precipitant. Crystals diffract to 1.6 A resolution on a synchrotron-radiation source and belong to the monoclinic space group P2(1), with unit-cell parameters a = 52.77, b = 79.63, c = 61.54 A, beta = 91.14 degrees.
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Affiliation(s)
- M. L. Rodrigues
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. República, Apt. 127, 2781-901 Oeiras, Portugal
| | - M. J. Bonifácio
- Department of Research and Development, BIAL, 4785 S. Mamede do Coronado, Portugal
| | - P. Soares-da-Silva
- Department of Research and Development, BIAL, 4785 S. Mamede do Coronado, Portugal
| | - M. A. Carrondo
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. República, Apt. 127, 2781-901 Oeiras, Portugal
| | - M. Archer
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. República, Apt. 127, 2781-901 Oeiras, Portugal
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11
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Enguita FJ, Marçal D, Martins LO, Grenha R, Bento I, Gato G, Lindley PF, Carrondo MA. Substrate and dioxygen binding to an endospore coat laccase from Bacillus subtilis. Acta Crystallogr A 2004. [DOI: 10.1107/s0108767304096813] [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: 04/03/2023] Open
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Macedo S, Mitchell EP, Matias PM, Romao CV, Liu MY, Xavier AV, Lindley PF, Le Gall J, Teixeira M, Carrondo MA. Bacterioferritin from Desulfovibrio desulfuricans: the identification of the ferroxidase centre. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302089766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Carrondo MA. Structural studies on the human androgen receptor ligand-binding domain. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302093005] [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: 11/11/2022] Open
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14
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Lindley PF, Aragao DG, Macedo S, Frazao C, Mitchell E, Romao CV, Teixeira M, Hagen WR, Carrondo MA. Hybrid cluster protein (HCP) from Desulfovibrio vulgarisand Desulfovibrio desulfuricans: aerobic, anaerobic and reduced structural studies. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302094886] [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: 11/10/2022] Open
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15
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Rodrigues ML, Archer M, Martel P, Jacquet A, Cravador A, Carrondo MA. Crystal structure of β-cinnamomin, a toxic protein fromPhytophthora cinnamomi. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302096885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Aragao DG, Macedo S, Frazao C, Mitchell E, Romao C, Teixeira M, Hagen WR, Carrondo MA, Lindley P. Hybrid cluster protein (HCP) from Desulfovibrio vulgarisand Desulfovibrio desulfuricans: aerobic, anaerobic and reduced structural studies. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302089699] [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: 11/10/2022] Open
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17
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Louro RO, Bento I, Matias PM, Catarino T, Baptista AM, Soares CM, Carrondo MA, Turner DL, Xavier AV. Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome. J Biol Chem 2001; 276:44044-51. [PMID: 11551953 DOI: 10.1074/jbc.m107136200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [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: 11/06/2022] Open
Abstract
Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. There is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates. Tetraheme cytochrome c(3) is a small soluble and monomeric protein that performs a central step in the bioenergetic metabolism of sulfate reducing bacteria, termed "proton-thrusting," linking the oxidation of molecular hydrogen with the reduction of sulfate. The mechano-chemical coupling involved in the transfer of multiple electrons and protons in cytochrome c(3) from Desulfovibrio desulfuricans ATCC 27774 is described using results derived from the microscopic thermodynamic characterization of the redox and acid-base centers involved, crystallographic studies in the oxidized and reduced states of the cytochrome, and theoretical studies of the redox and acid-base transitions. This proton-assisted two-electron step involves very small, localized structural changes that are sufficient to generate the complex network of functional cooperativities leading to energy transduction, while using molecular mechanisms distinct from those established for other Desulfovibrio sp. cytochromes from the same structural family.
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Affiliation(s)
- R O Louro
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6, Apt. 127, Oeiras 2780-156, Portugal
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Mendes J, Nagarajaram HA, Soares CM, Blundell TL, Carrondo MA. Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure. Biopolymers 2001; 59:72-86. [PMID: 11373721 DOI: 10.1002/1097-0282(200108)59:2<72::aid-bip1007>3.0.co;2-s] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [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: 11/06/2022]
Abstract
The performance of the self-consistent mean field theory (SCMFT) method for side-chain modeling, employing rotamer energies calculated with the flexible rotamer model (FRM), is evaluated in the context of comparative modeling of protein structure. Predictions were carried out on a test set of 56 model backbones of varying accuracy, to allow side-chain prediction accuracy to be analyzed as a function of backbone accuracy. A progressive decrease in the accuracy of prediction was observed as backbone accuracy decreased. However, even for very low backbone accuracy, prediction was substantially higher than random, indicating that the FRM can, in part, compensate for the errors in the modeled tertiary environment. It was also investigated whether the introduction in the FRM-SCMFT method of knowledge-based biases, derived from a backbone-dependent rotamer library, could enhance its performance. A bias derived from the backbone-dependent rotamer conformations alone did not improve prediction accuracy. However, a bias derived from the backbone-dependent rotamer probabilities improved prediction accuracy considerably. This bias was incorporated through two different strategies. In one (the indirect strategy), rotamer probabilities were used to reject unlikely rotamers a priori, thus restricting prediction by FRM-SCMFT to a subset containing only the most probable rotamers in the library. In the other (the direct strategy), rotamer energies were transformed into pseudo-energies that were added to the average potential energies of the respective rotamers, thereby creating hybrid energy-based/knowledge-based average rotamer energies, which were used by the FRM-SCMFT method for prediction. For all degrees of backbone accuracy, an optimal strength of the knowledge-based bias existed for both strategies for which predictions were more accurate than pure energy-based predictions, and also than pure knowledge-based predictions. Hybrid knowledge-based/energy-based methods were obtained from both strategies and compared with the SCWRL method, a hybrid method based on the same backbone-dependent rotamer library. The accuracy of the indirect method was approximately the same as that of the SCWRL method, but that of the direct method was significantly higher.
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Affiliation(s)
- J Mendes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, Av. da República, 2781-901, Oeiras, Portugal
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Mendes J, Baptista AM, Carrondo MA, Soares CM. Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants. J Comput Aided Mol Des 2001; 15:721-40. [PMID: 11718477 DOI: 10.1023/a:1012279810260] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [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: 11/12/2022]
Abstract
The Atomic Solvation Parameter (ASP) model is one of the simplest models of solvation, in which the solvation free energy of a molecule is proportional to the solvent accessible surface area (SAS) of its atoms. However, until now this model had not been incorporated into the Self-Consistent Mean Field Theory (SCMFT) method for modelling sidechain conformations in proteins. The reason for this is that SAS is a many-body quantity and, thus, it is not obvious how to define it within the Mean Field (MF) framework, where multiple copies of each sidechain exist simultaneously. Here, we present a method for incorporating an SAS-based potential, such as the ASP model, into SCMFT. The theory on which the method is based is exact within the MF framework, that is, it does not depend on a pairwise or any other approximation of SAS. Therefore, SAS can be calculated to arbitrary accuracy. The method is computationally very efficient: only 7.6% slower on average than the method without solvation. We applied the method to the prediction of sidechain conformation, using as a test set high-quality solution structures of 11 proteins. Solvation was found to substantially improve the prediction accuracy of well-defined surface sidechains. We also investigated whether the methodology can be applied to prediction of folding free energies of protein mutants, using a set of barnase mutants. For apolar mutants, the modest correlation observed between calculated and observed folding free energies without solvation improved substantially when solvation was included, allowing the prediction of trends in the folding free energies of this type of mutants. For polar mutants, correlation was not significant even with solvation. Several other factors also responsible for the correlation were identified and analysed. From this analysis, future directions for applying and improving the present methodology are discussed.
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Affiliation(s)
- J Mendes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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20
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Rodrigues ML, Archer M, Bonifácio MJ, Soares-da-Silva P, Carrondo MA. Crystallization and preliminary crystallographic characterization of catechol-O-methyltransferase in complex with its cosubstrate and an inhibitor. Acta Crystallogr D Biol Crystallogr 2001; 57:906-8. [PMID: 11375525 DOI: 10.1107/s0907444901006539] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Received: 03/13/2001] [Accepted: 04/17/2001] [Indexed: 11/10/2022]
Abstract
Catechol-O-methyltransferase (COMT) is involved in the metabolism of catecholamines, catechol steroids and xenobiotic catechols. A precise knowledge of the enzyme-inhibitor structural interactions could help in the design of better inhibitors. Soluble rat COMT was expressed in Escherichia coli and the recombinant protein was crystallized with a new tight-binding inhibitor, BIA 3-335 [1-(3,4-dihydroxy-5-nitrophenyl)-3-(n-3'-trifluoromethylphenyl)piperazine-1-propanone dihydrochloride]. The crystals were obtained by the sitting-drop vapour-diffusion method using PEG 6K as a precipitant. These crystals diffracted to better than 1.9 A and belong to the trigonal space group P3(2)21. The unit-cell parameters for the crystal measured at room temperature were a = b = 51.5, c = 168.3 A; each shrank by about 1 A on freezing.
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Affiliation(s)
- M L Rodrigues
- Instituto de Biologia Experimental e Tecnológica (IBET), Apt. 12, 2748-901 Oeiras, Portugal
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21
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Learmonth DA, Benes J, Parada A, Hainzl D, Beliaev A, Bonifácio MJ, Matias PM, Carrondo MA, Garrett J, Soares-da-Silva P. Synthesis, anticonvulsant properties and pharmacokinetic profile of novel 10,11-dihydro-10-oxo-5H-dibenz/b,f/azepine-5-carboxamide derivatives. Eur J Med Chem 2001; 36:227-36. [PMID: 11337101 DOI: 10.1016/s0223-5234(01)01220-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [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: 10/27/2022]
Abstract
A series of novel derivatives of oxcarbazepine (5), 10,11-dihydro-10-oxo-5H-dibenz/b,f/azepine-5-carboxamide was synthesised and evaluated for their anticonvulsant activity and sodium channel blocking properties. The oxime 8 was found to be the most active compound from this series, displaying greater potency than its geometric isomer 9 and exhibiting also the highest protective index value. Importantly, the metabolic profile of 8 differs from the already established dibenz/b,f/azepine-5-carboxamide drugs such as 1 and 5 which undergo rapid and complete conversion in vivo to several biologically active metabolites. In contrast 8 is metabolised to only a very minor extent leading to the conclusion that the observed anti-convulsant effect is solely attributable to 8. It is concluded that 8 may be as effective as 1 and 5 at controlling seizures and that the low toxicity and consequently high protective index should provide the compound with an improved side-effect profile.
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Affiliation(s)
- D A Learmonth
- Department of Research & Development, Laboratory of Chemistry, BIAL, 4785 S., Mamede do Coronado, Portugal
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22
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Frazão C, Enguita FJ, Coelho R, Sheldrick GM, Navarro JA, Hervás M, De la Rosa MA, Carrondo MA. Crystal structure of low-potential cytochrome c549 from Synechocystis sp. PCC 6803 at 1.21 A resolution. J Biol Inorg Chem 2001; 6:324-32. [PMID: 11315568 DOI: 10.1007/s007750100208] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [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: 11/30/2022]
Abstract
The crystal structure of low-potential cytochrome c549, an extrinsic component of the photosystem II (PS II) from Synechocystis sp. PCC 6803, was obtained directly from single-wavelength 1.21 A resolution diffraction data. This is the first monodomain bis-histidinyl monoheme cytochrome c to be structurally characterized. The extended N-terminal region of c549 builds up a two-strand antiparallel beta-sheet in a hairpin motif, which extends through two molecules owing to crystal packing. Both peptide termini are involved in crystal contacts, which may explain their protrusion out of the globular fold. The C-terminus is preceded by a 9 A-long hydrophobic finger extending from a positively charged base and could be involved in PSII interactions, as well as a protruding negative patch built by a set of conserved acidic residues among c549 sequences.
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Affiliation(s)
- C Frazão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
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23
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Coelho AV, Macedo S, Matias PM, Thompson AW, LeGall J, Carrondo MA. Structure determination of bacterioferritin from Desulfovibrio desulfuricans by the MAD method at the Fe K-edge. Acta Crystallogr D Biol Crystallogr 2001; 57:326-9. [PMID: 11173495 DOI: 10.1107/s0907444900015286] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Received: 08/23/2000] [Accepted: 10/25/2000] [Indexed: 11/10/2022]
Abstract
Bacterioferritins constitute a subfamily of heme ferritins, proteins involved in iron storage and homeostasis. The protein isolated from Desulfovibrio desulfuricans ATCC 27774 is a homodimer of mass 52 kDa. The monomers are linked by an iron-coproporphyrin group and each monomer contains a diferric center. The 24-monomer clusters found in the crystal are probably the functional particles. MAD data from cubic bacterioferritin crystals were collected at the K-shell iron edge. Preliminary phasing was performed using the positions of 23 of the 40 Fe atoms expected in the asymmetric unit. Further MAD phasing allowed the identification of individual iron sites. Clear and interpretable electron-density maps were obtained after density modification.
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Affiliation(s)
- A V Coelho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, Apartado 127, 2781-901 Oeiras, Portugal
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24
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Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA. [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome c3. J Biol Inorg Chem 2001; 6:63-81. [PMID: 11191224 DOI: 10.1007/s007750000167] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.9] [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: 10/27/2022]
Abstract
The primary and three-dimensional structures of a [NiFe] hydrogenase isolated from D. desulfitricans ATCC 27774 were determined, by nucleotide analysis and single-crystal X-ray crystallography. The three-dimensional structural model was refined to R=0.167 and Rfree=0.223 using data to 1.8 A resolution. Two unique structural features are observed: the [4Fe-4S] cluster nearest the [NiFe] centre has been modified [4Fe-3S-3O] by loss of one sulfur atom and inclusion of three oxygen atoms; a three-fold disorder was observed for Cys536 which binds to the nickel atom in the [NiFe] centre. Also, the bridging sulfur atom that caps the active site was found to have partial occupancy, thus corresponding to a partly activated enzyme. These structural features may have biological relevance. In particular, the two less-populated rotamers of Cys536 may be involved in the activation process of the enzyme, as well as in the catalytic cycle. Molecular modelling studies were carried out on the interaction between this [NiFe] hydrogenase and its physiological partner, the tetrahaem cytochrome c3 from the same organism. The lowest energy docking solutions were found to correspond to an interaction between the haem IV region in tetrahaem cytochrome c3 with the distal [4Fe-4S] cluster in [NiFe] hydrogenase. This interaction should correspond to efficient electron transfer and be physiologically relevant, given the proximity of the two redox centres and the fact that electron transfer decay coupling calculations show high coupling values and a short electron transfer pathway. On the other hand, other docking solutions have been found that, despite showing low electron transfer efficiency, may give clues on possible proton transfer mechanisms between the two molecules.
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Affiliation(s)
- P M Matias
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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25
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Frazão C, Silva G, Gomes CM, Matias P, Coelho R, Sieker L, Macedo S, Liu MY, Oliveira S, Teixeira M, Xavier AV, Rodrigues-Pousada C, Carrondo MA, Le Gall J. Structure of a dioxygen reduction enzyme from Desulfovibrio gigas. Nat Struct Biol 2000; 7:1041-5. [PMID: 11062560 DOI: 10.1038/80961] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Desulfovibrio gigas is a strict anaerobe that contains a well-characterized metabolic pathway that enables it to survive transient contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to water in a direct and safe way. The 2.5 A resolution crystal structure of ROO shows that each monomer of this homodimeric enzyme consists of a novel combination of two domains, a flavodoxin-like domain and a Zn-beta-lactamase-like domain that contains a di-iron center for dioxygen reduction. This is the first structure of a member of a superfamily of enzymes widespread in strict and facultative anaerobes, indicating its broad physiological significance.
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Affiliation(s)
- C Frazão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apartado 127, 2781-901 Oeiras, Portugal
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26
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Matias PM, Donner P, Coelho R, Thomaz M, Peixoto C, Macedo S, Otto N, Joschko S, Scholz P, Wegg A, Bäsler S, Schäfer M, Egner U, Carrondo MA. Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations. J Biol Chem 2000; 275:26164-71. [PMID: 10840043 DOI: 10.1074/jbc.m004571200] [Citation(s) in RCA: 414] [Impact Index Per Article: 17.3] [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: 11/06/2022] Open
Abstract
The crystal structures of the human androgen receptor (hAR) and human progesterone receptor ligand-binding domains in complex with the same ligand metribolone (R1881) have been determined. Both three-dimensional structures show the typical nuclear receptor fold. The change of two residues in the ligand-binding pocket between the human progesterone receptor and hAR is most likely the source for the specificity of R1881 to the hAR. The structural implications of the 14 known mutations in the ligand-binding pocket of the hAR ligand-binding domains associated with either prostate cancer or the partial or complete androgen receptor insensitivity syndrome were analyzed. The effects of most of these mutants could be explained on the basis of the crystal structure.
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Affiliation(s)
- P M Matias
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780 Oeiras, Portugal
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27
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Frazão C, Silva G, Gomes CM, Matias P, Coelho R, Sieker L, Macedo S, Liu MY, Oliveira S, Teixeira M, Xavier AV, Rodrigues-Pousada C, Carrondo MA, Le Gall J. Dioxygen reduction in strict anaerobes. Crystal structure of rubredoxin: oxygen oxidoredutase (ROO) from Desulfovibrio gigas. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300022583] [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: 11/11/2022] Open
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28
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Macedo S, Matias PM, Mitchell E, Coelho A, Le Gall J, Lindley P, Carrondo MA. Structural determination of Bacterioferritin from Desulfovibrio DesulfuricansATCC 27774. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300025952] [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: 11/10/2022] Open
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29
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Archer M, Rodrigues ML, Aurélio M, Cravador A, Carrondo MA. Crystal structure of β-cinnamomin, a protein elicitor produced by a phytopathogenic fungus. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300025757] [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: 04/03/2023] Open
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30
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Matias PM, Coelho R, Thomaz M, Peixoto C, Macedo S, Carrondo MA. Structural evidence for ligand specificity in the binding domain of the human Androgen receptor. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300025691] [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: 11/10/2022] Open
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31
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Enguita FJ, Frazão C, Coelho R, Navarro J, Hervás M, De la Rosa M, Sheldrick GM, Carrondo MA. Ab initiocrystal structure of low potentialcytochrome c549from Synechocistissp. PCC6803. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300025939] [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: 11/10/2022] Open
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32
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Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA. [NiFe] Hydrogenase from Desulfovibrio desulfuricansATCC 27774: Gene sequencing, three-dimensional structure determination and refinement at1.8 Å and modelling studies of its interaction with the tetra-haem cytochrome c3. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300026003] [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: 11/11/2022] Open
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33
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Archer M, Rodrigues ML, Aurélio M, Biemans R, Cravador A, Carrondo MA. Crystallization and preliminary x-ray diffraction analysis of beta-cinnamomin, an elicitin secreted by the phytopathogenic fungus Phytophthora cinnamomin. Acta Crystallogr D Biol Crystallogr 2000; 56:363-5. [PMID: 10713528 DOI: 10.1107/s0907444900000366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Cinnamomin (CIN) belongs to a family of 10 kDa proteins designated as elicitins. Some of these proteins induce a hypersensitive response in diverse plant species, leading to resistance against fungal and bacterial plant pathogens. CIN was crystallized by the vapour-diffusion method using either ammonium sulfate or polyethyleneglycol (PEG) as precipitants in solutions buffered at around pH 7. These crystals are isomorphous and belong to the triclinic space group, with unit-cell parameters a = 31.69, b = 36. 99, c = 44.09 A, alpha = 76.86, beta = 84.41, gamma = 80.26 degrees. A frozen crystal diffracted X-rays beyond 1.45 A resolution on a synchrotron-radiation source.
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Affiliation(s)
- M Archer
- Instituto de Tecnologia Química e Biológica (ITQB), Av. Republica, Apt 127, 2781-901 Oeiras, Portugal
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34
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Abstract
Side-chain modeling has a widespread application in many current methods for protein tertiary structure determination, prediction, and design. Of the existing side-chain modeling methods, rotamer-based methods are the fastest and most efficient. Classically, a rotamer is conceived as a single, rigid conformation of an amino acid sidechain. Here, we present a flexible rotamer model in which a rotamer is a continuous ensemble of conformations that cluster around the classic rigid rotamer. We have developed a thermodynamically based method for calculating effective energies for the flexible rotamer. These energies have a one-to-one correspondence with the potential energies of the rigid rotamer. Therefore, the flexible rotamer model is completely general and may be used with any rotamer-based method in substitution of the rigid rotamer model. We have compared the performance of the flexible and rigid rotamer models with one side-chain modeling method in particular (the self-consistent mean field theory method) on a set of 20 high quality crystallographic protein structures. For the flexible rotamer model, we obtained average predictions of 85.8% for chi1, 76.5% for chi1+2 and 1.34 A for root-mean-square deviation (RMSD); the corresponding values for core residues were 93.0%, 87.7% and 0.70 A, respectively. These values represent improvements of 7.3% for chi1, 8.1% for chi1+2 and 0.23 A for RMSD over the predictions obtained with the rigid rotamer model under otherwise identical conditions; the corresponding improvements for core residues were 6.9%, 10.5% and 0.43 A, respectively. We found that the predictions obtained with the flexible rotamer model were also significantly better than those obtained for the same set of proteins with another state-of-the-art side-chain placement method in the literature, especially for core residues. The flexible rotamer model represents a considerable improvement over the classic rigid rotamer model. It can, therefore, be used with considerable advantage in all rotamer-based methods commonly applied to protein tertiary structure determination, prediction, and design and also in predictions of free energies in mutational studies.
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Affiliation(s)
- J Mendes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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35
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Burke DF, Deane CM, Nagarajaram HA, Campillo N, Martin-Martinez M, Mendes J, Molina F, Perry J, Reddy BV, Soares CM, Steward RE, Williams M, Carrondo MA, Blundell TL, Mizuguchi K. An iterative structure-assisted approach to sequence alignment and comparative modeling. Proteins 1999; Suppl 3:55-60. [PMID: 10526352 DOI: 10.1002/(sici)1097-0134(1999)37:3+<55::aid-prot8>3.3.co;2-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http:/(/)www-cryst.bioc.cam.ac.uk/ approximately homstrad) and protein superfamilies (CAMPASS, http:/(/)www-cryst.bioc.cam.ac.uk/ approximately campass), in which structure-based alignments are analyzed and formatted with the program JOY (http:/(/)www-cryst.bioc.cam.ac.uk/ approximately joy) to reveal conserved local structural features. The databases facilitate the recognition of a family or superfamily, they assist in the selection of useful parent structures, they are helpful in alignment of the target sequences with the parent set, and are useful for deriving relationships that can be used in validating models. In the iterative approach, a model is constructed on the basis of the proposed sequence alignment and this is then reexpressed in the JOY format and realigned with the parent set. This is repeated until the model and sequence alignment is optimized. We examine the case for comparison and use of multiple structures of family members, rather than a single parent structure. We use the targets attempted by our group in CASP3 to assess the value of such procedures.
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Affiliation(s)
- D F Burke
- Department of Biochemistry, University of Cambridge, United Kingdom
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36
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Frazão C, Bento I, Costa J, Soares CM, Veríssimo P, Faro C, Pires E, Cooper J, Carrondo MA. Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic proteinase from the flowers of Cynara cardunculus L. J Biol Chem 1999; 274:27694-701. [PMID: 10488111 DOI: 10.1074/jbc.274.39.27694] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [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: 11/06/2022] Open
Abstract
Aspartic proteinases (AP) have been widely studied within the living world, but so far no plant AP have been structurally characterized. The refined cardosin A crystallographic structure includes two molecules, built up by two glycosylated peptide chains (31 and 15 kDa each). The fold of cardosin A is typical within the AP family. The glycosyl content is described by 19 sugar rings attached to Asn-67 and Asn-257. They are localized on the molecular surface away from the conserved active site and show a new glycan of the plant complex type. A hydrogen bond between Gln-126 and Manbeta4 renders the monosaccharide oxygen O-2 sterically inaccessible to accept a xylosyl residue, therefore explaining the new type of the identified plant glycan. The Arg-Gly-Asp sequence, which has been shown to be involved in recognition of a putative cardosin A receptor, was found in a loop between two beta-strands on the molecular surface opposite the active site cleft. Based on the crystal structure, a possible mechanism whereby cardosin A might be orientated at the cell surface of the style to interact with its putative receptor from pollen is proposed. The biological implications of these findings are also discussed.
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Affiliation(s)
- C Frazão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-Oeiras, Portugal
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37
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Pereira MM, Santana M, Soares CM, Mendes J, Carita JN, Fernandes AS, Saraste M, Carrondo MA, Teixeira M. The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: a HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel. Biochim Biophys Acta 1999; 1413:1-13. [PMID: 10524259 DOI: 10.1016/s0005-2728(99)00073-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The respiratory chain of the thermohalophilic bacterium Rhodothermus marinus contains a novel complex III and a high potential iron-sulfur protein (HiPIP) as the main electron shuttle (Pereira et al., Biochemistry 38 (1999) 1268-1275 and 1276-1283). In this paper, one of the terminal oxidases expressed in this bacterium is extensively characterised. It is a caa3-type oxidase, isolated with four subunits (apparent molecular masses of 42, 19 and 15 kDa and a C-haem containing subunit of 35 kDa), which has haems of the A(s) type. This oxidase is capable of using TMPD and horse heart cytochrome c as substrates, but has a higher turnover with HiPIP, being the first example of a HiPIP:oxygen oxidoreductase. The oxidase has unusually low reduction potentials of 260 (haem C), 255 (haem A) and 180 mV (haem A3). Subunit I of R. marinus caa3 oxidase has an overall significant homology with the subunits I of the COX type oxidases, namely the metal binding sites and most residues considered to be functionally important for proton uptake and pumping (K- and D-channels). However, a major difference is present: the putative essential glutamate (E278 in Paraccocus denitrificans) of the D-channel is missing in the R. marinus oxidase. Homology modelling of the R. marinus oxidase shows that the phenol group of a tyrosine residue may occupy a similar spatial position as the glutamate carboxyl, in relation to the binuclear centre. Moreover, sequence comparisons reveal that several enzymes lacking that glutamate have a conserved substitution pattern in helix VI: -YSHPXV- instead of -XGHPEV-. These observations are discussed in terms of the mechanisms for proton uptake and it is suggested that, in these enzymes, tyrosine may play the role of the glutamate in the proton channel.
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Affiliation(s)
- M M Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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38
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Mendes J, Soares CM, Carrondo MA. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. Biopolymers 1999; 50:111-31. [PMID: 10380336 DOI: 10.1002/(sici)1097-0282(199908)50:2<111::aid-bip1>3.0.co;2-n] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [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: 11/11/2022]
Abstract
With the objective of improving side-chain conformation prediction, we have analyzed the influence of various factors on prediction by the Self-Consistent Mean Field Theory method, applied to a set of high resolution x-ray protein structure models. These factors may be classed as variations in the mean field optimization protocol, variations in the potential energy function, and variations in rotamer library completeness. We have developed an optimization protocol that consistently reached lower mean field conformational free energies than two other protocols. This protocol led to an important improvement in prediction. We observed a major improvement in prediction with two more detailed van der Waals parameter sets, which we found to be due mainly to the introduction of scaling of 1-4 interactions. In a comparison of two knowledge-based rotamer libraries of considerably different size, we observed an unexpected decrease in prediction with an increase in library completeness. However, when we introduced a torsion potential term in the potential energy function, we found an important increase in average prediction and in the prediction of almost all residue types with a more complete rotamer set. The two knowledge-based rotamer libraries now became equivalent in terms of average prediction. The results we obtained in an analysis of the effect of the introduction of an additional electrostatic term in the potential energy function were largely inconclusive. However, we found a small increase in average prediction for an electrostatic potential term with a fixed dielectric constant of 15. The combined effect of all the factors we analyzed in this study resulted in average prediction accuracies of 79.9% for X1, 68.1% for X1 + 2, and 1.590 A for global rms deviation (RMSD); the corresponding values for core residues were 88.2%, 78.6%, and 1.171 A. These values represent improvements in average prediction of 6.5% for X1, 9.1% for X1 + 2, and 0.163 A for global RMSD over the original conditions; the corresponding improvements in the core were 5.9%, 9.0%, and 0.180 A, respectively.
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Affiliation(s)
- J Mendes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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39
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Frazão C, Sieker L, Coelho R, Morais J, Pacheco I, Chen L, LeGall J, Dauter Z, Wilson K, Carrondo MA. Crystallization and preliminary diffraction data analysis of both single and pseudo-merohedrally twinned crystals of rubredoxin oxygen oxidoreductase from Desulfovibrio gigas. Acta Crystallogr D Biol Crystallogr 1999; 55:1465-7. [PMID: 10417417 DOI: 10.1107/s0907444999006216] [Citation(s) in RCA: 2] [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] [Indexed: 11/10/2022]
Abstract
Crystals of rubredoxin oxygen oxidoreductase have been obtained and characterized. They belong to space group P2(1)2(1)2, with unit-cell dimensions a = 88.24 (15), b = 101.25 (7), c = 90.80 (3) A. The homodimer (86 kDa) in the asymmetric unit is related by a non-crystallographic twofold rotation axis parallel to the ab 'diagonal' direction, as shown by the self-rotation maximum in the section with chi = 180 degrees. This pseudo-crystallographic symmetry element was also found to be the twinning axis of pseudo-merohedrally twinned crystals, leading to apparent pseudo-tetragonal P42(1)2 crystal symmetry.
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Affiliation(s)
- C Frazão
- Instituto de Tecnologia Química e Biológica, Apartado 127, 2780-Oeiras, Portugal
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Matias PM, Saraiva LM, Soares CM, Coelho AV, LeGall J, Carrondo MA. Nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774:primary sequence determination, crystallographic refinement at 1.8 and modelling studies of its interaction with the tetrahaem cytochrome c3. J Biol Inorg Chem 1999; 4:478-94. [PMID: 10555582 DOI: 10.1007/s007750050334] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [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: 10/28/2022]
Abstract
A monomeric nine-haem cytochrome c (9Hcc) with 292 amino acid residues was isolated from cells of the sulfate- and nitrate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 grown under both nitrate- and sulfate-respiring conditions. The nucleotide sequence encoding the 292 residues was determined, allowing the correction of about 10% of the previous primary structure, determined from 1.8 A electron density maps. The refinement at 1.8 A resolution of the structural model was completed, giving an R-value of 16.5%. The nine haem groups are arranged into two tetrahaem clusters, located at both ends of the molecule, with Fe-Fe distances and local protein fold very similar to tetrahaem cytochromes c3, and the extra haem is located asymmetrically between the two regions. The new primary sequence determination confirmed the 39% sequence homology found between this cytochrome and the C-terminal region (residues 229-514) of the high-molecular-weight cytochrome c (Hmc) from D. vulgaris Hildenborough, providing strong evidence of structural similarity between 9Hcc and the C-terminal region of Hmc. The interaction between 9Hcc and the tetrahaem cytochrome c3 from the same organism was studied by modelling methods, and the results suggest that a specific interaction is possible between haem 4 of tetrahaem cytochrome c3 and haem 1 or haem 2 of 9Hcc, in agreement with previous kinetic experiments which showed the catalytic effect of the tetrahaem cytochrome c3 upon the reduction of 9Hcc by the [NiFe] hydrogenase from D. desulfuricans ATCC 27774. These studies suggest a role for 9Hcc as part of the assembly of redox proteins involved in recycling the molecular hydrogen released by the cell as a result of substrate oxidation.
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Affiliation(s)
- P M Matias
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Frazão C, Sieker L, Sheldrick G, Lamzin V, LeGall J, Carrondo MA. Ab initio structure solution of a dimeric cytochrome c3 from Desulfovibrio gigas containing disulfide bridges. J Biol Inorg Chem 1999; 4:162-5. [PMID: 10499086 DOI: 10.1007/s007750050299] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [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: 10/28/2022]
Abstract
The 1.2 A resolution crystal structure of the 29 kDa di-tetrahaem cytochrome c3 from the sulfate reducing bacterium Desulfovibrio gigas was solved by ab initio methods, making this the largest molecule to be solved by this procedure. The actual refined model of the cysteine-linked dimeric molecule reveals that this molecule is very similar to the non-covalently linked symmetrical dimer of the di-tetrahaem cytochrome c3 from Desulfomicrobium norvegicum. Each monomer has the typical polypeptide fold, haem arrangement and iron coordination found for the tetrahaem cytochrome c3 molecules. The interface between the covalently linked monomers in the asymmetric unit of the crystal shows a pseudo two-fold arrangement, disturbed from symmetry by crystal packing forces. The fact that D. gigas contains a dimeric tetrahaem cytochrome with solvent accessible disulfide bridges and that this cytochrome specifically couples hydrogen oxidation to thiosulfate reduction in bacterial extracts provides an interesting aspect related to disulfide exchange reactions in this microorganism.
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Affiliation(s)
- C Frazão
- Department of Biological Structure, University of Washington Seattle 98195, USA
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Matias PM, Coelho R, Pereira IA, Coelho AV, Thompson AW, Sieker LC, Gall JL, Carrondo MA. The primary and three-dimensional structures of a nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 reveal a new member of the Hmc family. Structure 1999; 7:119-30. [PMID: 10368280 DOI: 10.1016/s0969-2126(99)80019-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [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: 10/17/2022]
Abstract
BACKGROUND Haem-containing proteins are directly involved in electron transfer as well as in enzymatic functions. The nine-haem cytochrome c (9Hcc), previously described as having 12 haem groups, was isolated from cells of Desulfovibrio desulfuricans ATCC 27774, grown under both nitrate- and sulphate-respiring conditions. RESULTS Models for the primary and three-dimensional structures of this cytochrome, containing 292 amino acid residues and nine haem groups, were derived using the multiple wavelength anomalous dispersion phasing method and refined using 1.8 A diffraction data to an R value of 17.0%. The nine haem groups are arranged into two tetrahaem clusters, with Fe-Fe distances and local protein fold similar to tetrahaem cytochromes c3, while the extra haem is located asymmetrically between the two clusters. CONCLUSIONS This is the first known three-dimensional structure in which multiple copies of a tetrahaem cytochrome c3-like fold are present in the same polypeptide chain. Sequence homology was found between this cytochrome and the C-terminal region (residues 229-514) of the high molecular weight cytochrome c from Desulfovibrio vulgaris Hildenborough (DvH Hmc). A new haem arrangement in domains III and IV of DvH Hmc is proposed. Kinetic experiments showed that 9Hcc can be reduced by the [NiFe] hydrogenase from D. desulfuricans ATCC 27774, but that this reduction is faster in the presence of tetrahaem cytochrome c3. As Hmc has never been found in D. desulfuricans ATCC 27774, we propose that 9Hcc replaces it in this organism and is therefore probably involved in electron transfer across the membrane.
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Affiliation(s)
- P M Matias
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780 OEIRAS, Portugal
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Martel PJ, Soares CM, Baptista AM, Fuxreiter M, Náray-Szabó G, Louro RO, Carrondo MA. Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods. J Biol Inorg Chem 1999; 4:73-86. [PMID: 10499105 DOI: 10.1007/s007750050291] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [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: 11/25/2022]
Abstract
A comparative study of the pH-dependent redox mechanisms of several members of the cytochrome c3 family has been carried out. In a previous work, the molecular determinants of this dependency (the so-called redox-Bohr effect) were investigated for one species using continuum electrostatic methods to find groups with a titrating range and strength of interaction compatible with a mediating role in the redox-Bohr effect. Here we clarify these aspects in the light of new and improved pKa calculations, our findings supporting the hypothesis of propionate D from heme I being the main effector in the pH-dependent modulation of the cytochrome c3 redox potentials in all the c3 molecules studied here. However, the weaker (but significant) role of other titrating groups cannot be excluded, their importance and identity changing with the particular molecule under study. We also calculate the relative redox potentials of the four heme centers among the selected members of the c3 family, using a continuum electrostatic method that takes into account both solvation and interaction effects. Comparison of the calculated values with available data for the microscopic redox potentials was undertaken, the quality of the agreement being dependent upon the choice of the dielectric constant for the protein interior. We find that high dielectric constants give best correlations, while low values result in better magnitudes for the calculated potentials. The possibility that the crystallographic calcium ion in c3 from Desulfovibrio gigas may be present in the solution structure was tested, and found to be likely.
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Affiliation(s)
- P J Martel
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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Bento I, Frazão C, Coelho R, Wilson K, Dauter Z, Carrondo MA. Crystallization and preliminary X-ray crystallographic studies of the plant aspartic proteinase cardosin A. Acta Crystallogr D Biol Crystallogr 1998; 54:991-3. [PMID: 9757116 DOI: 10.1107/s0907444998001048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plant aspartic proteinase cardosin A was crystallized using vapour diffusion. Crystals belong to the monoclinic space group C2, cell dimensions a = 116.9 (2), b = 87.2 (8), c = 81.3 (1) A, beta = 104.4 (4) degrees, and contain two molecules in the asymmetric unit related by a non-crystallographic twofold axis. Diffraction data were collected at room temperature with radiation from a synchrotron source up to 2.85 A resolution. When the crystals were flash cooled to 110 K in a nitrogen stream the same resolution limit could also be obtained on a rotating-anode source. Recently, synchrotron radiation together with flash cooling led to an improvement of the diffraction data to 1.72 A resolution.
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Affiliation(s)
- I Bento
- Instituto de Tecnologia Química e Biológica, Apartado 127, 2780-Oeiras, Portugal
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Bento I, Coelho R, Frazão C, Costa J, Faro C, Veríssimo P, Pires E, Cooper J, Dauter Z, Wilson K, Carrondo MA. Crystallisation, structure solution, and initial refinement of plant cardosin-A. Adv Exp Med Biol 1998; 436:445-52. [PMID: 9580380 DOI: 10.1007/978-1-4615-5373-1_61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- I Bento
- Dep. Bioquímica, Fac. Ciências e Tecnologia, Univ. Coimbra, Portugal
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Soares CM, Martel PJ, Mendes J, Carrondo MA. Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations. Biophys J 1998; 74:1708-21. [PMID: 9545034 PMCID: PMC1299516 DOI: 10.1016/s0006-3495(98)77882-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [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: 02/07/2023] Open
Abstract
The tetraheme cytochrome c3 from Desulfovibrio vulgaris Hildenborough is studied using molecular dynamics simulation studies in explicit solvent. The high heme content of the protein, which has its core almost entirely made up of c-type heme, presents specific problems in the simulation. Instability in the structure is observed in long simulations above 1 ns, something that does not occur in a monoheme cytochrome, suggesting problems in heme parametrization. Given these stability problems, a partially restrained model, which avoids destruction of the structure, was created with the objective of performing free energy calculations of heme reduction, studies that require long simulations. With this model, the free energy of reduction of each individual heme was calculated. A correction in the long-range electrostatic interactions of charge groups belonging to the redox centers had to be made in order to make the system physically meaningful. Correlation is obtained between the calculated free energies and the experimental data for three of four hemes. However, the relative scale of the calculated energies is different from the scale of the experimental free energies. Reasons for this are discussed. In addition to the free energy calculations, this model allows the study of conformational changes upon reduction. Even if the precise details of the structural changes that take place in this system upon individual heme reduction are probably out of the reach of this study, it appears that these structural changes are small, similarly to what is observed for other redox proteins. This does not mean that their effect is minor, and one example is the conformational change observed in propionate D from heme I when heme II becomes reduced. A motion of this kind could be the basis of the experimentally observed cooperativity effects between heme reduction, namely positive cooperativity.
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Affiliation(s)
- C M Soares
- Instituto de Tecnologia Química e Biologica, Oeiras, Portugal.
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Costa J, Ashford DA, Nimtz M, Bento I, Frazäo C, Esteves CL, Faro CJ, Kervinen J, Pires E, Veríssimo P, Wlodawer A, Carrondo MA. The glycosylation of the aspartic proteinases from barley (Hordeum vulgare L.) and cardoon (Cynara cardunculus L.). Eur J Biochem 1997; 243:695-700. [PMID: 9057834 DOI: 10.1111/j.1432-1033.1997.t01-1-00695.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Plant aspartic proteinases characterised at the molecular level contain one or more consensus N-glycosylation sites [Runeberg-Roos, P., Tŏrmäkangas, K. & Ostman, A. (1991) Eur. J. Biochem. 202, 1021-1027; Asakura, T., Watanabe, H., Abe, K. & Arai, S. (1995) Eur. J. Biochem, 232, 77-83; Veríssimo, P., Faro, C., Moir, A. J. G., Lin, Y., Tang, J. & Pires, E. (1996) Eur. J. Biochem. 235, 762-768]. We found that the glycosylation sites are occupied for the barley (Hordeum vulgare L.) aspartic proteinase (Asn333) and the cardoon (Cynara cardunculus L.) aspartic proteinase, cardosin A (Asn70 and Asn363). The oligosaccharides from each site were released from peptide pools by enzymatic hydrolysis with peptide-N-glycanase A or by hydrazinolysis and their structures were determined by exoglycosidase sequencing combined with matrix-assisted laser desorption/ionization time of flight mass spectrometry. It was observed that 6% of the oligosaccharides from the first glycosylation site of cardosin A are of the oligomannose type. Modified type glycans with proximal Fuc and without Xyl account for about 82%, 14% and 3% of the total oligosaccharides from the first and the second glycosylation sites of cardosin A and from H. vulgare aspartic proteinase, respectively. Oligosaccharides with Xyl but without proximal Fuc were only detected in the latter proteinase (4%). Glycans with proximal Fuc and Xyl account for 6%, 86% and 92% of total oligosaccharides from the first and second glycosylation sites of cardosin A and from H. vulgare aspartic proteinase, respectively.
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Affiliation(s)
- J Costa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Coelho AV, Matias PM, Sieker LC, Morais J, Carrondo MA, Lampreia J, Costa C, Moura JJ, Moura I, Le Gall J. Preliminary crystallographic analysis and further characterization of a dodecaheme cytochrome c from Desulfovibrio desulfuricans ATCC 27774. Acta Crystallogr D Biol Crystallogr 1996; 52:1202-8. [PMID: 15299587 DOI: 10.1107/s090744499600738x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Dodecaheme cytochrome c has been purified from Desulfovibrio (D.) desulfuricans ATCC 27774 cells grown under both nitrate and sulfate-respiring conditions. Therefore, it is likely to play a role in the electron-transfer system of both respiratory chains. Its molecular mass (37768 kDa) was determined by electrospray mass spectrometry. Its first 39 amino acids were sequenced and a motif was found between amino acids 32 and 37 that seems to exist in all the cytochromes of the c(3) type from sulfate-reducing bacteria sequenced at present. The midpoint redox potentials of this cytochrome were estimated to be -68, -120, -248 and -310 mV. Electron paramagnetic resonance spectroscopy of the oxidized cytochrome shows several low-spin components with a g(max) spreading from 3.254 to 2.983. Two crystalline forms were obtained by vapour diffusion from a solution containing 2% PEG 6000 and 0.25-0.75 M acetate buffer pH = 5.5. Both crystals belong to monoclinic space groups: one is P2(1), with a = 61.00, b = 106.19, c = 82.05 A, beta = 103.61 degrees, and the other is C2 with a = 152.17, b = 98.45, c = 89.24 A, beta = 119.18 degrees. Density measurements of the P2(1) crystals suggest that there are two independent molecules in the asymmetric unit. Self-rotation function calculations indicate, in both crystal forms, the presence of a non-crystallographic axis perpendicular to the crystallographic twofold axis. This result and the calculated values for the volume per unit molecular weight of the C2 crystals suggest the presence of two or four molecules in the asymmetric unit.
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Affiliation(s)
- A V Coelho
- Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
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Matias PM, Coelho A, Carrondo MA, Fülöp V, Gonzalez A, Thompson A. A novel iron center in desulfoferrodoxin from D. desulfuricansATCC 27774: crystal structure at 1.8 Å resolution. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396096237] [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: 11/10/2022] Open
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50
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Coelho A, Matias PM, Carrondo MA, Fülöp V, Gonzalez A, Thompson A. MAD phasing used in the structure determination of desulfoferrodoxin. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396096742] [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: 11/10/2022] Open
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