Universidade Nova de Lisboa - CERMAX - ITQB

UNL
CERMAX - Centro de Ressonância Magnética António Xavier
ITQB - Instituto de Tecnologia Química e Biológica
Av. da República - EAN, Apartado 127
2780-156 Oeiras
Portugal

NMR Equipment
  • Bruker Avance II+ 800
  • Bruker Avance III 500
  • Bruker Avance II 500
  • Bruker Avance 400
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UNL - CERMAX-ITQB

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Main Research Topics

Helena Santos - In vivo metabolomics and protein NMR

Since 1986 Prof. Helena Santos is the leader of a research group (Cell Physiology and NMR), which applies NMR as the main tool to investigate cell metabolism and regulation. Her research team has pioneered the use in Portugal of in vivo NMR techniques to study metabolism of lactic acid bacteria and brain cells. Also, since 1993 she coordinated several projects in the area of stress responses in hyperthermophiles, which lead to the identification by NMR of several novel compatible solutes in thermophiles and hyperthermophiles, the discovery of their biosynthetic pathways, and the characterization of key-genes and enzymes. Her extensive expertise in NMR covers such diverse areas as in vivo NMR, metabolomics, structural studies in heme proteins, small molecule structural determination, protein dynamics and structural studies, and the discovery of new metabolic pathways by NMR.

David Turner - paramagnetic systems, Haem proteins and protein structure

Prof. David Turner had used high field NMR to investigate redox- and pH-related conformational changes in proteins that couple electron and proton transfer. In-house software is used to determine solution structures of paramagnetic as well as diamagnetic proteins. The thermodynamic properties of multihaem proteins are obtained from the dependence of carbon and proton chemical shifts of the haems on redox state and pH. Similar experiments to those used to cross assign haem signals in different redox states also provide information on the rate of electron transfer between protein molecules and the rate of proton exchange with the solvent. The aim of these studies is to understand how changes in protein conformation control energy transduction.

Carlos Romão - Organometalic compounds

Prof. Carlos Romão has directed its NMR studies to the structural identification of mainly organometallic complexes, that act as catalysts, potential pharmaceuticals, namely anti-tumoral drugs, as well as the identification of reaction products, intermediates and mechanisms involved in the catalytic reactions.

Ana Rute Neves - In vivo metabolomics

The study of metabolic and transcriptional regulation of sugar metabolism in lactic acid bacteria (LAB) and low-GC human pathogens is at the core Ana Rute’s research interests. Characterization of metabolic and regulatory networks requires data obtained at different cellular levels (mRNA, protein and metabolites). Different NMR techniques have been used to obtain reliable, good quality data on metabolite concentrations and carbon fluxes. During the last decade, Ana Rute has engaged on the application of in vivo NMR to probe biological processes directly in living cells. Through this effort she has gained substantial expertise in metabolite profiling and metabolic elucidation using NMR.

Ricardo Louro - Heamproteins

Dr. Ricardo O. Louro has focused his research studies on the bioenergetic metabolism of organisms that use metal compounds as sources or sinks of electrons. In the case of respiration this has been named extracellular respiration and involves the participation of complex electron transfer networks where heme proteins play key roles. NMR is used for the structural and functional characterization of these proteins, complemented by other biophysical and biochemical techniques.

Pedro Lamosa - Protein structure and dynamics

Having devoted his research to the adaptation of microorganisms to high temperatures, Dr. Pedro Lamosa has mainly used NMR to study protein stabilization by compatible solutes. These studies have focused in the discovery of novel compatible solutes accumulated by hyperthermophiles and their structure determination, and their action upon protein structure and protein dynamics. Through this effort he gain expertise in 3D protein structure determination by NMR, protein dynamics studies using H/D exchange and 15N relaxation studies, and the determination of the structure of small molecules using conventional 2D NMR techniques.

Patrick Groves - Molecular interactions

Dr Patrick Groves joined CERMAX (and the ITQB) in February 2008 after conducting research in the UK, Sweden, Poland and Spain. His experience in chemistry, biochemistry and NMR spectroscopy is currently concentrated on transfer-NMR (TR-NMR) methods that are used to define the molecular interactions of small molecules or ligands in the presence of biomolecules. Diffusion NMR (DOSY) can select which ligand from a mixture binds to a biomolecules. Saturation Transfer Difference (STD) NMR gives us the interaction surface for the bound molecule. Transfer nuclear Overhauser effect spectroscopy (TR-NOESY) gives us the bound conformation around flexible bonds. The samples typically contain around a ten micromolar solution of biomolecule and one millimolar ligand. TR-NMR methods are used to screen small molecule libraries (pharmaceutical applications) and to investigate specific ligands (biochemical applications).

Manolis Matzapetakis - Biomolecular NMR

Our focus is the application of NMR to various biomolecular problems. We are interested in protein structure determination - dynamics, protein-protein interactions including the study of metalloproteins and large proteins. Topics of research include the: Study or ferrous transport mechanisms in pathogenic bacteria. While significant amount of research has been done in the field of sequestering and transport system of iron we are still discovering new proteins that seem to function as transporters. We are interested in the structural and functional characterization of such proteins with an emphasis in pathogenic bacteria. Development of protocols for NMR based structural proteomics, Develop protocols for high throughput use of high field NMR in proteomics. Application of fast NMR acquisition and automated structure determination. Optimization of NMR friendly, high throughput protocols for protein production. Use in-cell NMR as a quick way to evaluate protein folding inside the cell

Selected Publications

  1. Alves P.M., Flögel U., Brand A., Leibfritz D., Carrondo M.J.T., Santos H. and Sonnewald U. (1996) Immobilization of primary astrocytes and neurons for on line monitoring of biochemical processes by NMR Developmental Neuroscience, 18, 478-483.

  2. Ramos A. and Santos H. (1999) NMR studies of wine chemistry and wine bacteria Annual Reports on NMR Spectroscopy, 37, 179-202.

  3. Xavier K.B., da Costa M.S. and Santos H. (2000) Demonstration of a novel glycolytic pathway in the hyperthermophilic archaeon Thermococcus zilligii by 13C-labeling experiments and NMR analysis. Journal of Bacteriology, 182, 4632-4636.

  4. Alves P.M., Fonseca L.L., Peixoto C.C., Almeida A.C., Carrondo M.J.T. and Santos H. (2000) NMR studies on energy metabolism of immobilized primary neurons and astrocytes during hypoxia, ischemia and hypoglycemia. NMR in Biomedicine, 13, 438-448.

  5. Neves A.R., Ventura R., Mansour N., Shearman C., Gasson M.J., Maycock C., Ramos A. and Santos H. (2002) Is the glycolytic flux in Lactococcus lactis primarily controlled by the redox charge? Kinetics of NAD+ and NADH pools determined in vivo by 13C-NMR. Journal of Biological Chemistry, 277, 28088-28098.

  6. Voit E.O., Neves A.R. and Santos H. (2006) The Intricate Side of Systems Biology. Proc. Nat. Acad. Sci. USA. 103:9452-9457.

  7. Lemos P.C., Dai Y., Yuan Z., Keller J., Santos H. and Reis A.M. (2007) Elucidation of metabolic pathways in glycogen-accumulating organisms with in vivo 13C nuclear magnetic resonance. Environmental Microbiology, 9, 2694-2706.

  8. Borges N., Gafeira L.G., Rodrigues M.V., Ventura R., Maycock C., Lamosa,P. and Santos H. (2006) Biosynthetic pathways of inositol and glycerol phosphodiesters used for stress adaptation in Archaeoglobus fulgidus. Journal of Bacteriology, 188, 8128-8135.

  9. Jorge C., Lamosa P. and Santos H. (2007) α-d-mannopyranosyl-(1→2)-α-d-glucopyranosyl-(1→2)-glycerate in the thermophilic bacterium Petrotoga miotherma: structure, cellular content and function. FEBS Journal, 274, 3120-3127.

  10. Lamosa P., Gonçalves L.G., Rodrigues M., Martins L.O., Raven N., and Santos H. (2006) Occurrence of 1-glyceryl-1-myo-inosityl-phosphate in hyperthermophiles. Applied and Environmental Microbiology: 72:6169-73.

  11. Pais T.M., Lamosa P., dos Santos W., LeGall J., Turner D.L. and Santos H. (2005) Structural determinants of protein stabilization by solutes: the importance of the hairpin loop in rubredoxins. European Journal of Biochemistry, 272, 999-1011.

  12. Lamosa P., Brennan L., Vis H., Turner D.L., and Santos H. (2001) NMR Structure of Desulfovibrio gigas Rubredoxin – A Model for Studying Protein Stabilisation by Compatible Solutes. Extremophiles. 5:301-11.

  13. Lamosa P., Turner D.L., and Santos H. (2003) Protein Stabilization by Compatible Solutes: Effect of Diglycerol Phosphate in the Backbone Dynamics of Desulfovibrio gigas Rubredoxin. Eur. J. Biochem. 270:4606-14.

  14. Messias A.C., Kastrau D.H.W., Costa H.S., LeGall J., Turner D.L., Santos H. and Xavier A.V. (1998) Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c3: structural basis for functional cooperativity Journal of Molecular Biology, 281, 719-739.

  15. Turner D.L., Brennan L., Meyer H.E., Lohaus C., Siethoff C., Costa H.S., Gonzalez B., Santos H. and Suárez J.E. (1999) Solution structure of plantaricin c, a novel lantibiotic European Journal of Biochemistry, 264, 833-839.

  16. Brennan L., Turner D.L., Messias A.C., Teodoro M.L., LeGall J., Santos H. and Xavier A.V. (2000) Structural basis for the network of functional cooperativities in cytochrome c3 from Desulfovibrio gigas: solution structures of the oxidised and reduced states. Journal of Molecular Biology, 298, 61-82.

  17. Brennan L., Turner D.L., Fareleira P. and Santos H. (2001) Solution structure of Methylophilus methylotrophus cytochrome c”: insights into the structural basis of haem-ligand detachment. Journal of Molecular Biology, 308, 353-365.

  18. Turner, D.L., Salgueiro, C.A., Catarino, T., Legall, J. and Xavier, A.V. (1996) NMR studies of cooperativity in the tetrahaem cytochrome c(3) from Desulfovibrio vulgaris. European Journal of Biochemistry 241:723-731.

  19. Messias, A.C., Aguiar, A.P., Brennan, L., Salgueiro, C.A., Saraiva, L.M., Xavier, A.V. and Turner, D.L. (2006) Solution structures of tetrahaem ferricytochrome c(3) from Desulfovibrio vulgaris (Hildenborough) and its K45Q mutant: The molecular basis of cooperativity. Biochimica Et Biophysica Acta-Bioenergetics 1757:143-153.

  20. Paquete, C.M., Pereira, P.M., Catarino, T., Turner, D.L., Louro, R.O. and Xavier, A.V. (2007) Functional properties of type I and type II cytochromes c3 from Desulfovibrio africanus, Biochim Biophys Acta 1767:177-188.

  21. Paquete, C.M., Reis, C., Louro, R.O., Xavier, A.V., Catarino, T. and Turner, D.L. (2005) characterization of a nine heme cytochrome by NMR, Ann. Magn. Reson., 4:100-104.

  22. Pessanha, M.J, Salgueiro, C.A., Rothery, E.L., Chapman, S.K, Louro, R.O., Turner, D.L., Xavier, A.V., Miles, C.S. and Reid, G.A. (2005) Elucidation of the functional redox behaviour of the fumarate reductase of Shewanella frigidimarina by NMR, Ann. Magn. Reson. 4:24-28.

  23. Salgueiro, C.A., Morgado, L., Fonseca, B., Lamosa, P., Catarino, T., Turner, D.L., Louro, R.O. (2005) Binding of ligands originates small perturbations on the microscopic thermodynamic properties of a multicentre redox protein, FEBS J. 272:2251-2260.

  24. Paquete, C.M., Pereira, P.M., Catarino, T., Turner, D.L., Louro, R.O. and Xavier, A.V. (2007) Functional properties of type I and type II cytochromes c3 from Desulfovibrio africanus, Biochim Biophys Acta 1767:177-188.

  25. Correia, I.J., Paquete, C.M., Coelho, A., Almeida, C., Catarino, T., Louro, R.O., Frazão, C., Saraiva, L.M., Carrondo, M.A., Turner, D.L. and Xavier, A.V. (2004) Proton assisted two-electron transfer in natural variants of tetraheme cytochromes from Desulfomicrobium sp., J. Biol. Chem. 279:52227-52237.

  26. Louro, R.O., Pessanha, M., Reid, G.A., Chapman, S.K., Turner, D.L. and Salgueiro, C.A. (2002) Determination of the orientation of the axial ligands and of the magnetic properties of the haems in the tetrahaem ferricytochrome from Shewanella frigidimarina, FEBS Letts., 531:520-524.

  27. Pereira, P. M., Pacheco, I., Turner, D. L. and Louro, R. O. (2002) Structure-function relationship in type II cytochrome c3 from Desulfovibrio africanus: a novel function in a familiar heme core, J.Biol.Inorg.Chem. 7:815-822.

  28. Louro, R.O., de Waal, H., Ubbink, M. and Turner, D.L. (2002) Replacement of the methionine axial ligand by a lysine: effects on the haem electronic structure, FEBS Lett. 510:185-188.

  29. Louro, R.O. (2007) Proton thrusters: overview of the structural and functional features of soluble tetrahaem cytochromes c3, J. Biol. Inorg. Chem. 12:1-10.
    Pessanha, M., Morgando, L., Louro, R.O., Londer, Y.Y., Pokkuluri, P.R., Schiffer, M. and Salgueiro, C.A. (2006) Thermodynamic characterization of triheme cytochrome PpcA from Geobacter sulfurreducens: evidence for a role played in e-/H+ energy transduction, Biochemistry, 45:13910-13917.

  30. Pereira, M., Jones, K.L., Campos, M.G., Melo, A.M.P., Saraiva L.M., Louro, R.O., Wittung-Stafshede, P. and Teixeira, M. (2002) A ferredoxin from the thermohalophilic bacterium Rhodothermus marinus, Biochim.Biophys.Acta, 1601:1-8.

  31. P. Groves, S. Offermann, M.O. Rasmussen, F.J. Cañada, J.J. Bono, H. Driguez, A. Imberty and J. Jiménez-Barbero (2005) The relative orientation of the lipid and carbohydrate moieties of lipochitooligosaccharides related to nodulation factors depends on lipid chain saturation, Org. Biomol. Chem., 3:1381–86.

  32. M.I. Chavez, C. Andreu, P. Vidal, N. Aboitiz, F. Freire, P. Groves, J-L- Asensio, G. Asensio, M. Muraki, F.J. Cañada, J. Jiménez-Barbero (2005)On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins. NMR Studies of the Structure and Binding Affinity of AcAMP2-Like Peptides with non Natural Napthyl and Fluoroaromatic Residues, Chem. Eur. J., 11:7060-74.

  33. F. Chevalier, J. Lopez-Prados, P. Groves, S. Perez, M. Martín-Lomas and P.M. Nieto (2006) Structure and dynamics of the conserved protein GPI anchor core inserted into detergent micelles, Glycobiol., 16:969-980.

  34. M. Politi, J. Alvaro-Blanco, P. Groves, A. Prieto, J.A. Leal, F.J. Cañada and J. Jiménez-Barbero (2006) Screening garlic water extract for binding activity with Cholera Toxin B pentamer by NMR. An old remedy giving a new surprise, Eur. J. Org. Chem., 2067-73.

  35. P. Groves, M. Palczewska, M.D. Molero, G. Batta, F.J. Cañada and J. Jiménez-Barbero (2004) Protein Molecular weight standards can compensate systematic errors in Diffusion Ordered Spectroscopy, Anal. Biochem., 331:395-7.

  36. P. Groves, M. O. Rasmussen, M. D. Molero, E. Samain, F. J. Canada, H. Driguez and J. Jimenez-Barbero (2004) Diffusion ordered spectroscopy as a complement to size exclusion chromatography in oligosaccharide analysis, Glycobiology, 14: 451-6.

  37. P. Groves, K.E. Kövér, S. André, J. Bandorowicz-Pikula, G. Batta, M. Bruix, R. Buchet, A. Canales, F.J. Cañada, H-J. Gabius, D.V. Laurents, J.R. Naranjo, M. Palczewska, S. Pikula, E. Rial, A. Strzelecka-Kiliszek, and J. Jiménez-Barbero (2007) Effect of temperature in Saturation Transfer Difference NMR experiments, Magn. Reson. Chem., 45:745-8.

  38. K.E. Kövér, P. Groves, J. Jiménez-Barbero and G. Batta (2007) Molecular recognition and screening using STD NMR: 15N-group selective STD NMR experiment to study intermolecular interactions in heavily overlapped spectra, J. Am. Chem. Soc., 129:11579-82.

  39. M. Palczewska, G. Batta, P. Groves, S. Linse, and J. Kuźnicki (2005) Localization of the Ca(2+)- and H(+)-dependent hydrophobic properties of calretinin”, Protein Sci., 14:1879-87.

  40. Bermel, W., I. Bertini, I.C. Felli, M. Matzapetakis, R. Pierattelli, E.C. Theil, P. Turano (2007) A method for C direct-detection in protonless NMR. J. Mag. Res., 188:301-10.

  41. Matzapetakis, M., P. Turano, E.C. Theil,I. Bertini, (2007) (13)C- (13)C NOESY spectra of a 480 kDa protein: solution NMR of ferritin. J Biomol NMR, 38:237-42.