MX Structural Genomics Lab

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Publications

2017

• A.I. Coelho, E. Rubio-Gozalbo, J.B. Vicente, and I.A. Rivera (2017) "Sweet and sour: "Sweet and sour: an update on classic galactosemia",
  J Inherit Metab Dis, in press

J.B. Vicente, H.G. Colaço, F. Malagrinò, P.E. Santo, A. Gutierres, T.M. Bandeiras, P. Leandro, J.A. Brito, and A. Giuffrè (2017) "A clinically relevant variant of the human hydrogen sulfide-synthesizing enzyme cystathionine β-synthase: increased CO reactivity as a novel molecular mechanism of pathogenicity?", Oxid Med Cell Longev, in press


2016

J.B. Vicente, F. Malagrinò, M. Arese, E. Forte, P. Sarti, and A. Giuffrè* (2016) " Bioenergetic relevance of hydrogen sulfide and the interplay between gasotransmitters at human cystathionine -synthase", BBA Bioenergetics, in press
http://www.ncbi.nlm.nih.gov/pubmed/27039165

• E. Forte, V. Borisov, M. Falabella, H.G. Colaço, M. Tinajero-Trejo, R. Poole, J.B. Vicente, P. Sarti, and A. Giuffrè (2016) "The Terminal Oxidase Cytochrome bd Promotes Sulfide-resistant Bacterial Respiration and Growth", Sci Reports, in press
http://dx.doi.org/10.1038/srep23788

• H.G. Colaço, P.E. Santo, P.M. Matias, T.M. Bandeiras, J.B. Vicente (2016) "Roles of Escherichia coli ZinT in cobalt, mercury and cadmium resistance and structural insights into the metal binding mechanism" Metallomics 8:327-336.
http://dx.doi.org/10.1039/C5MT00291E

C.M. Romão, J.B. Vicente, C. Frazão, and M. Teixeira (2016) "The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases", J Biol Inorg Chem 21(1): 39-52.
http://dx.doi.org/10.1007/s00775-015-1329-4

J.B. Vicente, H.G. Colaço, P. Sarti, P. Leandro, and A. Giuffrè* (2015) "S-Adenosyl-L-methionine modulates CO and NO· binding to the human H2S-generating enzyme cystathionine ß-synthase", J Biol Chem 291(2): 572-81.
http://dx.doi.org/10.1074/jbc.M115.681221


2015

• R. Ponnusamy, M.V. Petoukhov, B. Correia, T.F. Custodio, F. Juillard, M. Tan, M. Pires de Miranda, M.A. Carrondo, J.P. Simas, K.M. Kaye, D.I. Svergun, C.E. McVey (2015) "KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA." Nucleic Acids Res. 43 (20): 10039-54.
http://dx.doi.org/10.1093/nar/gkv987

• C.M. Sousa, P. Carpentier, P.M. Matias, F. Testa, F. Pinho, P. Sarti, A. Giuffrè, T.M. Bandeiras, C.V. Romão (2015) “Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre highly sensitive to photo-reduction” Acta Crystallographica D 71:2236-2247.
http://dx.doi.org/10.1107/S1399004715015825

• Pedersen, H. L., Johnson, K. A., McVey, C. E., Leiros, I. &, Moe E. (2015). “Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA”. Acta Crystallogr D Biol Crystallogr 71: 2137-49
http://dx.doi.org/10.1107/S1399004715014157

Moe, E., Assefa, N. G., Leiros, I., Torseth, K. J., Smalås, A. O. & Willassen, N. P. (2015). “Reduced Hydrophobicity of the Minor Groove Intercalation Loop is Critical for Efficient Catalysis by Cold Adapted Uracil-DNA N-Glycosylase from Atlantic Cod”. J Thermodyn Catal 6:155
http://dx.doi.org/10.4172/2157-7544.1000155

• C. G. Fernandes, D. Plácido, D. Lousa, J. A. Brito, A. Isidro, C. M.  Soares, J. Pohl, M. A. Carrondo, M. Archer, A. O. Henriques (2015, “Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking”, Biochemistry 54(37):5723-34.
http://dx.doi.org/10.1021/acs.biochem.5b00661

M.I. Mendes, D.E. Smith, J.B. Vicente, I. Tavares De Almeida, T. Ben-Omran, G.S. Salomons, I.A. Rivera, P. Leandro, H.J. Blom (2015) "Small aminothiol compounds improve the function of Arg to Cys variant proteins: effect on the human cystathionine ß-synthase p.R336C", Hum Mol Genet 24(25): 7339-48.
http://dx.doi.org/10.1093/hmg/ddv431

• Sarre, A., Ökvist, M., Klar, T., Hall, D., Smalas, A., McSweeney, S., Timmins, J. &, Moe E. (2015). «Structure/function studies of two unusual Endonuclease III enzymes from the extreme radiation and desiccation resistant bacterium Deinococcus radiodurans”. J Struct Biol. 191: 87-99
http://dx.doi.org/10.1016/j.jsb.2015.05.009

Niiranen, L., Lian, K., K., J. & Moe, E. (2015). «Crystal structure determination of DNA polymerase III b-subunit from the extreme radiation and desiccation resistant bacterium Deinococcus radiodurans”. BMC structural biology 15:5
http://dx.doi.org/10.1186/s12900-015-0032-6

Lian, K., Leiros, H. K. & Moe, E. (2015). “MutT from the fish pathogen Aliivibrio salmonicida is a cold-active nucleotide-pool sanitization enzyme with unexpectedly high thermostability”. FEBS Open Bio 5: 107-16
http://dx.doi.org/10.1016/j.fob.2015.01.006

Moe, E., Sezer, M., Hildebrandt, P. & Todorovic, S. (2015). “Surface enhanced vibrational spectroscopic evidence for an alternative DNA-independent redox activation of endonuclease III”. Chem Commun (Camb) 51: 3255-7
http://dx.doi.org/10.1039/c4cc09498k


 

2014

• P.T. Borges, C. Frazão, C.S. Miranda, M.A. Carrondo, and C.V. Romão, "Structure of the mono-functional heme catalase DR1998 from Deinococcus radiodurans", FEBS J. (2014), 281(18):4138-4150.

• P.T. Borges, C.S. Miranda, S.P. Santos, J.N. Carita, C. Frazão and C.V. Romão, "Purification, crystallization and phase determination of the DR1998 haem b catalase  from Deinococcus radiodurans", Acta Cryst. (2014) F70(5): 659-662.

• A.T. Marques, S.P. Santos, C.S. Miranda, M.J. Rosa, M.A. Rodrigues, I.A. Abreu, C. Frazão and C.V. Romão, "Expression, purification and crystallization of MnSOD from Arabidopsis thaliana", Acta Cryst. (2014) F70(5): 669-672.

• C.E. McVey, M.J. Ferreira, B. Correia, S. Lahiri, D. de Sanctis, M.A. Carrondo, P.F. Lindley, I. de-Sá-Nogueira, C.M. Soares and I. Bento, "The importance of the Abn2 calcium cluster in the endo-1,5-arabinanase activity from Bacillus subtilis", JBIC (2014), 19: 505-513.

 

2013

 

• A.M. Gonçalves, S. Mendes, D. de Sanctis, L.O. Mendes and I. Bento, "The Crystal Structure of Pseudomonas putida Azoreductase: the active site revisited." , FEBS J. (2013) 280(24):6643-6657.

B. Correia, S.A. Cerqueira, C. Beauchemin, M. Pires de Miranda, S. Li, R. Ponnusamy, L. Rodrigues, T. R. Schneider, M. A. Carrondo, K. M. Kaye, J. P. Simas and C. E. McVey “Crystal structure of the gamma-2 herpesvirus LANA DNA binding domain identifies charged surface residues which impact viral latency", PlosPath. (2013), 9(10): e1003673. doi:10.1371/journal.ppat.1003673.

• M. Pires de Miranda, F. B. Lopes, C. E. McVey, X. R. Bustelo,and J. P. Simas. "Role of Src-homology domain binding in signaling complexes assembled by the murid gammaherpesvirus M2 protein."J. Biol. Chem. 2013 vol. 288 (6) p. 3858-3870.

 

 

2012

• S. Gonçalves, S.P. Miller, M.A. Carrondo, A.M. Dean and P.M. Matias, "Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase", Biochemistry (2012), 51:7098–7115. 

• A.R. Marques, L. Kromer, D.J. Gallo, N. Penacho, S.S. Rodrigues, J.D. Seixas, G.J.L. Bernardes, P.M. Reis, S.L. Otterbein, R.A. Ruggieri, A.S.G. Gonçalves, A.M.L. Gonçalves, M.N. De Matos, I. Bento, L.E. Otterbein, W.A. Blättler, and C.C. Romão, “Generation of Carbon Monoxide Releasing Molecules (CO-RMs) as Drug Candidates for the Treatment of Acute Liver Injury: Targeting of CO-RMs to the Liver”, Organometallics (2012), 31 (16): 5810–5822.

• A.M. Gonçalves, C.S. Silva, T.I. Madeira, R. Coelho, D. de Sanctis, M.V. San Romão and I. Bento, "Endo-beta-D-1,4-mannanase from Chrysonilia sitophila displays a novel loop arrangement for substrate selectivity", Acta Cryst. (2012), D68, 1468-1478.

• C.N. Santos, M.M. Alves, I. Bento and R.B. Ferreira "Missing pieces in protein deposition and mobilization inside legume seed storage vacuoles: calcium and magnesium ions",  Seed Science Research (2012), in press

• S.P. Santos, T.M. Bandeiras, A.F. Pinto, M. Teixeira, M.A. Carrondo, C.V. Romão, “Thermofluor-based optimisation strategy for the stabilsation and crystallisation of Campylobacter jejuni desulforubrerythrin”,  Protein Exp. Purif. (2012), 81(2): 193-200.

• C.S. Silva, J.M. Damas, Z. Chen, V. Brissos, L.O. Martins, C.M. Soares, P.F. Lindley and I. Bento, “The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase: assistance during the proton-transfer mechanism ”, Acta Cryst. (2012), D68(2): 186-193.

• C.S. Silva, P. Durão, A. Fillat, P.F. Lindley, L.O. Martins, I. Bento, “Crystal structure of the multicopper oxidase from the pathogenic bacterium Campylobacter jejuni CGUG11284: characterization of a metallo-oxidase”, Metallomics (2012), 4(1): 37-47. (Front cover

 

Book Chapters:

• C.V. Romão, M. Archer, S.A. Lobo, R.O. Louro, I.A.C. Pereira, L.M. Saraiva, M. Teixeira and P.M. Matias "Diversity of Heme Proteins in Sulfate Reducing Bacteria" in HANDBOOK OF PORPHYRIN SCIENCE - With Applications to Chemistry, Physics, Materials Science, Engineering, Biology and Medicine (2012) (K.M. Kadish, K.M. Smith and R. Guilard, eds.), 19(89), pp 139-230, World Scientific Publishing Co. Pte. Ltd., Singapore.

 

• M.A. Carrondo and P. Spadon (eds) “Macromolecular Crystallography: Deciphering the structure, function and dynamics of biological molecules”, NATO Science for Peace and Security Series A: Chemistry and Biology(2012),Springer: Dordrecht (ISBN 978-94-007-2529-4) XIV, 208 p. 95 illus. DOI: 10.1007/978-94-007-2530-0.

 

• S. Gorynia, T.M. Bandeiras, P.M. Matias, F.G. Pinho, C. McVey, P. Donner and M.A. Carrondo “RuvBL1 and RuvBL2 and their complex proteins implicated in many cellular pathways”, in Macromolecular Crystallography: Deciphering the structure, function and dynamics of biological molecules (2012), (M.A Carrondo and P. Spadon, eds) NATO Science for Peace and Security Series A: Chemistry and Biology, pp. 55-63. DOI: 10.1007/978-94-007-2530-0_5.

 

2011

• S. Gorynia, T.M. Bandeiras, F.G. Pinho, C.E. McVey, C. Vonrhein, A. Round, D.I. Svergun, P. Donner, P.M. Matias and M.A. Carrondo, “Structural and functional insights into a dodecameric molecular machine - the RuvBL1/RuvBL2 complex”, J. Struct. Biol. (2011), 176(3): 279-291.

• F.G. Pinho, A.F. Pinto, L. Pinto, H. Huber, C.V. Romão, M. Teixeira, P.M. Matias and T.M. Bandeiras, “Superoxide Reductase from Nanoarchaeum equitans: expression, purification, crystallization and preliminary X-ray crystallographic analysis”, Acta Cryst. (2011), F67(5): 591-595.

• A.T. Fernandes, M.M. Pereira, C.S. Silva, P.F. Lindley, I. Bento, E.P. Melo and L.O. Martins, “The removal of a disulfide bridge in CotA-laccase changes the slower motion dynamics involved in copper binding but has no effect on the thermodynamic stability”, J. Biol. Inorg. Chem. (2011), 16(4): 641-651.

• A.F. Pinto, S. Todorovic, P. Hildebrandt, M. Yamazaki, F. Amano, S. Igimi, C.V. Romão and M. Teixeira, “Desulforubrerythrin from Campylobacter jejuni, a novel multi-domain protein”, J. Biol. Inorg. Chem. (2011), 16(3): 501-510.

• B. Correia, Z. Chen, S. Mendes, L.O. Martins and I. Bento, “Crystallization and preliminary X-ray diffraction analysis of the Azoreductase PpAzoR from Pseudomonas putida MET94”, Acta Cryst. (2011) F67(1): 121-123.

• C.V. Romão, D. Ladakis, S.A.L. Lobo, M.A. Carrondo, A.A. Brindley, E. Deery, P.M. Matias, R.W. Pickersgill, L.M. Saraiva and M.J. Warren, “Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization”, PNAS (2011), 108(1): 97-102.

 

Book Chapters:

• J.B. Vicente, M.A. Carrondo, M. Teixeira and C. Frazão “Flavodiiron Proteins: Nitric Oxide and/or Oxygen Reductases”, in Handbook of Metalloproteins (2011), Vol 4 & 5, Ed. A. Messerschmidt, Chichester, UK: John Wiley & Sons, Ltd., pp 277-295.

• I. Bento, R.O. Louro, C.M. Soares, M.A. Carrondo, “Tetraheme Cytochrome c3”, in Handbook of Metalloproteins (2011), Vol 4 & 5, Ed. A. Messerschmidt, Chichester, UK: John Wiley & Sons, Ltd., pp 5-15.

 

2010

• D. de Sanctis, J.M. Inácio, P.F. Lindley, I. de Sá Nogueira and I. Bento, “New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases”, FEBS J. (2010) 277(21): 4562-4574.

• I. Bento, C.S. Silva, Z. Chen, L.O. Martins, P.F. Lindley and C.M. Soares, “Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer”, BMC Structural Biology (2010), 10(28): 1-14.

• M. de Rosa, D. de Sanctis, M. Archer, A. Rich, A. Athanasiadis and M.A. Carrondo, “Crystal structure of a junction between two Z-DNA helices”, PNAS (2010), 107(20): 9088-9092.

• F.G. Pinho, C.V. Romão, A.F. Pinto, L.M. Saraiva, H. Huber, P.M. Matias, M.A. Carrondo, M. Teixeira and T.M. Bandeiras, “Cloning, purification, crystallization and X-ray crystallographic analysis of Ignicoccus hospitalis neelaredoxin”, Acta Cryst. (2010) F66(5): 605-607.

• T.M. Bandeiras, C.V. Romão, J.V. Rodrigues, M. Teixeira, P.M. Matias, “Purification, crystallization and X-ray crystallographic analysis of Archaeoglobus fulgidus neelaredoxin”, Acta Cryst. (2010) F66(3): 316-319.

• J. Rocha, A.O. Popescu, I. Sá-Correia, A.M. Fialho and C. Frazão, “Cloning, expression, purification, crystallization and preliminary crystallographic studies of BceC, a UDP-glucose dehydrogenase from Burkholderia cepacia IST408”, Acta Cryst. (2010) F66(3): 269-271.

• Z. Chen, P. Durão, C.S. Silva, M.M. Pereira, S. Todorovic, P. Hildebrandt, I. Bento, P.F. Lindley and L.O. Martins, “The role of Glu498 in the dioxygen reactivity of CotA-laccase from Bacillus subtilis”, Dalton Trans. (2010) 39(11): 2875-2882.

 

2009

• A.T. Gonçalves, D. Marçal, M.A. Carrondo and F.J. Enguita “Crystallization and preliminary X-ray characterization of a glycerol dehydrogenase from the human pathogen Salmonella enterica serovar Typhimurium”, Acta Cryst. (2009) F65(7), 698–701.

• D. de Sanctis, C.E. McVey, F.J. Enguita and M.A. Carrondo “Crystal structure of the full-length sorbitol operon regulator, SorC from Klebsiella pneumoniae: structural evidence for a novel transcriptional regulation mechanism” J. Mol. Biol. (2009), 387(3): 759-770.

• D. Marçal, A.T. Rêgo, M.A. Carrondo and F.J. Enguita “1,3-propanediol-dehydrogenase from Klebsiella pneumoniae: decameric quaternary structure and possible subunit cooperativity” J. Bacteriol. (2009), 191(4): 1143-1151.

• L. Toussaint, M.G. Cuypers, L. Bertrand, L. Hue, C.V. Romão, L.M. Saraiva, M. Teixeira, W. Meyer-Klaucke, M.C. Feiters and R.R. Crichton, “Comparative Fe and Zn K-edge X-ray absorption spectroscopic study of the ferroxidase centres of human H-chain ferritin and bacterioferritin from Desulfovibrio desulfuricansJ. Biol. Inorg. Chem. (2009), 14(1): 35-49.

 

2008

• M. V. Petoukhov, J. B. Vicente, P. B. Crowley, M. A. Carrondo, M. Teixeira, D. I. Svergun, “Quaternary structure of Flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering”, Structure (2008), 16(9):1428-36.

• S. Gorynia, P. M. Matias, T. M. Bandeiras, P. Donner and M. A. Carrondo, "Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1–RuvBL2 complex", Acta Cryst. (2008) F64, 840–846.

• D. de Sanctis, I. Bento, J.M. Inácio, S. Custódio, I. de Sá-Nogueira, M.A.Carrondo, "Overproduction, crystallization and preliminary X-ray characterization of Abn2, an endo-1,5-alpha-arabinanase from Bacillus subtilis" Acta Cryst. (2008) F64, 636-638.

• D. Aragão, E. Mitchell, C. Frazão, M.A. Carrondo and P. Lindley “Structural and Functional Relationships in the Hybrid Cluster Protein Family: the Structure of the Anaerobically Purified Hybrid Cluster Protein from Desulfovibrio vulgaris at 1.35A Resolution”, Acta Cryst. (2008) D64, 665-674.

• P. Durão, Z. Chen, C.S. Silva, C.M. Soares, M.M. Pereira, S. Todorovic, P. Hildebrandt, I. Bento, P.F. Lindley, and L.O. Martins, "Proximal mutations at the type 1 copper site of CotA laccase: Spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants", Biochem. J. (2008), 412(2): 339-46.

• S.A.L. Lobo, A.A. Brindley, C.V. Romão, H.K. Leech, M.J. Warren and L.M. Saraiva, “Two distinct roles for two functional cobaltochelatases (CbiK) in Desulfovibrio vulgaris Hildenborough”, Biochemistry (2008), 47(21):5851–5857.

• D. Plácido, C. G. Fernandes, A. Isidro, M. A. Carrondo, A. O. Henriques, M. Archer “Auto-induction and purification of a Bacillus Subtilis transglutaminase (Tgl) and its preliminary crystallographic characterization”, Protein Expres. Purif., (2008), 59: 1-8.

• T. M. Bandeiras, R. C. Hillig, P. M. Matias, U. Eberspaecher, J. Fanghänel, M. Thomaz, S. Miranda, K. Crusius, V. Pütter, P. Amstutz, M. Gulotti-Georgieva, H. K. Binz, C. Holz, A. A. P. Schmitz, C. Lang, P. Donner, U. Egner, M. A. Carrondo and B. Müller-Tiemann, “Structure of Wild-Type Plk-1 Kinase Domain in Complex with a Selective DARPin” Acta Cryst. (2008) D64, 339-353.

• C. Frazão, D. Aragão, R. Coelho, S. S. Leal, C. M. Gomes, M. Teixeira and M. A. Carrondo, “Crystallographic analysis of the intact metal centres [3Fe4S]1+/0 and [4Fe4S]2+/1+ in a Zn2+-containing ferredoxin” FEBS Letters (2008), 582(5):763-767.

• A.M.D. Gonçalves, A.T. Rêgo, M. Thomaz, F.J. Enguita and M.A. Carrondo, "Expression, purification, crystallization and preliminary X-ray characterization of two crystal forms of stationary-phase survival E protein from Campylobacter jejuni" Acta Cryst. (2008) F64, 213-216.

• D. de Sanctis, A. T. Rêgo, D. Marçal, C. E. McVey, M. A. Carrondo and F. J. Enguita “Overexpression, purification and crystallization of the tetrameric form of SorC sorbitol operon regulator” Acta Cryst. (2008) F64, 22-24.

 

Book Chapters:

•  M.L. Rodrigues, I.A.C. Pereira and M. Archer, “The NrfH Cytochrome c Quinol Dehydrogenase”, in Handbook of Metalloproteins, Ed. A. Messerschmidt, John Wiley & Sons, Ltd. (2008), DOI: 10.1002/0470028637.met221.

• J. B. Vicente, M. A. Carrondo, M. Teixeira and C. Frazão, “Structural Studies on Flavodiiron Proteins”, in Methods in Enzymol. (2008), Globins and other Nitric Oxide-Reactive Proteins Part B, 437:3-19.

• G. Leonard, D. Nurizzo, C. Dieckmann-Mueller, E. Mitchell, J. McCarthy, D. Flot, I. Bento and P. Lindley, "Crystallographic Research Developments" in Astrophysics and Condensed Matter – Horizons in World Physics, (2008) Ed. T.G. Hardwell, Nova Science Publishers, Inc., Vol. 262, pp 11-69.

 

2007

• M.G. Cuypers, E.P. Mitchell, C.V. Romão and S.M. McSweeney, "The crystal structure of the Dps2 from Deinococcus radiodurans reveals an unusual pore profile with a non-specific metal binding site" J. Mol. Biol. (2007), 371(3): 787-799.

• J. Andrade, A. Karmali, M. A. Carrondo, and C. Frazão “Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state”, J. Biol. Chem. (2007), 282: 19598-605.

• J. Tatur, W.R. Hagen and P. M. Matias, “Crystal structure of the ferritin from the hyperthermophilic archaeal anaerobe Pyrococcus furiosus”, J. Biol. Inorg. Chem. (2007), 12(5):615-630.

• S. Cooray, M.W. Bahar, N.G. Abrescia, C.E. McVey, N.W. Bartlett, R.A. Chen, D.I. Stuart, J.M. Grimes, G.L. Smith, "Functional and structural studies of the vaccinia virus virulence factor N1 reveal a Bcl-2-like anti-apoptotic protein", J. Gen. Virol. (2007), 88(6):1656-66.

• M. A. Carrondo, I. Bento, P. M. Matias and P. F. Lindley "Crystallographic evidence for dioxygen interactions with iron proteins", J. Biol. Inorg. Chem. (2007), 12: 429-442.

• D. Marçal, A. T. Rêgo, M. J. Fogg, K. S. Wilson, M. A. Carrondo and F. J. Enguita "Crystallization and preliminary X-ray characterization of 1,3-propanediol dehydrogenase from the human pathogen Klebsiella pneumoniae" Acta Cryst. (2007) F63, 249-251.

• J. Andrade, A. Karmali, M. A. Carrondo and C. Frazão “Crystallization, diffraction data collection and preliminary crystallographic analysis of hexagonal crystals of Pseudomonas aeruginosa amidase”, Acta Cryst. (2007) F63, 214-216.

• I. Bento, C. Peixoto, V. N. Zaitsev and P. F. Lindley. "Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites" Acta Cryst. (2007) D63, 240-248.

 

2006

• P. M. Matias, S. Gorynia, P. Donner, M. A. Carrondo, “Crystal structure of the human AAA+ protein RuvBL1” J. Biol. Chem. (2006), 281: 38918-29.

• C.C. Almeida, C.V. Romão, P.F. Lindley, M. Teixeira and L.M. Saraiva “The role of the hybrid cluster protein in oxidative stress defense” J. Biol. Chem. (2006), 281: 32445-50.

• A.V. Lyashenko, I. Bento, V.N. Zaitsev, N.E. Zhukhlistova, Y.N. Zhukova, A.G. Gabdoulkhakov, E.Y. Morgunova, W. Voelter, G.S. Kachalova, E.V. Stepanova, O.G. Koroleva, V.S. Lamzin, V.I. Tishkov, C. Betzel, P.F Lindley, A.B. Mikhailov. “X-ray structural studies of the fungal laccase from Cerrena maxima”, J. Biol. Inorg. Chem. (2006), 11: 963-973.

• F.C. Teixeira, H. Ramos, I.F. Antunes, M.J. Curto, M.T. Duarte, I. Bento, “Synthesis and structural characterization of 1- and 2-substituted indazoles: ester and carboxylic acid derivatives” Molecules. (2006), 11(11):867-89.

• M.J. Fogg, P. Alzari, M. Bahar, I. Bertini, J. M. Betton, W. P. Burmeister, C. Cambillau, B. Canard, M. Carrondo, M. Coll, S. Daenke, O. Dym, M. P. Egloff, F. J. Enguita, A. Geerlof, A. Haouz, T. A. Jones, Q. Ma, S. N. Manicka, M. Migliardi, P. Nordlund, R. J. Owens, Y. Peleg, G. Schneider, R. Schnell, D. I. Stuart, N. Tarbouriech, T. Unge, A. J. Wilkinson, M. Wilmanns, K. S. Wilson, O. Zimhony and J. M. Grimes, “Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens”, Acta Cryst. (2006) D62, 1196-1207.

• A. Geerlof, J. Brown, B. Coutard, M. P. Egloff, F. J. Enguita, M. J. Fogg, R.J.C. Gilbert, M.R. Groves, A. Haouz, J. E. Nettleship, P. Nordlund, R. J. Owens, M. Ruff, S. Sainsbury, D.I. Svergun and M. Wilmanns, "The impact of protein characterization in structural proteomics" Acta Cryst. (2006) D62, 1125-1136.

• A.V. Lyashenko, N.E. Zhukhlistova, A.G. Gabdoulkhakov, Y.N. Zhukova, W. Voelter, V.N. Zaitsev, I. Bento, E.V. Stepanova,  G.S. Kachalova, O.V. Koroleva, E.A. Cherkashyn, V.I. Tishkov, V.S. Lamzin, K. Schirwitz, E.Y. Morgunova, C. Betzel, P.F. Lindley,  A.M. Mikhailov. “Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima.”, Acta Cryst. (2006) F62, 954-7.

• D. Aragão, A.R. Marques, C. Frazão, F.J. Enguita, M.A. Carrondo, A.M. Fialho, I. Sa-Correia, E.P. Mitchell "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 Cryst. (2006) F62, 930-934.

• C. Frazão, C. E. McVey, M. Amblar, A. Barbas, C. Vonrhein, C. M. Arraiano and M.A. Carrondo “Unravelling the dynamics of RNA degradation by RNAse II and its RNA- bound complex”, Nature (2006), 443: 110-114.

• I. Bento, M. A. Carrondo, P. F. Lindley, “Reduction of dioxygen by enzymes containing copper”, J. Biol. Inorg. Chem. (2006), 11: 539-547.

• C.E. McVey, M. Amblar, A. Barbas, F. Cairrão, R. Coelho, C. Romão, C.M. Arraiano, M.A. Carrondo and C. Frazão “Expression, purification, crystallization and preliminary diffraction data characterization of Escherichia coli ribonuclease II (RNase II).”, Acta Cryst. (2006) F62, 684-687.

• P.N. Palma, M. L. Rodrigues, M. Archer, M. J. Bonifácio, A. I. Loureiro, D. Learmonth, M. A. Carrondo and P. Soares-da-Silva, “Comparative study of ortho- and meta- nitrated inhibitors of catechol-O-methyltransferase. Interactions with the active site and regioselectivity of O-methylation” Molecular Pharmacology (2006), 70: 143-153.

• P. Durão, I. Bento, A.T. Fernandes, E.P. Melo, P.F. Lindley, L.O. Martins. “Perturbations of the T1 copper site in the CotA laccase from Bacillus subtilis: structural, biochemical, enzymatic and stability studies” J. Biol. Inorg. Chem. (2006), 11: 514-26.

• J. Lachwa, I. Bento, M.T. Duarte, J.N. Lopes, L.P. Rebelo. “Condensed phase behaviour of ionic liquid-benzene mixtures: congruent melting of a [emim][NTf2].C6H6 inclusion crystal” Chem. Commun. (2006), 23: 2445-7.

• F.J. Enguita, E. Pohl, D.L. Turner, H. Santos, M.A. Carrondo, "Structural evidence for a proton transfer pathway coupled with haem reduction of cytochrome c'' from Methylophilus methylotrophus" J. Biol. Inorg. Chem. (2006), 11: 189-196.

• M.L. Rodrigues, M. Archer, P. Martel, S. Miranda, M. Thomaz, F.J. Enguita, R.P. Baptista, E. Pinho e Melo, N. Sousa, A. Cravador, M.A. Carrondo, "Crystal structures of the free and sterel-bound forms of b-cinnamomin", Biochimica et Biophysica Acta – Proteins and Poteomics (2006), 1764(1): 110-121.

• S. Gorynia, P.M. Matias, S. Gonçalves, R. Coelho, G.L. Gato, M. Thomaz, M. Huber, B. Haendler, P. Donner and M.A. Carrondo, "Expression, purification, crystallization and preliminary X-ray analysis of the human RuvB-like protein RuvBL1" Acta Cryst. (2006) F62, 61-66.

 

2005

• I. Bento, L. O. Martins, G. G. Lopes, M. A. Carrondo and P. F. Lindley “Dioxygen reduction by multi-copper oxidases; a structural perspective”, Roy. Chem. Soc. Dalton Trans. (2005), 21:3507-3513.

• P. M. Matias, I. A. C. Pereira, C. M. Soares and M. A. Carrondo “Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview”, Progress in Biophysics and Molecular Biology (2005), 89: 292-329.

• P.M. Matias, J. Tatur, M.A. Carrondo and W.R. Hagen, "Crystallization and preliminary X-ray characterization of a ferritin from the hyperthermophilic archaen and anaerobe Pyrococcus furious" Acta Cryst. (2005) F61, 503-506.

• C. Frazão, D.C. Simes, R. Coelho, D. Alves, M.K. Williamson, P.A. Price, M.L. Cancela and M.A. Carrondo “Structural evidence of a fourth Gla residue in fish osteocalcin: Biological implications” Biochemistry (2005), 44: 1234-1242.

• M. L. Rodrigues, M. J. Bonifácio, P. Soares-da-Silva, M. A. Carrondo, M. Archer “Crystallization and preliminary X-ray diffraction studies of a catechol-O- methyltransferase/inhibitor complex”, Acta Cryst. (2005) F61, 118-120.

 

2004

• I. J. Correia, C. M. Paquete, A. Coelho, C. C. Almeida, T. Catarino, R. O. Louro, C. Frazão, L. M. Saraiva, M. A. Carrondo, D. L. Turner and A. V. Xavier, “Proton assisted two-electron transfer in natural variants of tetraheme cytochromes from Desulfomicrobium sp.” J. Biol. Chem. (2004), 279: 52227-37.

• F. J. Enguita, D. Marçal, L. O. Martins, R. Grenha, A. O. Henriques, P. F. Lindley and M. A. Carrondo "Substrate and dioxygen binding to the endospore coat laccase from Bacillus subtilis", J. Biol. Chem. (2004), 279: 23472-23476.

• P. Crowley and M.A. Carrondo, “The Architecture of the Binding Site in Redox Protein Complexes: Implications for Fast Dissociation”, Proteins: Structure, Function and Bioinformatics (2004), 55: 603-612.

• I. Bento, P. M. Matias, A. M. Baptista, P. N. da Costa, W. M. A. M. van Dongen, L. M. Saraiva, T. R. Schneider, C. M. Soares and M. A. Carrondo “Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modelling studies of oxidised and reduced high-resolution structures at pH 7.6” Proteins: Structure, Function and Bioinformatics (2004), 54: 135-152.

 

2003

• I. Bento, V. H. Teixeira, A. M. Baptista, Cláudio M. Soares, P. M. Matias and M. A. Carrondo “Redox-Bohr and other cooperativity effects in the nine heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies”. J. Biol. Chem. (2003), 278: 36455-36469.

• F. J. Enguita, L. O. Martins, A. O. Henriques and M. A. Carrondo “Crystal structure of a bacterial endospore coat component: a laccase with enhanced thermostability properties” J. Biol. Chem. (2003), 278: 19416-19425.

• M. A. Carrondo “Ferritins, Iron Uptake and Storage from the Bacterioferritin Viewpoint” EMBO J. (2003), 22: 1959-1968.

• D. Aragão, S. Macedo, E. P. Mitchell, C. V. Romão, M. Y. Liu, C. Frazão, L. M. Saraiva, A. V. Xavier, J. LeGall, W. M.A.M. van Dongen, W. R. Hagen, M. Teixeira, M. A. Carrondo and P. Lindley “Reduced Hybrid Cluster Proteins (HCP) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough). X-ray Structures at High Resolution using Synchrotron Radiation”, J. Biol. Inorg. Chem. (2003), 8: 540-548.

• S. Macedo, C. V. Romão, E. Mitchell , P. M. Matias, M. Y. Liu , A. V. Xavier , J. LeGall , M. Teixeira, P. Lindley and M. A. Carrondo “The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricansNature Struct. Biol (2003), 10: 285-290.

• D. Aragão, C. Frazão, L. Sieker, G. M. Sheldrick, J. LeGall, and M. A. Carrondo “Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Å resolution” Acta Cryst. (2003) D59, 644-653.

• F. J. Enguita, L. Rodrigues, M. Archer, L. Sieker, A. Rodrigues, D. L. Turner, H. Santos and M. A. Carrondo “Crystallization and Preliminary X-Ray Characterization of Cytochrome c” from the obligate methylotroph Methylophilus methylotrophusActa Cryst. (2003) D59, 580-583.

• I. A. Abreu, A. I. Lourenço, A. V. Xavier, J. LeGall, A. V. Coelho, P. M. Matias, D. M. Pinto, M. A. Carrondo, M. Teixeira and L. M. Saraiva “A novel iron centre in the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774” J. Biol. Inorg. Chem. (2003), 8: 360-370.

 

2002

• P. M. Matias, A. V. Coelho, F. M. A. Valente, D. Plácido, J. LeGall, A. V. Xavier, I. A. C. Pereira and M. A. Carrondo “Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme Cytochrome c HmcA at 2.5 Å resolution and a view of its role in transmembrane electron transfer” J. Biol. Chem. (2002), 277(49): 47907-47916.

• M. J. Bonifácio, M. Archer, M. L. Rodrigues, P. M. Matias, D. A. Learmonth, M. A. Carrondo and P. Soares-da-Silva “Kinetics and Crystal Structure of Catechol-O-Methyltransferase Complex with Co-Substrate and a Novel Inhibitor with Potential Therapeutic Application” Molecular Pharmacology (2002), 62: 795-805.

• F.J. Enguita, P.M. Matias, L.O. Martins, D. Plácido, A. O. Henriques and M.A. Carrondo “Spore coat Laccase CotA from Bacillus subtilis: Crystallization and Preliminary X-Ray Characterization by the MAD method" Acta Cryst. (2002) D58, 1490-1493.

• M. L. Rodrigues, M. Archer, P. Martel, A. Jacquet, A. Cravador, and Maria A. Carrondo, “Crystal structure of beta-cinnamomin, a toxic protein for some plant species”, Acta Cryst. (2002) D58, 1314-1321.

• S. Macedo, E. P. Mitchell, C. V. Romão, S. J. Cooper, R. Coelho, M. Y. Liu, A. V. Xavier, J. LeGall, S. Bailey, C. D. Garner, W. R. Hagen, M. Teixeira, M.A. Carrondo and P. Lindley, “Hybrid cluster proteins (HCPs) from Desulfovibrio desulfuricans ATCC 2774 and Desulfovibrio vulgaris (Hildenborough): X-ray structures at 1.25 Å resolution using synchrotron radiation” J. Biol. Inorg. Chem. (2002), 7:514-525.

• C. M. Gomes, C. Frazão, A. V. Xavier, J. Legall and M. Teixeira "Functional control of the binuclear metal site in the metallo-beta-lactamase-like fold by subtle amino acid replacements" Protein Science (2002), 11:707-712.

• P. M. Matias, M. A. Carrondo, R. Coelho, M. Thomaz, X.-Y. Zhao, A. Wegg, K. Crusius, U. Egner, and P. Donner “Structural basis for the glucocorticoid response in a mutant human androgen receptor (ARccr) derived from an androgen-independent prostate cancer”, J. Med. Chem. (2002), 45: 1439-1446.

 

2001

• R. O. Louro, I. Bento, P. M. Matias, T. Catarino, A. M. Baptista, C. M. Soares, M. A. Carrondo, D. L. Turner, A. V. Xavier, “Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytchrome” J. Biol. Chem. (2001), 276: 44044-44051.

• J. Mendes, A.M. Baptista, M.A. Carrondo, C.M. Soares, "Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants", J. Comp. Aid. Mol. Des. (2001), 15: 721-740.

• J. Mendes, H. Nagarajaram, C.M. Soares, T. L. Blundell and M.A. Carrondo “Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure”, Biopolymers (2001), 59:72-86.

• M. L. Rodrigues, M. Archer, M. J. Bonifácio, P. Soares-da-Silva and M. A. Carrondo “Crystallisation and preliminary crystallographic characterisation of catechol-O-methyltransferase in complex with its co-substrate and an inhibitor” Acta Cryst. (2001) D57, 906-908.

• D. A. Learmonth, J. Benes, A. Parada, D. Hainzl, A. Beliaev, M. J. Bonifácio, P. M. Matias, M. A. Carrondo, J. Garret and P. Soares-da-Silva “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: 227-236.

• C. Frazão, F. J. Enguita, R. Coelho, G. M. Sheldrick, J. A. Navarro, M.Hervás, M. A. De la Rosa, M. A. Carrondo “Crystal structure of low-potential cytochrome c549 from Synechocystis sp. PCC 6803, at 1.21 Å resolution” J. Biol. Inorg. Chem. (2001), 6:324-332.

• A.V. Coelho, S. Macedo, P. M. Matias, A. W. Thompson, J. LeGall and M.A. Carrondo “Structure determination of Bacterioferritin from Desulfovibrio desulfuricans by the MAD method at the Fe K-edge” Acta Cryst. (2001) D57, 326-329.

• P.M. Matias, C. M. Soares, L. M. Saraiva, R. Coelho, J. Morais, J. Le Gall and M.A. Carrondo, “[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774: Gene sequencing, three-dimensional structure determination and refinement at 1.8 Å and modelling studies of its interaction with the tetra-haem cytochrome c3” J. Biol. Inorg. Chem. (2001), 6: 63-81.

 

Book Chapters:

• M. A. Carrondo, C. M. Soares, P.M. Matias “Nine-heme Cytochrome c”, in Handbook of Metalloproteins, Ed. K. Wieghardt, R. Huber, T. L. Poulos, A. Messerschmidt, John Wiley & Sons, Ltd. (2001), pp 147-158.

 

Patents:

• P. Donner, U. Egner, M. A. Carrondo and P.M. Matias ”Crystal” World Intellectual Property Organization, International Publication Number WO 01/66599 A1, publication date 13/09/2001.

 

Pedagogical publications:

• C. Frazão, C. M. Gomes, G. Silva, S. Oliveira, A.V. Xavier, J. LeGall, M. Teixeira and M. A. Carrondo “ Utilização de oxigénio em organismos anaeróbicos – Estrutura da rubredoxina:oxigénio oxidoreductase, o protótipo de uma nova família de metaloenzimas” Boletim de Biotecnologia (2001), 70: 2-6.

 

2000

• C. Frazão, G. Silva, C. M. Gomes, P. M. Matias, R. Coelho, L. Sieker, S. Macedo, M. Y. Liu, S. Oliveira, M. Teixeira, A. V. Xavier, C. Rodrigues-Pousada, M. A. Carrondo, and J. Le Gall, “Structure of a dioxygen reduction enzyme from Desulfovibrio gigas”, Nature Struct. Biol. (2000), 7: 1041-1045.

• P.M. Matias, P. Donner, R. Coelho, M. Thomaz, C. Peixoto, S. Macedo, N. Otto, S. Joschko, P. Scholz, A. Wegg, S. Bäsler, M. Schäfer, U. Egner and M.A. Carrondo, “Structural evidence for ligand specificity in the binding domain of the human Androgen receptor: implications for phatogenic gene mutations” J. Biol. Chem. (2000), 275: 26164-26171.

• M. Archer, M.L. Rodrigues, M. Aurélio, R. Biemans, A. Cravador and M.A. Carrondo, “Crystallisation and preliminary X-ray diffraction analysis of beta-cinnamomin, an elicitin secreted by the phytopathogenic fungus Phytophthora cinnamomin”, Acta Cryst. (2000) D56, 363-365.

 

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Structural Genomics | Macromolecular Crystallography Unit 2011

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