Publications

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1997
Romao, MJ, I. Kolln, JM Dias, AL Carvalho, A. Romero, P. F. Varela, L. Sanz, E. Topfer-Petersen, and JJ Calvete. "Crystal structure of acidic seminal fluid protein (aSFP) at 1.9 angstrom resolution: a bovine polypeptide of the spermadhesin family." Journal of Molecular Biology. 274 (1997): 650-660. Abstract

We report the three-dimensional crystal structure of acidic seminal fluid protein (aSFP), a 12.9 kDa poly-peptide of the spermadhesin family isolated from bovine seminal plasma, solved by the multiple isomorphous replacement method and refined with data to 1.9 Angstrom resolution with a final R-factor of 17.3%. aSFP is built by a single CUB domain architecture, a 100 to 110 amino-acid-residue extracellular module found in 16 functionally diverse proteins. The structure of aSFP reveals that the CUB domain displays a beta-sandwich topology organised into two 5-stranded beta-sheets, each of which contain two parallel and four antiparallel strands. The structure of aSFP is almost identical to that of porcine spermadhesins PSP-I and PSP-II, which in turn show limited structural similarity with jellyroll topologies of certain virus capsid proteins. Essentially, topologically conserved residues in these proteins are those internal amino acids forming the hydrophobic core of the CUB and the jellyroll domains, suggesting their importance in maintaining the integrity of these protein folds, On the other hand, the structure of aSFP shows structural features that are unique to this protein and which may provide a structural ground for understanding the distinct biological properties of different members of the spermadhesin protein family. (C) 1997 Academic Press Limited.

Romero, A., MJ Romao, P. F. Varela, I. Kolln, JM Dias, AL Carvalho, L. Sanz, E. TopferPetersen, and JJ Calvete. "The crystal structures of two spermadhesins reveal the CUB domain fold." Nature Structural Biology. 4 (1997): 783-788. Abstract

Spermadhesins, 12,000-14,000 M-r mammalian proteins, include lectins involved in sperm-egg binding and display a single CUB domain architecture. We report the crystal structures of porcine seminal plasma PSP-I/PSP-II, a heterodimer of two glycosylated spermadhesins. and bovine aSFP at 2.4 Angstrom and 1.9 Angstrom resolution respectively.

Dias, JM, AL Carvalho, I. Kolln, JJ Calvete, E. TopferPetersen, P. F. Varela, A. Romero, C. Urbanke, and MJ Romao. "Crystallization and preliminary x-ray diffraction studies of aSFP, a bovine seminal plasma protein with a single CUB domain architecture." Protein Science. 6 (1997): 725-727. Abstract

{Bovine acidic seminal fluid protein (aSFP) is a 12.9 kDa polypeptide of the spermadhesin family built by a single CUB domain architecture. The CUB domain is an extracellular module present in 16 functionally diverse proteins. To determine the three-dimensional structure of aSFP, the protein was crystallized at 21 degrees C by vapor diffusion in hanging drops, using ammonium sulfate, pH 4.7, and polyethyleneglycol 4000 as precipitants, containing 10% dioxane to avoid the formation of clustered crystals. Elongated prismatic crystals with maximal size of 0.6 x 0.3 x 0.2 mm(3) diffract to beyond 1.9 Angstrom resolution and belong to space group P2(1)2(1)2, with cell parameters a = 52.4 Angstrom

1999
Archer, M., AL Carvalho, S. Teixeira, I. Moura, JJG Moura, F. Rusnak, and MJ Romao. "Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein." Protein Science. 8 (1999): 1536-1545. Abstract
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2001
Carvalho, AL, JM Dias, L. Sanz, A. Romero, JJ Calvete, and MJ Romao. "Purification, crystallization and identification by X-ray analysis of a prostate kallikrein from horse seminal plasma." Acta Crystallographica Section D-Biological Crystallography. 57 (2001): 1180-1183. Abstract

The purification, crystallization and identification by X-ray diffraction analysis of a horse kallikrein is reported. The protein was purired from horse seminal plasma. Crystals belong to space group C2 and the structure was solved by the MIRAS method, with two heavy-atom derivatives of mercury and platinum. X-ray diffraction data to 1.42 Angstrom resolution were collected at the ESRF synchrotron-radiation source.

2002
Carvalho, AL, L. Sanz, D. Barettino, A. Romero, JJ Calvete, and MJ Romao. "Crystal structure of a prostate kallikrein isolated from stallion seminal plasma: A homologue of human PSA." Journal of Molecular Biology. 322 (2002): 325-337. Abstract
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2003
Carvalho, AL, FMV Dias, JAM Prates, T. Nagy, HJ Gilbert, GJ Davies, LMA Ferreira, MJ Romao, and CMGA Fontes. "Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex." Proceedings of the National Academy of Sciences of the United States of America. 100 (2003): 13809-13814. Abstract
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2004
Carvalho, AL, A. Goyal, JAM Prates, DN Bolam, HJ Gilbert, VMR Pires, LMA Ferreira, A. Planas, MJ Romao, and CMGA Fontes. "The family 11 carbohydrate-binding module of Clostridium thermocellum Lic26A-Cel5E accommodates beta-1,4- and beta-1,3-1,4-mixed linked glucans at a single binding site." Journal of Biological Chemistry. 279 (2004): 34785-34793. Abstract
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2005
Carvalho, AL, VMR Pires, TM Gloster, JP Turkenburg, JAM Prates, LMA Ferreira, MJ Romao, GJ Davies, CMGA Fontes, and HJ Gilbert. "Insights into the structural determinants of cohesin dockerin specificity revealed by the crystal structure of the type II cohesin from Clostridium thermocellum SdbA." Journal of Molecular Biology. 349 (2005): 909-915. Abstract
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Santos-Silva, T., J. Trincao, AL Carvalho, C. Bonifacio, F. Auchere, I. Moura, JJG Moura, and MJ Romao. "Superoxide reductase from the syphilis spirochete Treponema pallidum: crystallization and structure determination using soft X-rays." Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 61 (2005): 967-970. Abstract
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2006
Santos-Silva, T., J. Trincao, AL Carvalho, C. Bonifacio, F. Auchere, P. Raleiras, I. Moura, JJG Moura, and MJ Romao. "The first crystal structure of class III superoxide reductase from Treponema pallidum." Journal of Biological Inorganic Chemistry. 11 (2006): 548-558. Abstract
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Najmudin, S., CIPD Guerreiro, AL Carvalho, JAM Prates, MAS Correia, V. D. Alves, LMA Ferreira, MJ Romao, HJ Gilbert, DN Bolam, and CMGA Fontes. "Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains." Journal of Biological Chemistry. 281 (2006): 8815-8828. Abstract
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2007
Carvalho, Ana Luisa, Fernando M. V. Dias, Tibor Nagy, Jose A. M. Prates, Mark R. Proctor, Nicola Smith, Edward A. Bayer, Gideon J. Davies, Luis M. A. Ferreira, Maria J. Romao, Carlos M. G. A. Fontes, and Harry J. Gilbert. "Evidence for a dual binding mode of dockerin modules to cohesins." Proceedings of the National Academy of Sciences of the United States of America. 104 (2007): 3089-3094. Abstract
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Coelho, Catarina, Pablo J. Gonzalez, Jose Trincao, Ana L. Carvalho, Shabir Najmudin, Thomas Hettman, Stephan Dieckman, Jose J. G. Moura, Isabel Moura, and Maria J. Romao. "Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis." Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 63 (2007): 516-519. Abstract
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2008
Viegas, Aldino, Natercia F. Bras, Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Jose A. M. Prates, Carlos M. G. A. Fontes, Marta Bruix, Maria Joao Romao, Ana Luisa Carvalho, Maria Joao Ramos, Anjos L. Macedo, and Eurico J. Cabrita. "Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach." Febs Journal. 275 (2008): 2524-2535. Abstract
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2009
Godinho, M. H., D. Filip, I. Costa, A. - L. Carvalho, J. L. Figueirinhas, and E. M. Terentjev. "Liquid crystalline cellulose derivative elastomer films under uniaxial strain." Cellulose. 16 (2009): 199-205. Abstract
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Freire, Filipe, Maria Joao Romao, Anjos L. Macedo, Susana S. Aveiro, Brian J. Goodfellow, and Ana Luisa Carvalho. "Preliminary structural characterization of human SOUL, a haem-binding protein." Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65 (2009): 723-726. Abstract
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Viciosa, M. T., N. T. Correia, M. Salmeron Sanchez, AL Carvalho, MJ Romao, J. L. Gomez Ribelles, and M. Dionisio. "Real-Time Monitoring of Molecular Dynamics of Ethylene Glycol Dimethacrylate Glass Former." Journal of Physical Chemistry B. 113 (2009): 14209-14217. Abstract
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2010
Carvalho, Ana Luísa, José Trincão, and Maria João Romão. "X-Ray Crystallography in Drug Discovery." Methods in molecular biology (Clifton, N.J.). Vol. 572. 2010. 31-56. Abstract

Macromolecular X-ray crystallography is an important and powerful technique in drug discovery, used by pharmaceutical companies in the discovery process of new medicines. The detailed analysis of crystal structures of protein-ligand complexes allows the study of the specific interactions of a particular drug with its protein target at the atomic level. It is used to design and improve drugs. The starting point of these studies is the preparation of suitable crystals of complexes with potential ligands, which can be achieved by using different strategies described in this chapter. In addition, an introduction to X-ray crystallography is given, highlighting the fundamental steps necessary to determine the three-dimensional structure of protein-ligand complexes, as well as some of the tools and criteria to validate crystal structures available in databases.

2011
Garcia-Alvarez, Begona, Roberto Melero, Fernando M. V. Dias, Jose A. M. Prates, Carlos M. G. A. Fontes, Steven P. Smith, Maria Joao Romao, Ana Luisa Carvalho, and Oscar Llorca. "Molecular Architecture and Structural Transitions of a Clostridium thermocellum Mini-Cellulosome." Journal of Molecular Biology. 407 (2011): 571-580. Abstract
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Bras, Joana L. A., Alan Cartmell, Ana Lusia M. Carvalho, Genny Verze, Edward A. Bayer, Yael Vazana, Marcia A. S. Correia, Jose A. M. Prates, Supriya Ratnaparkhe, Alisdair B. Boraston, Maria J. Romao, Carlos M. G. A. Fontes, and Harry J. Gilbert. "Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis (vol 108, pg 5237, 2011)." Proceedings of the National Academy of Sciences of the United States of America. 108 (2011): 8525. Abstract
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2012
Pinheiro, B. A., J. L. A. Bras, S. Najmudin, AL Carvalho, LMA Ferreira, JAM Prates, and CMGA Fontes. "Flexibility and specificity of the cohesin-dockerin interaction: implications for cellulosome assembly and functionality." Biocatalysis and Biotransformation. 30 (2012): 309-315. AbstractWebsite

Cellulosomes are highly elaborate multi-enzyme complexes of Carbohydrate Active enZYmes (CAZYmes) secreted by cellulolytic microorganisms, which very effectively degrade the most abundant polymers on Earth, cellulose and hemicelluloses. Cellulosome assembly requires that a non-catalytic dockerin module found in cellulosomal enzymes binds to one of the various cohesin domains located in a large molecular scaffold called Scaffoldin. A diversity of cohesin -dockerin binding specificities have been described, the combination of which may result in complex plant cell wall degrading systems, maximising the synergy between enzymes in order to improve catalytic efficiency. Structural studies have allowed the spatial flexibility inherent to the cellulosomal system to be determined. Recent progress achieved from the study of the fundamental cohesin and dockerin units involved in cellulosome assembly will be reviewed.

Kowacz, Magdalena, Abhik Mukhopadhyay, Ana Luisa Carvalho, Jose M. S. S. Esperanca, Maria J. Romao, and Luis Paulo N. Rebelo. "Hofmeister effects of ionic liquids in protein crystallization: Direct and water-mediated interactions." Crystengcomm. 14 (2012): 4912-4921. AbstractWebsite
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Bras, Joana L. A., Victor D. Alves, Ana Luisa Carvalho, Shabir Najmudin, Jose A. M. Prates, Luis M. A. Ferreira, David N. Bolam, Maria Joao Romao, Harry J. Gilbert, and Carlos M. G. A. Fontes. "Novel Clostridium thermocellum Type I Cohesin-Dockerin Complexes Reveal a Single Binding Mode." The Journal of biological chemistry. 287 (2012): 44394-405.Website
Bras, Joana L. A., Ana Luisa Carvalho, Aldino Viegas, Shabir Najmudin, Victor D. Alves, Jose A. M. Prates, Luis M. A. Ferreira, Maria J. Romao, Harry J. Gilbert, and Carlos M. G. A. Fontes. "Escherichia coli expression, purification, crystallization, and structure determination of bacterial cohesin-dockerin complexes." Methods in enzymology. Vol. 510. 2012. 395-415. Abstract

Cellulosomes are highly efficient nanomachines that play a fundamental role during the anaerobic deconstruction of complex plant cell wall carbohydrates. The assembly of these complex nanomachines results from the very tight binding of repetitive cohesin modules, located in a noncatalytic molecular scaffold, and dockerin domains located at the C-terminus of the enzyme components of the cellulosome. The number of enzymes found in a cellulosome varies but may reach more than 100 catalytic subunits if cellulosomes are further organized in polycellulosomes, through a second type of cohesin-dockerin interaction. Structural studies have revealed how the cohesin-dockerin interaction mediates cellulosome assembly and cell-surface attachment, while retaining the flexibility required to potentiate catalytic synergy within the complex. Methods that might be applied for the production, purification, and structure determination of cohesin-dockerin complexes are described here. Copyright 2012 Elsevier Inc. All rights reserved.