@article {16257, title = {The structure of a Bacteroides thetaiotaomicron carbohydrate-binding module provides new insight into the recognition of complex pectic polysaccharides by the human microbiome}, year = {2023}, note = {

n/a

}, month = {2023}, pages = {100084}, abstract = {

TheBacteroides thetaiotaomicronhas developed a consortium of enzymes capable of overcoming steric constraints and degrading, in a sequential manner, the complex rhamnogalacturonan II (RG-II) polysaccharide. BT0996 protein acts in the initial stages of the RGII depolymerisation, where its two catalytic modules remove the terminal monosaccharides from RG-II side chains A and B. BT0996 is modular and has three putative carbohydrate-binding modules (CBMs) for which the roles in the RG-II degradation are unknown. Here, we present the characterisation of themoduleat the C-terminal domain, which we designated BT0996C. The high-resolution structure obtained by X-ray crystallography reveals that the protein displays a typical β-sandwich fold with structural similarity to CBMs assigned to families 6 and 35. The distinctive features are: 1) the presence of several charged residues at the BT0996-C surface creating a large, broad positive lysine-rich patch that encompasses the putative binding site; and 2) the absence of the highly conserved binding-site signatures observed in CBMs from families 6 and 35, such as region A tryptophan and region C asparagine. These findings hint at a binding mode of BT0996-C not yet observed in its homologues. In line with this, carbohydrate microarrays and microscale thermophoresis show the ability of BT0996-C to bind α1-4-linked polygalacturonic acid, and that electrostatic interactions are essential for the recognition of the anionic polysaccharide. The results support the hypothesis that BT0996-C may have evolved to potentiate the action of BT0996 catalytic modules on the complex structure of RG-II by binding to the polygalacturonic acid backbone sequence.

}, keywords = {Carbohydrate Binding Module, Carbohydrates, Human Gut Microbiota, Rhamnogalacturonan II}, isbn = {2590-1524}, url = {https://www.sciencedirect.com/science/article/pii/S2590152422000253}, author = {Trov{\~a}o, Filipa and Correia, Viviana G. and Louren{\c c}o, Frederico M. and Ribeiro, Diana O. and Carvalho, Ana Lu{\'\i}sa and Palma, Angelina S. and Pinheiro, Benedita A.} } @article {15279, title = {Structural insights into the molecular recognition mechanism of the cancer and pathogenic epitope, LacdiNAc by immune-related lectins}, journal = {Chemistry {\textendash} A European JournalChemistry {\textendash} A European Journal}, volume = {n/a}, year = {2021}, note = {

https://doi.org/10.1002/chem.202100800

}, month = {2021}, publisher = {John Wiley \& Sons, Ltd}, abstract = {

Interactions of glycan-specific epitopes to human lectin receptors represent novel immune checkpoints for investigating cancer and infection diseases. By employing a multidisciplinary approach that combines isothermal titration calorimetry, NMR spectroscopy, molecular dynamics simulations, and X-ray crystallography, we disclosed the molecular determinants that govern the recognition of the tumour and pathogenic glycobiomarker LacdiNAc (GalNAc?1-4GlcNAc, LDN), including their comparison with the ubiquitous LacNAc epitope (Gal?1-4GlcNAc, LN), by two human immune-related lectins, galectin-3 (hGal-3) and the macrophage galactose C-type lectin (hMGL). A different mechanism of binding and interactions is observed for the hGal-3/LDN and hMGL/LDN complexes, which explains the remarkable difference in the binding specificity of LDN and LN by these two lectins. The new structural clues reported herein are fundamental for the chemical design of mimetics targeting hGal-3/hMGL recognition process.

}, keywords = {glycan-protein interactions, hGal-3, hMGL, LacdiNAc, molecular recognition}, isbn = {0947-6539}, url = {https://doi.org/10.1002/chem.202100800}, author = {Lima, Carlos D. L. and Helena Coelho and Gimeno, Ana and Trov{\~a}o, Filipa and Diniz, Ana and Dias, Jorge S. and Jes{\'u}s Jim{\'e}nez-Barbero and Corzana, Francisco and Carvalho, Ana Lu{\'\i}sa and Cabrita, Eurico J. and Marcelo, Filipa} } @article {15549, title = {Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus}, journal = {Microbiology SpectrumMicrobiology Spectrum}, year = {2021}, note = {

doi: 10.1128/Spectrum.01826-21

}, pages = {e01826-21}, publisher = {American Society for Microbiology}, abstract = {

n/a

}, url = {https://doi.org/10.1128/Spectrum.01826-21}, author = {Correia Viviana G. and Trov{\~a}o Filipa and Pinheiro Benedita A. and Br{\'a}s Joana L. A. and Silva Lisete M. and Nunes Cl{\'a}udia and Coimbra Manuel A. and Liu Yan and Feizi Ten and Fontes Carlos M. G. A. and Mulloy Barbara and Chai Wengang and Carvalho Ana Lu{\'\i}sa and Palma Angelina S.} } @article {12521, title = {Molecular recognition of a Thomsen-Friedenreich antigen mimetic targeting human galectin-3}, journal = {ChemMedChem}, volume = {Aug 9. doi: 10.1002/cmdc.201800525. [Epub ahead of print]}, year = {2018}, note = {

doi: 10.1002/cmdc.201800525

}, month = {2018}, publisher = {Wiley-Blackwell}, abstract = {

Overexpression of the Thomsen-Friedenreich (TF) antigen in cell membrane proteins occurs in 90\% of adenocarcinomas. Additionally, the binding of the TF-antigen to human galectin-3 (Gal-3), also frequently overexpressed in malignancy, promotes cancer progression and metastasis. In this context, structures that interfere with this specific interaction display the potential to prevent cancer metastasis. Herein, a multidisciplinary approach, combining the optimized synthesis of a TF-antigen mimetic with NMR, X-ray crystallography methods and isothermal titration calorimetry assays has been employed to unravel the molecular structural details that govern the Gal-3/TF-mimetic interaction. The TF-mimetic presents a binding affinity for Gal-3 similar to the TF-natural antigen and retains the binding epitope and the bioactive conformation observed for the native antigen. Furthermore, from a thermodynamic perspective a decrease in the enthalpic contribution was observed for the Gal-3/TF-mimetic complex, however this behaviour is compensated by a favourable entropy gain. From a structural perspective, these results establish our TF-mimetic as a scaffold to design multivalent solutions to potentially interfere with Gal-3 aberrant interactions and likely be used to hamper Gal-3-mediated cancer cells adhesion and metastasis.

}, keywords = {galectin-3, molecular recognition, NMR spectroscopy, Tumour-associated carbohydrate antigens, X-ray crystallography}, isbn = {1860-7179}, url = {https://doi.org/10.1002/cmdc.201800525}, author = {Santarsia, Sabrina and Grosso, Ana Sofia and Trov{\~a}o, Filipa and Jes{\'u}s Jim{\'e}nez-Barbero and Carvalho, Ana Lu{\'\i}sa and Nativi, Cristina and Marcelo, Filipa} } @article {ijms19041184, title = {The Crystal Structure of the R280K Mutant of Human p53 Explains the Loss of DNA Binding}, journal = {International Journal of Molecular Sciences}, volume = {19}, number = {4}, ARTICLE NUMBER = {1184}, year = {2018}, note = {n/a}, abstract = {

The p53 tumor suppressor is widely found to be mutated in human cancer. This protein is regarded as a molecular hub regulating different cell responses, namely cell death. Compelling data have demonstrated that the impairment of p53 activity correlates with tumor development and maintenance. For these reasons, the reactivation of p53 function is regarded as a promising strategy to halt cancer. In the present work, the recombinant mutant p53R280K DNA binding domain (DBD) was produced for the first time, and its crystal structure was determined in the absence of DNA to a resolution of 2.0 {\r A}. The solved structure contains four molecules in the asymmetric unit, four zinc(II) ions, and 336 water molecules. The structure was compared with the wild-type p53 DBD structure, isolated and in complex with DNA. These comparisons contributed to a deeper understanding of the mutant p53R280K structure, as well as the loss of DNA binding related to halted transcriptional activity. The structural information derived may also contribute to the rational design of mutant p53 reactivating molecules with potential application in cancer treatment.

}, issn = {1422-0067}, doi = {10.3390/ijms19041184}, url = {http://www.mdpi.com/1422-0067/19/4/1184}, author = {Gomes, Ana Sara and Trov{\~a}o, Filipa and Andrade Pinheiro, Benedita and Freire, Filipe and Gomes, Sara and Oliveira, Carla and Domingues, Luc{\'\i}lia and Rom{\~a}o, Maria Jo{\~a}o and Saraiva, Luc{\'\i}lia and Carvalho, Ana Lu{\'\i}sa} } @article {Kryshtafovych2017, title = {Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016)}, journal = {Proteins: Structure, Function, and Bioinformatics}, year = {2017}, note = {

n/a

}, month = {oct}, abstract = {

The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment. This article is protected by copyright. All rights reserved.

}, keywords = {CASP, NMR, protein structure prediction, X-ray crystallography}, issn = {08873585}, doi = {10.1002/prot.25392}, url = {http://www.ncbi.nlm.nih.gov/pubmed/28960539 http://doi.wiley.com/10.1002/prot.25392}, author = {Kryshtafovych, Andriy and Albrecht, Reinhard and Basl{\'e}, Arnaud and Bule, Pedro and Caputo, Alessandro T. and Carvalho, Ana Luisa and Chao, Kinlin L. and Diskin, Ron and Fidelis, Krzysztof and Fontes, Carlos M. G. A. and Fredslund, Folmer and Gilbert, Harry J. and Goulding, Celia W. and Hartmann, Marcus D. and Hayes, Christopher S. and Herzberg, Osnat and Hill, Johan C. and Joachimiak, Andrzej and Kohring, Gert-Wieland and Koning, Roman I. and {Lo Leggio}, Leila and Mangiagalli, Marco and Michalska, Karolina and Moult, John and Najmudin, Shabir and Nardini, Marco and Nardone, Valentina and Ndeh, Didier and Nguyen, Thanh H. and Pintacuda, Guido and Postel, Sandra and van Raaij, Mark J. and Roversi, Pietro and Shimon, Amir and Singh, Abhimanyu K. and Sundberg, Eric J. and Tars, Kaspars and Zitzmann, Nicole and Schwede, Torsten} } @article {8484, title = {Unravelling glucan recognition systems by glycome microarrays using the designer approach and mass spectrometry}, journal = {Mol Cell Proteomics}, year = {2015}, note = {

n/a

}, type = {Journal Article}, abstract = {

Glucans are polymers of D-glucose with differing linkages in linear or branched sequences. They are constituents of microbial and plant cell-walls and involved in important bio-recognition processes including immunomodulation, anti-cancer activities, pathogen virulence and plant cell-wall biodegradation. Translational possibilities for these activities in medicine and biotechnology are considerable. High-throughput micro-methods are needed to screen proteins for recognition of specific glucan sequences as a lead to structure-function studies and their exploitation. We describe construction of a glucome microarray, the first sequence-defined glycome-scale microarray, using a designer approach from targeted ligand-bearing glucans in conjunction with a novel high-sensitivity mass spectrometric sequencing method, as a screening tool to assign glucan recognition motifs. The glucome microarray comprises 153 oligosaccharide probes with high purity, representing major sequences in glucans. The negative-ion electrospray tandem mass spectrometry with collision-induced dissociation was used for complete linkage analysis of gluco-oligosaccharides in linear homo and hetero and branched sequences. The system is validated using antibodies and carbohydrate-binding modules known to target α- or β-glucans in different biological contexts, extending knowledge on their specificities, and applied to reveal new information on glucan recognition by two signalling molecules of the immune system against pathogens: Dectin-1 and DC-SIGN. The sequencing of the glucan oligosaccharides by the MS method and their interrogation on the microarrays provides detailed information on linkage, sequence and chain length requirements of glucan-recognizing proteins, and are a sensitive means of revealing unsuspected sequences in the polysaccharides.

}, issn = {1535-9484}, doi = {10.1074/mcp.M115.048272}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25670804}, author = {Palma, A. S. and Liu, Y. and Zhang, H. and Zhang, Y and McCleary, B. V. and Yu, G. and Huang, Q. and Guidolin, L. S. and Ciocchini, A. E. and Torosantucci, A. and Wang, D. and Carvalho, AL and Fontes, C. M. and Mulloy, B. and Childs, R. A. and Feizi, T. and Chai, W.} } @inbook {Carvalho2010, title = {X-Ray Crystallography in Drug Discovery}, booktitle = {Methods in molecular biology (Clifton, N.J.)}, volume = {572}, year = {2010}, note = {

n/a

}, pages = {31{\textendash}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.

}, issn = {1940-6029}, doi = {10.1007/978-1-60761-244-5_3}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79952112755{\&}partnerID=MN8TOARS http://www.ncbi.nlm.nih.gov/pubmed/20694684{\%}0Ahttp://link.springer.com/10.1007/978-1-60761-244-5{\_}3}, author = {Carvalho, Ana Lu{\'\i}sa and Trinc{\~a}o, Jos{\'e} and Rom{\~a}o, Maria Jo{\~a}o} } @article {1809, title = {Liquid crystalline cellulose derivative elastomer films under uniaxial strain}, journal = {Cellulose}, volume = {16}, number = {2}, year = {2009}, note = {n/a}, pages = {199-205}, abstract = {n/a}, author = {Godinho, M. H. and Filip, D. and Costa, I. and Carvalho, A. -L. and Figueirinhas, J. L. and Terentjev, E. M.} } @article {1805, title = {Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis}, journal = {Acta Crystallographica Section F-Structural Biology and Crystallization Communications}, volume = {63}, year = {2007}, note = {n/a}, pages = {516-519}, abstract = {n/a}, author = {Coelho, Catarina and Gonzalez, Pablo J. and Trincao, Jose and Carvalho, Ana L. and Najmudin, Shabir and Hettman, Thomas and Dieckman, Stephan and Moura, Jose J. G. and Moura, Isabel and Romao, Maria J.} } @article {1814, title = {The first crystal structure of class III superoxide reductase from Treponema pallidum}, journal = {Journal of Biological Inorganic Chemistry}, volume = {11}, number = {5}, year = {2006}, note = {n/a}, pages = {548-558}, abstract = {n/a}, author = {Santos-Silva, T and Trincao, J and Carvalho, AL and Bonifacio, C. and Auchere, F and Raleiras, P and Moura, I and Moura, JJG and Romao, MJ} } @article {1802, title = {Insights into the structural determinants of cohesin dockerin specificity revealed by the crystal structure of the type II cohesin from Clostridium thermocellum SdbA}, journal = {Journal of Molecular Biology}, volume = {349}, number = {5}, year = {2005}, note = {n/a}, pages = {909-915}, abstract = {n/a}, author = {Carvalho, AL and Pires, VMR and Gloster, TM and Turkenburg, JP and Prates, JAM and Ferreira, LMA and Romao, MJ and Davies, GJ and Fontes, CMGA and Gilbert, HJ} } @article {1813, title = {Superoxide reductase from the syphilis spirochete Treponema pallidum: crystallization and structure determination using soft X-rays}, journal = {Acta Crystallographica Section F-Structural Biology and Crystallization Communications}, volume = {61}, year = {2005}, note = {n/a}, pages = {967-970}, abstract = {n/a}, author = {Santos-Silva, T and Trincao, J and Carvalho, AL and Bonifacio, C. and Auchere, F and Moura, I and Moura, JJG and Romao, MJ} } @article {1796, title = {Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein}, journal = {Protein Science}, volume = {8}, number = {7}, year = {1999}, note = {n/a}, pages = {1536-1545}, abstract = {n/a}, author = {Archer, M and Carvalho, AL and Teixeira, S and Moura, I and Moura, JJG and Rusnak, F and Romao, MJ} } @article {1811, title = {Crystal structure of acidic seminal fluid protein (aSFP) at 1.9 angstrom resolution: a bovine polypeptide of the spermadhesin family}, journal = {Journal of Molecular Biology}, volume = {274}, number = {4}, year = {1997}, note = {

ISI Document Delivery No.: YP198 Times Cited: 33 Cited Reference Count: 32 Romao, MJ Kolln, I Dias, JM Carvalho, AL Romero, A Varela, PF Sanz, L Topfer-Petersen, E Calvete, JJ ACADEMIC PRESS LTD LONDON

}, pages = {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.

}, keywords = {bovine seminal plasma protein acidic seminal fluid protein aSFP spermadhesins CUB domain PELLUCIDA BINDING CHARACTERISTICS BOAR SPERMADHESINS PLASMA OLIGOSACCHARIDE LOCALIZATION LOCATION}, author = {Romao, MJ and Kolln, I. and Dias, JM and Carvalho, AL and Romero, A. and Varela, P. F. and Sanz, L. and Topfer-Petersen, E. and Calvete, JJ} } @article {1812, title = {The crystal structures of two spermadhesins reveal the CUB domain fold}, journal = {Nature Structural Biology}, volume = {4}, number = {10}, year = {1997}, note = {

ISI Document Delivery No.: YA203 Times Cited: 108 Cited Reference Count: 32 Romero, A Romao, MJ Varela, PF Kolln, I Dias, JM Carvalho, AL Sanz, L TopferPetersen, E Calvete, JJ NATURE PUBLISHING CO NEW YORK

}, pages = {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.

}, keywords = {SEMINAL FLUID PROTEIN BOAR SPERMADHESINS PSP-II PLASMA HETERODIMER LOCATION CLONING RNA}, author = {Romero, A. and Romao, MJ and Varela, P. F. and Kolln, I. and Dias, JM and Carvalho, AL and Sanz, L. and TopferPetersen, E. and Calvete, JJ} } @article {1806, title = {Crystallization and preliminary x-ray diffraction studies of aSFP, a bovine seminal plasma protein with a single CUB domain architecture}, journal = {Protein Science}, volume = {6}, number = {3}, year = {1997}, note = {

ISI Document Delivery No.: WM740 Times Cited: 7 Cited Reference Count: 22 Dias, JM Carvalho, AL Kolln, I Calvete, JJ TopferPetersen, E Varela, PF Romero, A Urbanke, C Romao, MJ CAMBRIDGE UNIV PRESS NEW YORK

}, pages = {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

}, keywords = {acidic seminal fluid protein analytical ultracentrifugation aSFP bovine seminal plasma crystallization CUB domain spermadhesin protein family X-ray diffraction analysis FLUID PROTEIN BOAR SPERMADHESINS ZONA-PELLUCIDA LOCALIZATION AWN-1}, author = {Dias, JM and Carvalho, AL and Kolln, I. and Calvete, JJ and TopferPetersen, E. and Varela, P. F. and Romero, A. and Urbanke, C. and Romao, MJ} }