Ribeiro, D. O., F. Bonnardel, A. S. Palma, A. L. M. Carvalho, and S. Perez. "
CBMcarb-DB: interface of the three-dimensional landscape of carbohydrate-binding modules."
Carbohydrate Chemistry: Chemical and Biological Approaches Volume 46. Eds. Amélia Pilar Rauter, Yves Queneau, and Angelina Sá Palma. Vol. 46. Royal Society of Chemistry, 2024.
AbstractCarbohydrate-binding-modules (CBMs) are discrete auxiliary protein modules with a non-catalytic carbohydrate-binding function and that exhibit a great diversity of binding specificities. CBMcarb-DB is a curated database that classifies the three-dimensional structures of CBM–carbohydrate complexes determined by single-crystal X-ray diffraction methods and solution NMR spectroscopy. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to describing the bound glycans using simple graphical representation and numerical format for cross-referencing to other glycosciences and functional data databases. CBMcarb-DB provides detailed information on CBMs and their bound oligosaccharides and features their interactions using several open-access applications. We also describe how the curated information provided by CBMcarb-DB can be integrated with AI algorithms of 3D structure prediction, facilitating structure–function studies. Also in this chapter, we discuss the exciting convergence of CBMcarb-DB with the glycan array repository, which serves as a valuable resource for investigating the specific binding interactions between glycans and various biomolecular targets. The interaction of the two fields represents a significant milestone in glycosciences. CBMcarb-DB is freely available at https://cbmdb.glycopedia.eu/ and https://cbmcarb.webhost.fct.unl.pt.
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.
AbstractCellulosomes 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.
Correia, Viviana G., Benedita A. Pinheiro, Ana Luísa Carvalho, and Angelina S. Palma. "
Resistance to Aminoglycosides."
Antibiotic Drug Resistance. John Wiley & Sons, Ltd, 2019. 1-38.
AbstractSummary The emergence of bacterial resistance to different antibiotics in clinical use, together with the knowledge on the mechanisms by which bacteria resist the action of aminoglycosides, have contributed to the renewed interest in these molecules as potential antimicrobials. Here, we give an overview on natural and semisynthetic aminoglycosides and their structural features and modes of action, focusing on the structural insight underlying resistance mechanisms. Developments on carbohydrate chemistry and microarray technology are highlighted as powerful approaches toward generation of new aminoglycosides and for screening their interactions with RNAs and proteins. The link between antibiotic uptake and the human gut microbiome is also addressed, focusing on gut microbiome function and composition, antibiotic-induced alterations in host health, and antibiotic resistance. In addition, strategies to modulate human microbiome responses to antibiotics are discussed as novel approaches for aminoglycoside usage and for the effectiveness of antibiotic therapy.
Ribeiro, Diana O., Benedita A. Pinheiro, Ana Luisa Carvalho, and Angelina S. Palma. "
Targeting protein-carbohydrate interactions in plant cell-wall biodegradation: the power of carbohydrate microarrays."
Carbohydrate Chemistry: Chemical and Biological Approaches Volume 43. Vol. 43. The Royal Society of Chemistry, 2018. 159-176.
AbstractThe plant cell-wall is constituted by structurally diverse polysaccharides. The biodegradation of these is a crucial process for life sustainability. Cellulolytic microorganisms are highly efficient in this process by assembling modular architectures of carbohydrate-active enzymes with appended non-catalytic carbohydrate-binding modules (CBMs). Carbohydrate microarrays offer high-throughput and sensitive tools for uncovering carbohydrate-binding specificities of CBMs{,} which is pivotal to understand the function of these modules in polysaccharide biodegradation mechanisms. Features of this technology will be here briefly reviewed with highlights of microarray approaches to study plant-carbohydrates and CBM-carbohydrate interactions{,} along with an overview of plant polysaccharides and microorganisms strategies for their recognition.
Carvalho, Ana Luísa, Teresa Santos-Silva, Maria João Romão, J. Eurico, and Filipa Marcelo. "
{CHAPTER 2 Structural Elucidation of Macromolecules}."
Essential Techniques for Medical and Life Scientists: A Guide to Contemporary Methods and Current Applications with the Protocols. BENTHAM SCIENCE PUBLISHERS, 2018. 30-91.
Abstract