Research Lab

XTAL - Macromolecular Crystallography

XTAL - Macromolecular Crystallography
29669
Research Interests

We use X-ray diffraction data to study proteins and protein-ligand complexes using X-ray Crystallography and SAXS methods as well as novel methodologies applied to glycomics, such as glycan microarrays. Our main foci of research are:

  1. Mechanistic studies and identification of ligands, at atomic level (metalloenzymes, in particular those containing Mo and Fe centers)
  2. Drug design and ligand discovery
  3. Glycan function, Glycan-protein and protein-protein interactions
  4. Novel strategies for improved protein crystallization
Research Highlights
Functional and structural insights into peptidoglycan amidation of Staphylococcus aureus

Peptidoglycan amidation, catalysed by the bi-enzymatic complex MurT-GatD, is crucial for the proper assembly of bacteria cell wall and has been associated with antibiotic resistance mechanisms. Combining X-ray Crystallography and NMR spectroscopy we identified the molecular determinants involved in the glutaminase step of Staphylococcus aureus MurT-GatD activity. The results allowed the establishment of the first structural-functional insight of this complex, shedding light into the reaction mechanism of peptidoglycan amidation. The ubiquitous presence of the complex in Gram-positive bacteria, specially the pathogenic Streptococcus pneumoniae, Clostridium perfringens and Mycobacterium tuberculosis makes MurT-GatD complex a potential target to fight different bacterial infections. The updated outcomes of our research, in combination with the recently published crystal structure of the whole complex (Scientific Reports 2018, 8(1):12953) are being used to identify hot spots for the development of new antibiotics able to integrate current therapeutics.

 

fig1Schematic representation of lipid II amidation in S. aureus including the functional outcomes of our research.

 

Targeting protein-carbohydrate interactions in plant cell-wall biodegradation

The plant cell wall is constituted by structurally diverse polysaccharides. Their biodegradation 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). In a book chapter for the Royal Society of Chemistry, we highlight how carbohydrate microarrays offer high-throughput and sensitive tools for uncovering carbohydrate-binding specificities of CBMs. This is pivotal to understand the function of these modules in polysaccharide biodegradation mechanisms (Ribeiro et al, In Carbohydrate Chemistry: Chemical and Biological Approaches Volume 43, The Royal Society of Chemistry, 2018).

 

fig2Schematic representation of a cellulosomal assembly from Clostridium thermocellum and its cellular location. The figure also depicts known 3D structures of selected modules determined by X-ray Crystallography

 

Representative Projects

  • “Glycan-human microbiome interaction: glycan diversity and recognition in the human gut with impact on health and nutrition”, FCT-MCTES, Total funding: €234,280, Unit funding: € 176,405 + € 15,625 (NZYTech) , Maria Angelina de Sá Palma (PI).
  • “Advances in MUC1 Glycan Cancer Antigens: From structure to function in the fight against cancer”, FCTMCTES, Total funding: €238,195, Unit funding: € 176,266 , Maria Angelina de Sá Palma (Co-PI).
  • “B.EST.CBM: an integrative structural biology approach to characterise the protein-carbohydrate microbial recognition”, FCT-MCTES, Total funding: €199,884, Unit funding: €120,684, Ana Luísa Carvalho (PI).
  • “Carbon monoxide guided shuttles (COGSs) to fight rheumatoid arthritis”, FCT-MCTES, Total funding: €199,996, Unit funding: €117,996, Teresa Santos-Silva (PI).
  • “Aldehyde oxidases in drug metabolism and biocatalysis: searching for the substrate specificity and catalytic mechanism”, FCT-MCTES, Total funding: €198,996, Unit funding: €162,792, Maria João Romão (PI).

Selected Publications

Rudkin, FM; Raziunaite, I; Workman, H; Essono, S; Belmonte, R; MacCallum, DM; Johnson, EM; Silva, L; Palma, AS; Feizi, T; Jensen, A; Erwig, LP; Gow, NAR. 2019. Single human B cell-derived monoclonal anti-Candida antibodies enhance phagocytosis and protect against disseminated candidiasis (vol 9, 5288, 2018). Nature Communications, 10, DOI: 10.1038/s41467-019-08392-x
Peixoto, D; Malta, G; Cruz, H; Barroso, S; Carvalho, AL; Ferreira, LM; Branco, PS. 2019. N-Heterocyclic Olefin Catalysis for the Ring Opening of Cyclic Amidine Compounds: A Pathway to the Synthesis of c-Caprolactamand -Lactam-Derived Amines. JOURNAL OF ORGANIC CHEMISTRY, 84, DOI: 10.1021/acs.joc.8b02823
Santarsia, S; Grosso, AS; Trovao, F; Jimenez-Barbero, J; Carvalho, AL; Nativi, C; Marcelo, F. 2018. Molecular Recognition of a Thomsen-Friedenreich Antigen Mimetic Targeting Human Galectin-3. ChemMedChem, 13, DOI: 10.1002/cmdc.201800525
Kumar, K; Correia, MAS; Pires, VMR; Dhillon, A; Sharma, K; Rajulapati, V; Fontes, CMGA; Carvalho, AL; Goyal, A. 2018. Novel insights into the degradation of beta-1,3-glucans by the cellulosome of Clostridium thermocellum revealed by structure and function studies of a family 81 glycoside hydrolase. INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 117, DOI: 10.1016/j.ijbiomac.2018.06.003
Kryshtafovych, A; Albrecht, R; Basle, A; Bule, P; Caputo, AT; Carvalho, AL; Chao, KL; Diskin, R; Fidelis, K; Fontes, CMGA; Fredslund, F; Gilbert, HJ; Goulding, CW; Hartmann, MD; Hayes, CS; Herzberg, O; Hill, JC; Joachimiak, A; Kohring, GW; Koning, RI; Lo Leggio, L; Mangiagalli, M; Michalska, K; Moult, J; Najmudin, S; Nardini, M; Nardone, V; Ndeh, D; Nguyen, TH; Pintacuda, G; Postel, S; van Raaij, MJ; Roversi, P; Shimon, A; Singh, AK; Sundberg, EJ; Tars, K; Zitzmann, N; Schwede, T. 2018. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 86, DOI: 10.1002/prot.25392