Matias Lab - Industry and Medicine Applied Crystallography

The Lab’s research is focused on the structural characterization of biomolecules with potential impact in industry and/or medicine.

We use several biophysical techniques directed towards the understanding of their mode of action, with the aim of designing variants with enhanced properties for industrial applications or contribute to drug discovery and development pipelines targeting proteins with human health implications.
The main technique used is X-ray crystallography, but we have also developed internal and external collaborations to complement the structural studies with biochemical and biophysical assays. We are also beginning the first steps towards using CryoElectron Microscopy in our research.

Highlights

Improving O2 tolerance in a [NiFeSe] hydrogenase

Hydrogenases are metalloenzymes that catalyse the reversible oxidation of one hydrogen molecule (H2) into two electrons and two protons. They are of great potential economic interest because they can produce hydrogen from biological sources to be used as fuel, or in bioelectrodes to produce an electrical current from hydrogen. [NiFeSe] hydrogenases, where selenocysteine is a ligand to the Ni atom in the active site, are much more active towards H2 production and are less inhibited by H2 than standard [NiFe] hydrogenases. Nevertheless, they can also be inhibited by O2. In the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough, O2 inactivation involves the irreversible oxidation of a terminal cysteine ligand to nickel in the active site to a sulfenate/sulfinate  (Marques et al., 2013) .

We designed mutations in this protein to constrict a solvent-filled hydrophilic channel that links the protein surface to this active site cysteine. Two of the variants created, G491A and G491S, show markedly increased tolerance to O2 inactivation, while retaining high catalytic activities for both H2 production and oxidation. Structural studies confirmed that in these variants, Cys75 oxidation was prevented or considerably slowed down. These results indicate that diffusion of O2 or ROS to the active site can occur through a hydrophilic water channel, contrary to the widely held assumption that only hydrophobic channels are used for diffusion of O2/ROS and active site inactivation (Zacarias et al., 2019).

This work shows that by a single-residue mutation it is possible to improve the O2-tolerance of a [NiFeSe] hydrogenase, while retaining high activity in both directions of H2 catalysis.

References

Marques, M. C., Coelho, R., Pereira, I. A. C. & Matias, P. M. (2013). International Journal of Hydrogen Energy 38, 8664-8682. http://dx.doi.org/10.1016/j.ijhydene.2013.04.132

Zacarias, S., Temporão, A., Barrio, M. d., Fourmond, V., Léger, C., Matias, P. M. & Pereira, I. A. C. (2019). ACS Catalysis, 8509-8519. http://dx.doi.org/10.1021/acscatal.9b02347

 

Team members

  • Pedro Matias, Ph.D., Lab Head
  • Tiago Bandeiras, Ph.D., iBET Merck Healthcare Lab Head
  • Patricia Borges, PhD, Junior Researcher
  • Dalila Fernandes, Ph.D. student (co-supervision with João Vicente)
  • Catarina Paiva, Ph.D. student (co-supervision with Tiago Bandeiras)
  • Ana Margarida Coito, Ph.D. student (co-supervision with Inês A. C. Pereira)

  

Collaborations

  • Inês Pereira Lab – Bacterial Energy Metabolism, ITQB NOVA
  • Lígia Saraiva Lab – Molecular Mechanisms of Pathogen Resistance, ITQB NOVA
  • Cláudio Soares Lab – Protein Modeling, ITQB NOVA
  • Maria Arménia Carrondo Lab – Structural Genomics, ITQB NOVA
  • Gonçalo J. L. Bernardes Lab – iMM, Lisbon, Portugal
  • Antonio de Lacey Lab – Instituto de Catálisis y Petroleoquímica (CSIC), Madrid, Spain
  • José María Carazo Lab - Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
  • Sarah Butcher Lab – University of Helsinki, Helsinki, Finland

 

Recent Publications

  • Gizardin-Fredon, H., Santo, P. E., Chagot, M. E., Charpentier, B., Bandeiras, T. M., Manival, X., Hernandez-Alba, O., and Cianferani, S. (2024) Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions, Nat Commun 15, 3516, 10.1038/s41467-024-47732-4.
  • Ferreira, I. C., Torrejon, E., Abecasis, B., Alexandre, B. M., Gomes, R. A., Verslype, C., van Pelt, J., Barbas, A., Simao, D., Bandeiras, T. M., Bortoluzzi, A., and Rebelo, S. P. (2024) Aldehyde Dehydrogenase 2 (ALDH2): A novel sorafenib target in hepatocellular carcinoma unraveled by the proteome-wide cellular thermal shift assay, SLAS Discov 29, 100154, 10.1016/j.slasd.2024.100154.
  • Pires, C., Marques, I. J., Valerio, M., Saramago, A., Santo, P. E., Santos, S., Silva, M., Moura, M. M., Matos, J., Pereira, T., Cabrera, R., Lousa, D., Leite, V., Bandeiras, T. M., Vicente, J. B., and Cavaco, B. M. (2024) CHEK2 germline variants identified in familial nonmedullary thyroid cancer lead to impaired protein structure and function, J Biol Chem 300, 105767, 10.1016/j.jbc.2024.105767.
  • Salgueiro, B. A., Saramago, M., Tully, M. D., Issoglio, F., Silva, S. T. N., Paiva, A. C. F., Arraiano, C. M., Matias, P. M., Matos, R. G., Moe, E., and Romão, C. V. (2024) SARS-CoV2 Nsp1 is a metal-dependent DNA and RNA endonuclease, BioMetals, https://doi.org/10.1007/s10534-024-00596-z.
  • A. Fernandes, A. Williamson, P.M. Matias, E. Moe (2023) Structure/function studies of the NAD+‑dependent DNA ligase from the poly‑extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding. Extremophiles. 27:26. https://doi.org/10.1007/s00792-023-01309-z
  • A.G. Gouveia, B.A. Salgueiro, D.O. Ranmar, W.D.T. Antunes, P. Kirchweger, O. Golani O, S.G. Wolf , M. Elbaum, P.M. Matias and C.V. Romão (2023) Unraveling the multifaceted resilience of arsenic resistant bacterium Deinococcus indicus. Front. Microbiol. 14:1240798. https://doi.org/10.3389/fmicb.2023.1240798
  • I.B. Trindade, F. Rollo, S. Todorovic, T. Catarino, E. Moe, P.M. Matias, M. Piccioli, R.O. Louro (2023) The structure of a novel ferredoxin – FhuF, a ferric-siderophore reductase from E. coli K-12 with a novel 2Fe-2S cluster coordination. BioRxiv. https://doi.org/10.1101/2023.07.04.547673
  • Paiva, A. C. F., Lemos, A. R., Busse, P., Martins, M. T., Silva, D. O., Freitas, M. C., Santos, S. P., Freire, F., Barrey, E. J., Manival, X., Koetzner, L., Heinrich, T., Wegener, A., Gradler, U., Bandeiras, T. M., Schwarz, D., and Sousa, P. M. F. (2023) Extract2Chip-Bypassing Protein Purification in Drug Discovery Using Surface Plasmon Resonance, Biosensors (Basel) 13, 10.3390/bios13100913
  • Gradler, U., Schwarz, D., Wegener, A., Eichhorn, T., Bandeiras, T. M., Freitas, M. C., Lammens, A., Ganichkin, O., Augustin, M., Minguzzi, S., Becker, F., and Bomke, J. (2023) Biophysical and structural characterization of the impacts of MET phosphorylation on tepotinib binding, J Biol Chem 299, 105328, 10.1016/j.jbc.2023.105328.
  • S. Zacarias, A. Temporão, P. Carpentier, P. van der Linden, I. A. C. Pereira, P. M. Matias (2020) Exploring the Gas Access Routes in a [NiFeSe] Hydrogenase using Crystals Pressurized with Krypton and Oxygen. J. Biol. Inorg. Chem. 25:863-874. http://dx.doi.org/10.1007/s00775-020-01814-y
  • Abel, A.C.F. Paiva, J. Bizarro, M.E. Chagot, P.E. Santo, M.C. Robert, M. Quinternet, F. Vandermoere, P.M.F. Sousa, P. Fort, B. Charpentier, X. Manival, T.M. Bandeiras, E. Bertrand, C. Verheggen (2021) NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis. Nucleic Acids Res. 2021 Jan 25;49(2):1094-1113. http://dx.doi.org/10.1093/nar/gkaa1226
  • D. Seixas, B. B. Sousa, M. C. Marques, A. Guerreiro, R. Traquete, T. Rodrigues, I. S. Albuquerque, M. Sousa, A. R. Lemos, P. M. F. Sousa, T. M. Bandeiras, D. Wu, S. K. Doyle, C. V. Robinson, A. N. Koehler, F. Corzana, P. M. Matias, G. J. L. Bernardes (2020) Structural and biophysical insights into the mode of covalent binding of rationally designed potent BMX inhibitors. RSC Chem. Biol., 1:251-262. http://dx.doi.org/10.1039/d0cb00033g

Social Media / Lab website

https://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography