Where Ideas grow

Macromolecular Structure


We use X-ray crystallography, in combination with other biophysical and biochemical approaches, to unveil two distinct biological problems: the molecular determinants of specific thrombin recognition and inhibition by natural anticoagulants from haematophagous animals, and the mechanism of action of unique enzymes from human pathogens, which are potential drug targets for therapeutic intervention.



Our current research interests concentrate in two main lines:

1. The molecular mechanisms of specific thrombin recognition and inhibition by natural anticoagulants from haematophagous animals. In this field, our work contributed to unveiling the mode of action of several unique anticoagulants (e.g., boophilin from the cattle tick, anophelin from the malaria mosquito, and madanin and chimadanin from the bush tick). In the scope of a long-term collaboration with Richard Payne (University of Sydney, Australia) we also disclosed the dramatic effect of a specific post-translational modification, tyrosine sulfation, on inhibitor binding affinity;


2. The functional and structural characterization of novel potential drug targets from human pathogens. We have been devoting our attention to a unique biosynthetic mycobacterial pathway, leading to the production of complex polysaccharides. In close collaboration with Nuno Empadinhas (CNBC, Portugal), we have identified and characterized functional and structurally several of the intervening enzymes, unveiling their molecular determinants of substrate specificity.


Tyrosine sulfation is a strong modulator of the anticoagulant activity of tick-derived thrombin inhibitors (MEROPS families I53 and I72)

Selected Publications

Macedo-Ribeiro S., Almeida C., Calisto B., Friedrich T., Mentele R., Stürzebecher J., Fuentes-Prior P., Pereira P.,
Isolation, cloning and structural characterization of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick. PLoS ONE3(2):1-17, 2008. [Journal: Article] [CI: 70]
DOI: 10.1371/journal.pone.0001624 SCOPUS: 45849130590. .

Pereira P., Empadinhas N., Albuquerque L., Sá-Moura B., da Costa M., Macedo-Ribeiro S.,
Mycobacterium tuberculosis glucosyl-3-phosphoglycerate synthase: Structure of a key enzyme in methylglucose lipopolysaccharide biosynthesis. PLoS ONE3(11):, 2008. [Journal: Article] [CI: 22]
DOI: 10.1371/journal.pone.0003748 SCOPUS: 56649112704. .

Figueiredo A., De Sanctis D., Gutiérrez-Gallego R., Cereija T., Macedo-Ribeiro S., Fuentes-Prior P., Pereira P.,
Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector. Proceedings of the National Academy of Sciences of the United States of America109(52):, 2012. [Journal: Article] [CI: 21] [IF: 9,7]
DOI: 10.1073/pnas.1211614109 SCOPUS: 84871839379. .

Figueiredo A., Clement C., Zakia S., Gingold J., Philipp M., Pereira P.,
Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors. PLoS ONE7(3):, 2012. [Journal: Article] [CI: 15] [IF: 3,7]
DOI: 10.1371/journal.pone.0034354 SCOPUS: 84858758675. .

Figueiredo A., de Sanctis D., Pereira P.,
The Tick-Derived Anticoagulant Madanin Is Processed by Thrombin and Factor Xa. PLoS ONE8(8):, 2013. [Journal: Article] [CI: 9] [IF: 3,5]
DOI: 10.1371/journal.pone.0071866 SCOPUS: 84881513163. .

Santos J., Alonso-Garciá N., Macedo-Ribeiro S., Barbosa Pereira P.,
The unique regulation of iron-sulfur cluster biogenesis in a Gram-positive bacterium. Proceedings of the National Academy of Sciences of the United States of America111(22):, 2014. [Journal: Article] [CI: 17] [IF: 9,7]
DOI: 10.1073/pnas.1322728111 SCOPUS: 84901821729. .

Thompson R., Liu X., Alonso-García N., Pereira P., Jolliffe K., Payne R.,
Trifluoroethanethiol: An additive for efficient one-pot peptide ligation - Desulfurization chemistry. Journal of the American Chemical Society136(23):8161-8164, 2014. [Journal: Article] [CI: 63] [IF: 12,1]
DOI: 10.1021/ja502806r SCOPUS: 84902270939. .

Meyer P., Socias S., Key J., Ransey E., Tjon E., Buschiazzo A., Lei M., Botka C., Withrow J., Neau D., Rajashankar K., Anderson K., Baxter R., Blacklow S., Boggon T., Bonvin A., Borek D., Brett T., Caflisch A., Chang C., Chazin W., Corbett K., Cosgrove M., Crosson S., Dhe-Paganon S., Di Cera E., Drennan C., Eck M., Eichman B., Fan Q., Ferré-D'Amaré A., Fromme J., Garcia K., Gaudet R., Gong P., Harrison S., Heldwein E., Jia Z., Keenan R., Kruse A., Kvansakul M., McLellan J., Modis Y., Nam Y., Otwinowski Z., Pai E., Pereira P., Petosa C., Raman C., Rapoport T., Roll-Mecak A., Rosen M., Rudenko G., Schlessinger J., Schwartz T., Shamoo Y., Sondermann H., Tao Y., Tolia N., Tsodikov O., Westover K., Wu H., Foster I., Fraser J., Maia F., Gonen T., Kirchhausen T., Diederichs K., Crosas M., Sliz P.,
Data publication with the structural biology data grid supports live analysis. Nature Communications7:, 2016. [Journal: Article] [CI: 48] [IF: 12,1]
DOI: 10.1038/ncomms10882 SCOPUS: 84960381776. .

Thompson R., Liu X., Ripoll-Rozada J., Alonso-García N., Parker B., Pereira P., Payne R.,
Tyrosine sulfation modulates activity of tick-derived thrombin inhibitors. Nature Chemistry9(9):909-917, 2017. [Journal: Article] [CI: 14] [IF: 26,2]
DOI: 10.1038/NCHEM.2744 SCOPUS: 85028339870. .

Merski M., Moreira C., Abreu R., Ramos M., Fernandes P., Martins L., Pereira P., Macedo-Ribeiro S.,
Molecular motion regulates the activity of the mitochondrial serine protease HtrA2. Cell Death and Disease8(10):, 2017. [Journal: Article] [CI: 2] [IF: 5,6]
DOI: 10.1038/cddis.2017.487 SCOPUS: 85031277139. .