The laboratory for structural and computational proteomics (LPEC) conducts research in development of computational and experimental approaches tailored toward biological mass spectrometry, especially proteomics and structural proteomics. We apply these methods to address biological questions such as cancer and the characterization of proteins, protein complexes, and large-scale protein-protein interaction. Complementary techniques such as x-ray crystallography and saxs are also frequently used.
Our Laboratory
Laboratory for structural and computational proteomics (LPEC)
Principal Investigators
holds a PhD in systems engineering and computer science from the Federal University of Rio de Janeiro and is a former member of the John R. Yates (h-index 174) Laboratory at the Scripps Research Institute, California, EUA. Among his awards, we highlight the Google Award for Academic Excellence, honourable mention provided by CAPES Tese 2010 for having his PhD thesis as one of the most prominent in Brazil for the year 2010, the Fleury Award for Innovation and the Institut Pasteur Talent Award. In 2012 he earned a position as a research scientist in proteomics at Fiocruz. Paulo published over 100 papers of which several of his first / last author ones being in journals such as Bioinformatics, Analytical Chemistry, Nature Protocols, and Nature Methods.. Paulo is a member of the faculty at the Federal University of Rio de Janeiro and Carlos Chagas Institute, an associate Researcher at Institut Pasteur – Montevideo, and Fiocruz, where he teaches computational proteomics at the graduate level. Paulo is founding member of the Brazilian Society for Proteomics and is part of its scientific committee. In October 2014, Paulo was nominated as an executive editor of the Journal of Proteomics (IF 3.9) which is the official journal of the European Proteomics Association. In 2016, he became part of the Features Panel of the prestigious Analytical Chemistry (IF 5.8) journal. During his career, Paulo has earned several national and international grants, coordinated several projects within the Fiocruz-Pasteur network; an example being the DiagnoProt in collaboration with Institute Pasteur Montevideo and Institute Pasteur Paris. He also leads projects with the industry; examples being with Nitto Aveccia (USA), Nova Analítica (Brazil), and O Boticario (Brazil). He has concluded the supervision of 6 MSc, 4PhDs, 1 post-doc, and currently supervises 4 MSc, 5 PhDs and 1 post-doc.
holds a PhD in Genetics and Molecular Biology from UNICAMP. Tatiana’s professional experience includes 7 years of activities at the Brazilian Center for research in Energy and Materials (CNPEM) where the national synchrotron source is located. During that period, she worked on studies aiming the structural and functional understanding of several protein families (examples: septins, nucleoside diphosphate kinases, infestins, metalloproteinase, GH51 α-L-arabinofuranosidase, phospholipases, subtilases, xyloglucan-specific endo-β-1,4-glucanase, thrombin-like, cyclophilins, insulin, GH1 β-glucosidases, peroxiredoxins, nek kinases). The development of such projects resulted in 42 deposits of structures in the PDB, obtained by X-ray crystallography. In 2012 she earned a position as a research scientist at Fiocruz. Tatiana published over 35 papers of which several of her first / last author ones being in journals such as Acta Crystallographica D, Journal of Biological Chemistry e Journal of Molecular Biology. In 2018, she became accredited into the highly competitive group of researchers officially sponsored by Brazil’s Research Council, owing to the high quality of his publications (pesquisador de produtividade CNPq). Due to the biomedical and biotechnological application of her projects, Tatiana is inventor in two patent deposits.
Research
Selected publications
For a complete list of publications please refer to the corresponding CVs
- LIMA, DIOGO B ; MELCHIOR, JOHN T ; MORRIS, JAMIE ; BARBOSA, VALMIR C ; CHAMOT-ROOKE, JULIA; FIORAMONTE, MARIANA ; SOUZA, TATIANA A C B ; FISCHER, JULIANA S G ; GOZZO, FABIO C ; DAVIDSON, W SEAN; CARVALHO, PAULO C ;. CHARACTERIZATION OF HOMODIMER INTERFACES WITH CROSS-LINKING MASS SPECTROMETRY AND ISOTOPICALLY LABELED PROTEINS. NATURE PROTOCOLS, V. 13, P. 431-458, 2018.
- CARVALHO, PAULO C; LIMA, DIOGO B ; LEPREVOST, FELIPE V ; SANTOS, MARLON D M ; FISCHER, JULIANA S G ; AQUINO, PRISCILA F ; MORESCO, JAMES J ; YATES, JOHN R ; BARBOSA, VALMIR C . INTEGRATED ANALYSIS OF SHOTGUN PROTEOMIC DATA WITH PATTERNLAB FOR PROTEOMICS 4.0. NATURE PROTOCOLS (PRINT), V. 11, P. 102-117, 2015.
- THE ROLE OF THE QUATERNARY STRUCTURE IN THE ACTIVATION OF HUMAN L-ASPARAGINASE AUTHOR LINKS OPEN OVERLAY ANELS.B.MORAISAR.A.S.PIROLLABN.F.FROTACM.R.LOURENZONICDF.C.GOZZOBT.A.C.B.SOUZA
- YATES, JOHN R ; PARK, SUNG KYU ROBIN ; DELAHUNTY, CLAIRE M ; XU, TAO ; SAVAS, JEFFREY N; COCIORVA, DANIEL ; CARVALHO, PAULO COSTA . TOWARD OBJECTIVE EVALUATION OF PROTEOMIC ALGORITHMS. NATURE METHODS, V. 9, P. 455-456, 2012
- DE CASTRO, EMANUELLA ; REUS, THAMILE LUCIANE ; DE AGUIAR, ALESSANDRA MELO ; ÁVILA, ANDREA RODRIGUES ; DE ARRUDA CAMPOS BRASIL DE SOUZA, TATIANA . PROCASPASE-ACTIVATING COMPOUND-1 INDUCES APOPTOSIS IN TRYPANOSOMA CRUZI. APOPTOSIS, V. 1, P. 1-14, 2017.
- SANTANA, ALINE GUIMARÃES ; GRACHER, ANA HELENA PEREIRA ; RÜDIGER, ANDRÉ LUIS ; ZANCHIN, NILSON IVO TONIN ; CARVALHO, PAULO COSTA ; CIPRIANI, THALES RICARDO ; DE ARRUDA CAMPOS BRASIL DE SOUZA, TATIANA . IDENTIFICATION OF POTENTIAL TARGETS FOR AN ANTICOAGULANT PECTIN. JOURNAL OF PROTEOMICS (PRINT), V. 1, P. 1-4, 2016.
News
Computational and Structural Proteomics
Awards
- Institut Pasteur Talent Award conferred to Paulo Costa Carvalho, 2019
- Fleury Award for Innovation, conferred to Paulo Costa Carvalho, 2018
- Prêmio Capes de Tese Doutorado as one of the top 3 PhD thesis in biological sciences in Brazil, conferred to former PhD student Diogo Borges Lima and his advisor, Paulo Costa Carvalho, 2017
- Award in 23rd Congress of the International Union for Biochemistry and Molecular Biology conferred to Tatiana de Arruda Campos Brasil de Souza, 2015
- AC Camargo Cancer Center award, conffered to Victor Maltese Stoco for his project on Asparaginase production