Research

 

Research Outline

Protein-protein interactions play a relevant role among the different functions of a cell. Identifying the protein-protein interaction network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. A paradox in protein-protein binding is to explain how the unbound proteins of a binary complex recognize each other among a large population within a cell and how they find their best docking interface in a short time-scale. We interrogate protein structure to unveil its function, generate the network of interactions and to relate genes/proteins with diseases by means of exploiting the topology of the network.

 

Current Projects

On the study of the relationship between sequence, structure and function of proteins: Characterization of the structural motifs involved in the function and interactions between proteins. Development of statistical potentials and analysis of physico-chemical potentials helping to describe the fold and function of proteins and its interactions with other macro-molecules.

On the prediction of protein-protein and protein-DNA interactions: Structural analysis of docking approaches and development of new techniques towards the prediction of binding sites and the mechanisms of interface selection of protein-protein and protein-DNA interactions.

On the analysis of protein interaction networks and its use on bio-medicine, helping to detect potential targets and prioritization of candidate disease-genes. Development of methods to study and integrate information for different types of networks and application on the study of metastasis. Prediction of signalling networks, such as the phosphorylation network and other post-transcriptional modifications, and integration with genomic data, such as microarrays.


Selected publications

  • Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions BMC Bioinformatics 22(1) 1-13, 2021
  • Ana Tapia-Abellán, Diego Angosto-Bazarra, Cristina Alarcón-Vila, María C Baños, Iva Hafner-Bratkovič, Baldomero Oliva, Pablo Pelegrín. Sensing low intracellular potassium by NLRP3 results in a stable open structure that promotes inflammasome activation. Scientific Advances 7(38), eabf4468, 2021
  • Maria Pallarès-Masmitjà, Dimitrije Ivančić, Júlia Mir-Pedrol, Jessica Jaraba-Wallace, Tommaso Tagliani, Baldomero Oliva, Amal Rahmeh, Avencia Sánchez-Mejías, Marc Güell. Find and cut-and-transfer (FiCAT) mammalian genome engineering. Nature communications 12(1) 1-9. 2021
  • Laura Artigas, Mireia Coma, Pedro Matos-Filipe, Joaquim Aguirre-Plans, Judith Farrés, Raquel Valls, Narcis Fernandez-Fuentes, Juan De La Haba-Rodriguez, Alex Olvera, Jose Barbera, Rafael Morales, Baldo Oliva, Jose Manuel Mas In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PLoS ONE  October 2, 2020 https://doi.org/10.1371/journal.pone.0240149
  • Patricia Mirela-Bota, Joaquim Aguirre-Plans, Alberto Meseguer, Cristiano Galletti, Joan Segura, Joan Planas-Iglesias, Javi Garcia-Garcia, Emre Guney, Baldo Oliva, Narcis Fernandez-Fuentes. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data. J Mol Biol. 2020 Sep 23;S0022-2836(20)30557-X. doi: 10.1016/j.jmb.2020.09.01
  • Priyanka Sharma, Antonios Lioutas, Narcis Fernandez-Fuentes, Javier Quilez, José Carbonell-Caballero, Roni HG Wright, Chiara Di Vona, François Le Dily, Roland Schüller, Dirk Eick, Baldomero Oliva, Miguel Beato. Arginine citrullination at the C-terminal domain controls RNA polymerase II transcription. Molecular cell 73(1) 84-96. e7 2019.
  • Alberto Meseguer, Filip Årman, Oriol Fornes, Ruben Molina-Fernández, Jaume Bonet, Narcis Fernandez-Fuentes, Baldo Oliva. On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF. NAR Genomics and Bioinformatics. 2020. 2(3): lqaa046. doi: 10.1093/nargab/lqaa046
  • Pol Picón-Pagès, Jaume Bonet, Javier García-García, Joan Garcia-Buendia, Daniela Gutierrez, Javier Valle, Carmen ES Gómez-Casuso, Valeriya Sidelkivska, Alejandra Alvarez, Alex Perálvarez-Marín, Albert Suades, Xavier Fernàndez-Busquets, David Andreu, Rubén Vicente, Baldomero Oliva, Francisco J Muñoz. Computational and structural biotechnology journal 17,963-971, 2019
  • Aguirre-Plans J, Piñero J, Sanz F, Furlong LI, Fernandez-Fuentes N, Oliva B, Guney E. GUILDify v2.0: A tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets. J Mol Biol, 2019. pii: S0022-2836 (19) 30117-2.. PMID: 30851278 . DOI: 10.1016/ j.jmb.2019.02.027
  • Bernat Blasco-Moreno, Leire de Campos-Mata, René Böttcher, José García-Martínez, Jennifer Jungfleisch, Danny D Nedialkova, Shiladitya Chattopadhyay, María-Eugenia Gas, Baldomero Oliva, José E Pérez-Ortín, Sebastian A Leidel, Mordechai Choder, Juana Díez. The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins Nature communications 10(1), 1-15 2019
  • ANTONIO CUADRADO, GINA MANDA, AHMED HASSAN, MARÍA JOSÉ ALCARAZ, CORAL BARBAS, ANDREAS DAIBER, PIETRO GHEZZI, RAFAEL LEÓN, MANUELA G LÓPEZ, BALDO OLIVA, MARTA PAJARES, ANA I ROJO, NATALIA ROBLEDINOS-ANTÓN, ANGELA M VALVERDE, EMRE GUNEY, HARALD HHW SCHMIDT. Transcription factor NRF2 as a therapeutic target for chronic diseases: a systems medicine approach. Pharmacological reviews 70 (2), 348-383 (2018)
  • GARCIA-GARCIA J, VALLS-COMAMALA V, GUNEY E, ANDREU D, MUÑOZ FJ, FERNANDEZ-FUENTES N, OLIVA B. iFraG: A protein-protein interface prediction server based on sequence fragments. J Mol Biol. 3;429(3):382-389. (2017)
  • RUBIO-PEREZ C, GUNEY E, AGUILAR D, PIÑERO J, GARCIA-GARCIA J, IADAROLA B, SANZ F, FERNANDEZ-FUENTES N, FURLONG LI, OLIVA B. Genetic and functional characterization of disease associations explains comorbidity. Sci Rep. 7(1):6207 (2017)
  • Gubern A, Joaquin M, Marquès M, Maseres P, Garcia-Garcia J, Amat R, González-Nuñez D, Oliva B, Real Fx, De Nadal E, Posas F. The N-Terminal Phosphorylation of RB by p38 Bypasses Its Inactivation by CDKs and Prevents Proliferation in Cancer Cells. Mol Cell. pii: S1097-2765(16) 30429-4 ( 2016)
  • Sieberts Sk, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín Ma, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao Ao, Suver C, Hoff B, Balagurusamy Vs, Dillenberger D, Neto Ec, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott Ca, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan Sa, Kramer Er, Marttinen P, Mezlini Am, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert Jp, Wang B, Wang T, Wennerberg K, Wineinger Ne, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members Of The Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, De Vries N, Tak Pp, Gerlag D, Huizinga Tw, Kurreeman F, Allaart Cf, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen Pk, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite Lm, Bridges Sl, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen Pk, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite Lm. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun. 7:12460 (2016)
  • Wright Rh, Lioutas A, Le Dily F, Soronellas D, Pohl A, Bonet J, Nacht As, Samino S, Font-Mateu J, Vicent Gp, Wierer M, Trabado Ma, Schelhorn C, Carolis C, Macias Mj, Yanes O, Oliva B, Beato M. ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling. Science. 352(6290):1221-5 (2016)
  • Hill Sm, Heiser Lm, Cokelaer T, Unger M, Nesser Nk, Carlin De, Zhang Y, Sokolov A, Paull Eo, Wong Ck, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova Lv, Favorov Av, Lee Ws, TaylorD, Hu Cw, Long Bl, Noren Dp, Bisberg Aj; Hpn-Dream Consortium, Mills Gb, Gray Jw, Kellen M, Norman T, Friend S, Qutub Aa, Fertig Ej, Guan Y, Song M, Stuart Jm, Spellman Pt, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Et Al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods. 13(4):310-8. (2016)
  • Bonet, J, Planas-Iglesias, J, Garcia-Garcia, J, Marin-Lopez,MA, Fernandez-Fuentes, N., Oliva, B. ArchDB 2014: structural classification of loops in proteins. Nucleic Acids Research, 2014; 42(Database issue):D315-9
  • Guney E, Oliva B. Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization. PLoS One, 2012, 7 (9) e43557
  • Garcia-Garcia J, Schleker S, Klein-Seetharaman J, Oliva B. BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference Nucleic Acids Res, 2012; 40 (W1):W147-W151

 

 

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