Protein Interactions and Docking

Algorithms for protein-protein docking based on FFT and Global Energy Optimization
We are integrating the energy function that we previously developed for scoring of rigid-body docking poses, in a grid search using Fast Fourier Transform algorithms to speed up calculations.

Prediction of protein interaction sites and hot-spots
We are extending our powerful binding site predictors, such as ODA and NIP, to the identification of hot-spot residues at binding interfaces. All these tools will be applied at proteomic scale.

Understanding protein-protein association mechanism
A deep understanding of protein-protein association will be essential, not only for accurate modelling and prediction of complex structure, but also for designing small-molecule inhibitors of protein-protein complexes. We are applying physical principles to study the energy landscape of the process of association between two proteins.

Flexible algorithms for protein-protein docking
Treatment of flexibility is currently the bottleneck in protein docking. We will use the capabilities of MareNostrum to develop new algorithms based on molecular dynamics approaches.

Prediction of electron-transfer complexes
In collaboration with other laboratories, we are modelling different complexes involved in electron transfer, such as the interaction between ferredoxin-NADP+ reductase and the proteins flavodoxin and ferredoxin, or the interaction between cythochrome c oxidase and the proteins plastocianin and cyt c6.

Prediction of multi-protein systems
We are also collaborating with many experimentalist groups, on modelling of challenging multi-protein systems such as the bacteria drug pump, signal transduction interactions, plant immune system, etc.

JOB OFFERS

We are always seeking for highly motivated people with a grade or doctorate in a scientific discipline (Chemistry, Physics, Bioinformatics, Biology, Biotechnology, Pharmacy) who want to do research at predoctoral and postdoctoral level in a multi-disciplinary field such as Structural Bioinformatics of Protein-Protein Interactions. Computer scientists and software engineers are also needed. If you are interested, please send your CV and a statement of interests to Dr. Juan Fernandez-Recio.

SELECTED PUBLICATIONS

(2005 - present)


Fernandez-Recio, J., Totrov, M., Skorodumov, C., Abagyan, R. (2005) Optimal Docking Area: a new method for predicting protein-protein interaction sites. Proteins 58, 134-143

Federici, L., Du, D., Walas, F., Matsumura, H., Fernandez-Recio, J., Borges-Walmsley, I., Luisi, B.F., Walmsley, A. (2005) The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 A resolution. J.Biol.Chem. 280, 15307-15314

Fernandez-Recio, J., Abagyan, R., Totrov, M. (2005) Improved CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 60, 308-313

Sicilia, F., Fernandez-Recio, J., Caprari, C., De Lorenzo, G., Tsernoglou, D., Cervone, F., Federici, L. (2005) The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endo-polygalacturonase PG1 of Botrytis cinerea. Plant Physiology 139, 1380-1388

Federici, L., Di Matteo, A., Fernandez-Recio, J., Tsernoglou, D., Cervone, F. (2006) Polygalacturonase inhibiting proteins: players in plant innate immunity? Trends Plant Sci. 11, 65-70

Noy A, Meyer T, Rueda M, Ferrer C, Valencia A, Perez A, de la Cruz X, Lopez-Bes JM, Pouplana R, Fernandez-Recio, J., Luque FJ, Orozco M. (2006) Data mining of molecular dynamics trajectories of nucleic acids. J Biomol Struct Dyn. 23, 447-456

Chelliah V, Blundell TL, Fernandez-Recio, J. (2006) Efficient Restraints for Protein-Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment. J.Mol.Biol. 357, 1669-1682

Yraola, F., Garcia-Vicente, S., Fernandez-Recio, J., Albericio, F., Zorzano, A., Marti, L., Royo, M. (2006) New Efficient Substrates for Semicarbazide-Sensitive Amine Oxidase/VAP-1 Enzyme: Analysis by SARs and Computational Docking. J.Med.Chem 49, 6197-6208

Casal, E., Federici, L., Zhang, W., Fernandez-Recio, J., Priego, E.M., Miguel, R.N., DuHadaway, J.B., Prendergast, G.C., Luisi, B.F., Laue, E.D. (2006) The Crystal Structure of the BAR Domain from Human Bin1/Amphiphysin II an Its Implications for Molecular Recognition. Biochemistry 45, 12917-12928

Bolanos-Garcia, V., Fernandez-Recio, J., Allende, J.E., Blundell, T.L. (2006) Identifying interaction motifs in CK2beta - a ubiquitous kinase regulatory subunit? Trends Biochem. Sci. 31, 654-661

Blundell, T.L., Fernandez-Recio, J. (2006) Brief encounters bolster contacts. Nature (News & Views) 444, 279-280

Chandran, V., Poljak, L., Vanzo, N.F., Leroy, A., Miguel, R.N., Fernandez-Recio, J., Parkinson, J., Burns, C., Carpousis, A.J., Luisi, B.F. (2007) Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. J.Mol.Biol. 367, 113-132.

Fernández, D., Vendrell, J., Avilés, F.X., Fernández-Recio, J. (2007) Structural and functional characterization of binding sites in metallopeptidases based on ODA analysis. Proteins.68, 131-144

Cheng, T., Blundell, T.L., Fernández-Recio, J. (2007) pyDockSER: scoring of rigid-body docking orientations by electrostatics and desolvation. Proteins 68, 503-515.

Fort, J., de la Ballina, L.R., Burghardt, H.E., Ferrer-Costa, C., Turnay, J., Ferrer-Orta, C., Usón, I., Zorzano, A., Fernández-Recio, J., Orozco, M., Lizarbe, M.A., Fita, I., Palacín, M. (2007) The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane. J.Biol.Chem. 282, 31444-31452

Grosdidier, S., Pons, C., Solernou, A., Fernandez-Recio, J. (2007) Prediction and scoring of docking poses with pyDock. Proteins 69, 852-858

Bonivento, D., Pontiggia, D., Matteo, A.D., Fernandez-Recio, J., Salvi, G., Tsernoglou, D., Cervone, F., de Lorenzo, G. and Federici, L. (2008) Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins. Proteins 70, 294-299.

Medina, M., Abagyan, R,, Gómez-Moreno, C. and Fernández-Recio, J. (2008) Docking analysis of transient complexes: Interaction of ferredoxin.NADP+ reductase with ferredoxin and flavodoxin. Proteins 72, 848-862.

Bavro, V., Pietras, Z., Furnham, N., Pérez-Cano, L., Fernández-Recio, J., Yuan Pei, X., Misra, R. and Luisi, B.. (2008) Channel opening and allostery in a bacterial drug efflux machine. Mol. Cell. 30, 114-121.

Fernández-Recio, J. and Verma, C. (2008) Theory and simulation. Editorial overview. Curr. Opin. Struct. Biol. (2008) 18, 131-133.

Degryse, B., Fernandez-Recio, J., Citro, V., Blasi, F. and Cubellis, M.V. (2008) In silico docking of urokinase plasminogen activator and integrins. BMC Bioinformatics 9 Suppl 2, S8

Pallarès, I., Fernández, D., Comellas-Bigler, M., Fernández-Recio, J., Ventura, S., Avilés, F.X., Bode, W. and Vendrell, J. (2008) Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid). Acta Crystallogr. D Biol. Crystallogr. 64, 784-791.

Hart, S.E., Howe, C.J., Mizuguchi, K. and Fernández-Recio, J. (2008) Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum. Protein Eng. Des. Sel. 21, 689-698.

Cheng, T.M.K.., Blundell, T.L. and Fernández-Recio, J. (2008) Structural assembly of two-domain proteins by rigid-body docking. BMC Bioinformatics 9, 441.

Grosdidier, S. and Fernández-Recio, J. (2008) Prediction of hot-spot residues in protein-protein interaction from rigid-body docking simulations. BMC Bioinformatics 9, 447.

Solernou, A. and Fernández-Recio, J. (2008) Computational tools for exploration of the energy landscape in protein-protein association. AIP Conf. Proc. 1071, 98-108.