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Alfonso Valencia CNB-CSIC Integración de datos evolutivos en la predicción de estructura y función Alfonso Valencia CNB - CSIC.

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Presentation on theme: "Alfonso Valencia CNB-CSIC Integración de datos evolutivos en la predicción de estructura y función Alfonso Valencia CNB - CSIC."— Presentation transcript:

1 Alfonso Valencia CNB-CSIC Integración de datos evolutivos en la predicción de estructura y función Alfonso Valencia CNB - CSIC

2 Alfonso Valencia CNB-CSIC ranrcc1 by J.A. G-Ranea

3 Alfonso Valencia CNB-CSIC Cluster of solutions 1 Cluster of solutions 2 Solution 3 Solution 4 by J.A. G-Ranea

4 Alfonso Valencia CNB-CSIC Ras Ral Rho Ras Ral Rho ranrcc1 by J.A. G-Ranea

5 Alfonso Valencia CNB-CSIC Model Mapping of tree determinants

6 Alfonso Valencia CNB-CSIC Azuma et al., J,Mol. Biol. 1999

7 Alfonso Valencia CNB-CSIC Model D44 GDP Mg++ H270 R206 H304 E157 D128 H78 H410 Green: Km, red: Kcat. Mapping of mutants (side view)

8 Alfonso Valencia CNB-CSIC Complex Ran SO4 Rcc1 Model and Xray Model Ran Mg++ GDP Rcc1

9 Alfonso Valencia CNB-CSIC 13 59 3 122 GRAMM results Ran (GDP-Mg++) Rcc1 Ran (SO4) Rcc1 Complex/Docking superposition Model/Docking superposition Complex: Model:

10 Alfonso Valencia CNB-CSIC Complex (Model on Vomplex superposition) Model GDP Mg++ D44 H78 D128 E157 R206 H270 H304 H78 H410 D44 GDP Mg++ H270 R206 H304 E157 D128 H78 H410 Green: Km, red: Kcat. Mapping of mutants (side view)

11 Alfonso Valencia CNB-CSIC Complex Model Mapping of tree determinants

12 Alfonso Valencia CNB-CSIC Ras Binding Domain folding Ras Rlip (coiled-coil) Ral Functional specificity in the ras superfamily By J.A. Ranea

13 Alfonso Valencia CNB-CSIC The space of sequences Yeast Two-Hybrid Experiments (Bauer et. al. JBC 1999) by J.A. G-Ranea Treedeterminants Ras Ral Rho Ras Ral Rho Sequencespace (Casari, Sander, Valencia, Nature. Str. Bio. 95) 36 and 37 main tree-determinant positions

14 Alfonso Valencia CNB-CSIC DnaK FtsA Actin Hexokinase Hsc70 MreB

15 Alfonso Valencia CNB-CSIC

16 A dimerization model for FtsA Carettoni, et al., (2002) Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA Proteins Löwe et al., Nature 00

17 Alfonso Valencia CNB-CSIC Information extracted from multiple sequence alignments Ras Ral Rho Correlated mutations Tree-determinant conserved

18 Alfonso Valencia CNB-CSIC Prediction of interaction regions AV..WYAV..WY aa...... Interface No 5,6,10,20,22,30 5 6 10 20 22 30 3D str. Surface patch Sequence profiles Multiple sequence alignment Fariselli, et al., (2002). Prediction of protein-protein interaction sites with neural networks. Eur J Biochem

19 Alfonso Valencia CNB-CSIC Prediction of protein interaction sites with neural networks Goal: Predict surface residue in contact with another protein. Method: Feed-forward neural network trained with standard back- propagation. Output layer: Single neuron representing contact / no contact Hidden layer: 4 nodes Input layer: - Patches in protein structures (sets of exposed neighbour residues) 11 residue-long window, central surface residue + 10 patch neighbours - Evolutionary information Residue coded as a vector corresponding to frequencies in the MSA Result: 73% average accuracy of correctly predicted interacting residues Fariselli, Pazos,Valencia, Casadio, Eur. J. Biochem. 02

20 Alfonso Valencia CNB-CSIC Results of the predictions of protein interaction sites Fariselli, Pazos,Valencia, Casadio, Eur. J. Biochem. 02

21 Alfonso Valencia CNB-CSIC NN predictions of interaction regions AB Carettoni, et al., (2002) Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA Proteins

22 Alfonso Valencia CNB-CSIC

23 DnaK FtsA Actin Hexokinase Hsc70 MreB

24 Alfonso Valencia CNB-CSIC Prediction of interaction regions AV..WYAV..WY aa...... Interface No 5,6,10,20,22,30 5 6 10 20 22 30 3D str. Surface patch Sequence profiles Multiple sequence alignment Fariselli, et al., (2002). Prediction of protein-protein interaction sites with neural networks. Eur J Biochem

25 Alfonso Valencia CNB-CSIC Prediction of protein interaction sites with neural networks Goal: Predict surface residue in contact with another protein. Method: Feed-forward neural network trained with standard back- propagation. Output layer: Single neuron representing contact / no contact Hidden layer: 4 nodes Input layer: - Patches in protein structures (sets of exposed neighbour residues) 11 residue-long window, central surface residue + 10 patch neighbours - Evolutionary information Residue coded as a vector corresponding to frequencies in the MSA Result: 73% average accuracy of correctly predicted interacting residues Fariselli, Pazos,Valencia, Casadio, Eur. J. Biochem. 02

26 Alfonso Valencia CNB-CSIC Results of the predictions of protein interaction sites Fariselli, Pazos,Valencia, Casadio, Eur. J. Biochem. 02

27 Alfonso Valencia CNB-CSIC A dimerization model for FtsA Carettoni, et al., (2002) Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA Proteins Löwe et al., Nature 00

28 Alfonso Valencia CNB-CSIC NN predictions of interaction regions AB Carettoni, et al., (2002) Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA Proteins

29 Alfonso Valencia CNB-CSIC Carnitine Acyl transferases 2dubE/CPTI/COT/CACP P. Gomez-Puertas / F. G. Hegardt lab Carnitine OctanoyltransferaseCarnitine Palmitoyltransferase I Octanoyl-CoA Malonyl-CoA A332 H327 (catalytic) A478 Palmitoyl-CoA Malonyl-CoA H473 (catalytic) Morillas et al. 2001. J.Biol.Chem. 276, 45001-8, 2001 in the press, and 2002 in the press

30 Alfonso Valencia CNB-CSIC Protein Design Group CNB-CSIC David de Juan Protein interactions Damien Devos Function prediction at genomic scale Rita Casadio Pierro Fariselli U. Bologna Antoine de Daruvar Lion, Heidelberg. Burkhard Rost Columbia U., NY Søren Brunak DTU, Copenhagen Christos Ouzounis EBI-EMBL, Cambridge Julio Collado-Vides UNAM, Cuernavaca. María González Genomics, Ecology Ramón Alonso Arabidopsis T. factors Juan Antonio G. Ranea ras signalling system Protein Design RAS E. Laue, Cambridge F. Wittinghoer, MPI Andrés Moya, Roeland van Ham U. Valencia Centro de Astrobiología Federico Abascal Function prediction CICYTbiotech Protein Structure Prediction CICYTFEDER www.pdg.cnb.uam.es DNA arrays EC V FP Manuela Helmer-Citterich U. TorVergata, Paulino Gómez Puertas Bacterial Cell Division Luis Sánchez-Pulido Sequence analysis Ramón Roca Homology modeling SANITAS Miguel Vicente CNB - CSIC Osvaldo Graña Threading / servers ALMA Bioinformática S.L. Armando Amat System management Bioinformatics support Information extraction Florencio Pazos Interaction networks Keith Harshman, Carlos Martínez D I O - C N B Genome analysis Amalia Muñoz binding specificity system Juan Carlos Sanchez TFs in Aspergilus Enrique Merino Centro Bioitecnología UNAM, Cuernavaca Javier Guijarro Interaction networks Manuel Gómez Bacterial Cell division II Prof. Hans Robert Kalbitzer U. Regensburg Visitors José María Fernandéz Database design REGIA J. Pazares, CNB-CSIC SH3 B. Distel, Amsterdam Ugo Bastolla Protein stability Fausto Edgarth U. Barcelona Michael Tress Threading Juan Carlos Oliveros Array data management Roderic Guigo IMIM, Barna Joaquin Dopazo Javier Herrero CNIO Javier Tamames Genome analysis TEMBLOREBI EC VFP Robert Hoffmann I.E. Biomedicine ORIELEMB0 EC VFP Information Extraction Christian Blaschke Information extraction Eduardo Leon Detection of protein names Systems Miguel A. Peñalva CIB-CSIC

31 Alfonso Valencia CNB-CSIC Protein interactions Text mining Biological examples

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