2. Using Sequence Information Into Protein Docking Procedure

3. What did we want to do ? Why did we want to do that ? How did we want to do that ?

4. What did we want to do? Incorporate sequence and experimental information into protein-protein or protein- ligand docking procedure Test the method by treating the case when two proteins are known to bind and 3D modells are available for both binding partners

5. Why did we want to do that? Importance of protein-protein interaction in cellular processes We therefore need accurate tools to predict such events Methods exist with attempt to predict protein-protein docking Base on : Shape complementarity (Shoichet & Kuntz, 1996; Janin et al., 1995) Surface match (Helmer-Citterich &Tramontano, 1994; Walls & Sternberg, 1992) Electrostatic (Gabdoulline & Wade, 1998; Vijayakumar et al., 1998) Combination of some of the above strategy (Gabb et al., 1997)

6. Sequence and structural data are actually on increase The need for combining sequence and structural information to: To predict protein-protein/ligand docking is urgent Improve existing methods Generate new approaches

7. How did we want to do that? Define type of protein sequence to use Find out conserved residues in that protein family or subfamily Find out experimental and structural information available in the literatures Combine sequence and experimental Information to select residues to use to define distance constraints in the sdabf program (gabdoulline and Wade, 2002)

8. Hope to make sampling more faster comparing to not using sequence and experimental information Hope to have correct docked structure and avoid false positives when sequence and experimental information are used

9. WW domain alignment WW domain alignment

10. The WW domain Definition: The WW domain is a protein-protein interaction module compose of 35-40 amino acids. It has 3 anti-parallel beta-sheet, and is stable in the absence of disulfide bonds, cofactor or ligands W34 W11 Y23 F25 P37

11. The domain binds proline-rich or proline containing ligands it is evolutionary well conserved and present in plants, yeast, worm, fly and vertebrates

12. Classification of WW domains Group I YAP65, Nedd4, Dystrophin Group II Formin Binding Proteins, FE65 Group III Formin Binding Proteins Group IV Ess1/Pin1 Group V Npw38/PQBP-1 PPPPPPL/RP Phospho-(S/T)P PPxY (PxxGMxPP)N Rx(x)PPGPPPxR PEBP2 transcriptional activator, ENaC sodium channel, beta-dystroglycan Formin, Mena, Bat2 Splicing factors: SmB, SmB', U1C RNA Pol II, Cdc25C, p53 NpwBP Consensus sequence of the ligandRepresentative ligands Groups/representatives http://www.bork.embl-heidelberg.de/Modules/ww_classes.html

13. Function of the WW domain Variety of target Therefore involve in variety of cellular processes such as: - Co-activation of transcription and modulation of RNA pol II - Mitotic regulation (G2/M transition) - Protein processing … Implicate in several human diseases such as: - Muscular Dystrophy - Alzheimer’s disease - Hypertension - Cancer …

14. Differences between the free and complexed pin1 WW domain

15. Script „pdbExtractor“ remove phosphates Sequence alignment, experimental information +PO3 - ; -HG of SER Script„do_all_whatif“: add the H-atoms with “Whatif” p2.pdb p1.pdb dephosphorylated peptide +H-atoms coordinates of the dephosphorylated peptide PDB-file 1f8a file with coordinates of the phosphorylated peptide file with coordinates of the WW-domain Script „do-run“ Script „rxnaEditor.py“ Script „do_bf_prepare”: UHBD, ECM, mk_ds_grid + other parameters (e.g. the distance constraint) sdabfcw sdabf12.in (input-file) start the simulation p1e.grd, p1.echa, p1ds.grd p2e.grd, p2.echa, p2ds.grd fort.xx* and other output-files p1.rxna p2.rxna Clustering and cluster analysis Nmrclust, twopdb2rmsd.f, clusteranalyse.f

16. could sampling be speed up using sequence/experimental information? constraints 0123 sampling time SDABF (grid sampling) 30.5h4-6h6-9h8-13h SDA (BD sampling) ca 2h 5-8min 1h (W34)? 6min1-2.5h

17. E 12 =  E coul +  E des  E 12 =  E coul +  E des +  E hyd  E 12 =  E coul

18. E 12 =  E coul +  E des  E 12 =  E coul +  E des +  E hyd  E 12 =  E coul

19. ComplexCenFreeCen Y23Y27

20. program RMSD free WW domaincomplexed WW domain SDABF (grid sampling) constraint 0Y230Y27 17.9 19.4 25.7 23.8 10.2 25.7 23.0 9.5 18.1 18.7 5.5 6.4 8.2 7.5 11.5 13.2 9.2 10.5 4.2 8.0 3.6 10.0 9.4 14.2 4.2 6.2 10.3 15.9 15.0 9.7 3.6 14.5 15.4 6.0 11.8 12.6 11.0 13.4 14.5 13.0 SDA (BD sampling) 18.1 17.8 18.5 24.9 19.0 18.9 17.3 25.9 26.1 9.7 12.3 7.2 7.1 13.5 9.3 5.0 14.5 12.9 12.1 2.8 2.7 2.4 3.0 3.4 3.7 2.5 3.0 3.1 3.0 2.4 3.0 2.4 2.9 3.2 2.8 3.0 2.2

21. Y27 W38 Y23W34

22. program RMSD free WW domaincomplexed WW domain SDABF (grid sampling) constraint W34Y23W38Y27 23.8 23.0 25.1 22.1 8.8 13.5 20.9 22.1 10.6 5.5 6.4 8.2 7.5 11.5 13.2 9.2 10.5 4.2 8.0 3.6 14.2 4.2 10.3 15.9 15.0 9.7 10.3 11.4 15.4 3.6 14.5 15.4 6.0 11.8 12.6 11.0 13.4 14.5 13.0 SDA (BD sampling) 8.1 24.3 24.8 20.5 10.3 25.8 8.2 18.4 22.9 22.4 9.7 12.3 7.2 7.1 13.5 9.3 5.0 14. 5 12.9 12.1 2.4 3.0 3.6 2.8 3.4 4.6 3.2 2.8 5.2 2.4 3.0 2.4 2.9 3.2 2.8 3.0 2.2

24. Program RMSD free WW domaincomplexed WW domain SDABF (grid sampling) ConstraintR17Y23W34Y23*R21Y27W38Y27 7.471 11.078 12.859 10.838 13.795 11.513 12.543 14.428 13.468 12.956 8.794 8.149 10.636 8.606 10.505 8.792 7.386 8.357 11.018 8.497 17.814 10.815 13.899 16.749 17.944 17.677 17.006 13.339 18.032 16.458 3.474 10.340 15.363 14.461 11.369 11.184 6.723 11.958 10.046 12.838 SDA (BD sampling) 7.210 6.573 10.384 6.314 9.314 10.434 16.834 8.327 10.045 16.688 *Independent distance = 6

25. R17Y23W34R21Y27W38 Grid sampling

26. R17Y23W34R21Y27W38 BD sampling

27. RMSD programR17Y23W34R21Y27W38 SDABF 17,737 17,809 4,221 4,192 4,628 3,072 6,713 15,895 4,935 4,412 4,510 6,674 11,710 15,191 15,835 13,062 13,853 10,941 11,070 11,476 SDA 6,214 17,543 4,241 2,430 4,945 3,669 15,556 5,661 4,266 3,063 2,808 2,749 2,362 3,041 2,364 3,401 3,504 3,656 2,455 3,342 ENERGY programR17Y23W34R21Y27W38 SDABF -6,4284 -6,4263 -6,1933 -6,1869 -6,1372 -6,0129 -5,9385 -5,6976 -5,6498 -5,6457 -13,523 -11,443 -10,171 -9,4154 -8,7401 -8,484 -7,9132 -7,5226 -7,3882 -6,8053 SDA -6,31 -5,98 -5,92 -5,8 -5,78 -5,76 -5,75 -5,74 -5,71 -5,69 -16,3 -16,2 -16,0 -15,9 -15,8 -15,7

28. Conclusion RMSD free WW domain constraint0W34Y23R17Y23W34Y23R17Y23W34 SDABF (grid sampling) 17.875 9.452 23.832 8.794 5.491 4.221 7.4718.794 7.4 17,737 3,072 SDA (BD sampling) 18.138 17.297 8.1179.714 5.021 7.210 6.314 6,214 2,430 RMSD docked WW domain constraint 0W38Y27R21Y27W38Y27R21Y27W38 SDABF (grid sampling) 3.586 3.61117.814 10.815 3.4744,510 SDA (BD sampling) 2.808 2.455 2.362 2.249 2,808 2,362 RUN TIME constraint0123 SDABF 30.5h4-6h6h40min8-13h SDA ca 2h5-8min 1h (W34)? 6min1-2.5h

29. Thanks to All the MCM -GROUP members Special thanks to Rebecca Wade Razif Gabdoulline Jan Lac and Ting Wang