Classification of Protein Complexes based on Biophysics of Association Sandor Vajda

1. Classification of Protein Complexes based on Biophysics of Association Sandor Vajda Boston University

2. “Tell me with whom you go, • and I'll tell you what you are.”Italian Proverb List of Interactions computational prediction of structure and specificity of protein – protein complexes • “FYI” filtered yeast interactome (Vidal 2004): • involves ~1500 proteins, • making ~2500 physical interactions Structure: Nature of Intreractions PDB: ~ 25’000 solved crystal structures; ~ 10% complexes H. Jeong et al, Nature 2001 • “Tell me how you contact your partners, • and I'll tell you who you are.”

3. Protein-protein docking • How proteins interact with each other? • Docking problem • Predict docking configuration from the structures of component proteins • Bound vs. unbound docking • Conformational change

4. Bound vs.unbound: at least side chain conformations change Fine details Receptor Ligand Coarse details Trypsin/APPI

5. Talk outline • What is the current state of docking? • What docking calculations tell us about the nature of protein - protein complexes? • How to deal with side chain flexibility?

6. Building Blocks: backbone & side chains • Proteins: Basics CASP CAPRI Sequence Monomers ADEFFGKLSTKK……. + Rigid body degrees of freedom 3 translation 3 rotation de novo docking Structure Prediction Structure Complex

8. Benchmark set of protein complexes: Chen, R. et al. (2003) A protein-protein docking benchmark. Proteins, 52, 88-91. • 22 enzyme-inhibitor • 19 antigen-antibody • 11 “other” types • 7 “difficult” cases Comeau, S. et al. (2003) ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics, 20, 45-50. Chen, R. et al. (2003) ZDOCK: An initial-stage protein-docking algorithm Proteins, 52, 80-87 Li, L. et al. (2003) RDOCK: Refinement of rigid-body protein docking predictions. Proteins, 53, 693-707. Gray, J.J. et al. (2003) Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Molec. Biol. 331, 281-299

9. Rigid Body Search Select docked structures with low energy Cluster retained conformations Refine structures Flexible side chains Submit 10 models to CAPRI How current protein docking programs work? Filter 1: 20,000 Filter 2: 2,000 Filter 3: 30 Filter 4: 1?

10. Algorithms of the 3 docking methods

11. Effect of the interface area uncertain easy very difficult difficult GOOD

12. Effect of hydrophobicity uncertain easy -4

13. Size vs. Hydrophobicity Type III uncertain Type IV difficult Type II easy Type V difficult Type I easy

14. Benchmark by type Type V difficult Type IV difficult difficult Type III uncertain Type II easy Type I easy

15. Type IV Difficult Type III Uncertain Antibody/ Antigen Type II Or Type V? Type V Hopeless Transitional complexes with substantial conformational change Type II Easy Large multienzyme complexes Desolvation free energy -4 Small signalling complexes Type I Easy Enzymes 1400 2000 3400 Interface Area

17. Classification of complexes

18. Type I: Enzyme-Inhibitor Complexes trypsin inhibitor variant 3 alpha-chymotrypsinogen

19. Interface in the complex of alpha-chymotrypsinogen with trypsin inhibitor

21. Classification of complexes

22. Type III: Antigen-Antibody Complexes chicken lysozyme Monoclonal antibody fab d44.1

23. Interface in the complex of chicken lysozyme with antibody fab d44.1

24. Type IV Difficult Type III Uncertain Antibody/ Antigen Type II Or Type V? Type V Hopeless Transitional complexes with substantial conformational change Type II Easy Large multienzyme complexes Desolvation free energy -4 Small signalling complexes Type I Easy Enzymes 1400 2000 3400 Interface Area

25. Classification of complexes

26. ribonuclease a Ribonuclease inhibitor

27. Interface in the complex of ribonuclease a with ribonuclease inhibitor

28. Type IV Difficult Type III Uncertain Antibody/ Antigen Type II Or Type V? Type V Hopeless Transitional complexes with substantial conformational change Type II Easy Large multienzyme complexes Desolvation free energy -4 Small signalling complexes Type I Easy Enzymes 1400 2000 3400 Interface Area

29. Classification of complexes

30. ras-interacting domain of ralgds GNP (5'-guanosyl-imido-triphosphate ras protein

31. Interface in the complex of ras-interacting domain with ras

32. Type IV Difficult Type III Uncertain Antibody/ Antigen Type II Or Type V? Type V Hopeless Transitional complexes with substantial conformational change Type II Easy Large multienzyme complexes Desolvation free energy -4 Small signalling complexes Type I Easy Enzymes 1400 2000 3400 Interface Area

33. Classification of complexes

34. Type V: Large interface and large conformational change Cyclin-A Cyclin-dependent kinase

35. Li, L. et al. (2003) RDOCK

36. Gray, J.J. et al. (2003)

37. 2: How the community is doing? Overall Success rates of participants in CAPRI 1-5

38. Classification of CAPRI 1-2 Targets

39. Overall Success rates of participants in CAPRI 1-5

40. Classification of CAPRI 3-5 Targets

41. Overall Success rates of participants in CAPRI 1-5

42. Expected Improvements Type IV Difficult Type III Uncertain Antibody/ Antigen Type II Or Type V? Type V Hopeless Transitional complexes with substantial conformational change Type II Easy Large multienzyme complexes Desolvation free energy Small signalling complexes -4 Type I Easy Enzymes Much improved 1400 2000 3400 Interface Area

43. 3. How to deal with side chain flexibility? Fine details Receptor Ligand Coarse details Trypsin/APPI

44. Recognition mechanisms: Lock-and-key vs. Induced fit Key-and-latch mechanism Rajamani, D., Thiel, S. Vajda, S. and C.J. Camacho. Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA, 101: 11287-11292, 2004. Key-Latch model KEYSwhich stay close to the bound conformation in solution LATCHES do not show preference to stay near bound conformation. key latch

45. Individually crystallized protein Predisposition Unbound Bound Simulated Solvated protein

46. RMSD of Arg39 of ribonuclease A with respect to the structure found in the complex (bound; PDB code 1DFJ) and in the individually crystallized ribonuclease A (unbound; PDB code 7RSA). The RMSD was computed for 2000 snapshots of a 4ns MD simulation of 7RSA.

47. Clustering of the conformations of Arg39 in ribonuclease A. The 16 largest clusters were derived from a pairwise RMSD analysis of the MD snapshots, and clustering using a radius of 2Å. The RMSD of the cluster center from the bound conformation is shown on the top/bottom of each bar. The bound conformation is shown in blue, unbound in red, and the dominant conformation from the MD simulations is shown in green.

48. Complex of trypsin with amyloid β-protein inhibitor (APPI). Key residue Arg-15 is a major contributor to the total binding free energy.

49. HIV-1 NEF/FYN tyrosine kinase SH3 domain complex. Trp-119 is within 1 and 2 Å of the bound conformation for 36% and 96% of the MD. It is stabilized in this native-like conformation by Tyr-93 (and therefore also native-like) in the free state. Thr-97 buries the second largest SASA (70 Å2). Thr97 Tyr93 Asp100 Trp119

50. Hyhel-5 Fab/lysozyme complex. Themain key residue, Arg-45, has a SASA value of 147 Å2; a second key residue, Lys-68, is found buried with a SASA = 93 Å2. Both side chains show native-like properties, sampling during 50% and 97% of the time conformations that were less than 2 Å rmsd from their corresponding bound rotamer. Lys68 Arg45