HOW TO UNBOIL AN EGG

1. HOW TO UNBOIL AN EGG

2. SOME REFLECTIONS ON LIVING THINGS. ..

4. Schroedinger: Order requires large numbers of particles e.g. alignment of magnetic dipoles.

7. Monod:

8. Monod: Specificity: Large number of weak interactions... Catalysis: ...that stabilize transition state.

9. ...but how is the necessary three-dimensional structure created?????

12. OPINIONS ON PROTEIN FOLDING. student postdoc Geneticist? professor

13. “Denatured protein disordered, exposing parts that are otherwise on the inside...”

17. Statistical Models of a Strongly Unfolded Protein

21. Trichter

23. Protein folding funnels A lecture from Achim Besser

24. Summary • A small course through history from Levinthal to pathways • The old and the new view of protein folding • The role of hydrophobic interaction during the folding process • The structure of funnels • The use of this knowledge for structure predictions (CGU)

25. The beginning • Experiments by Christian B. Anfinsen (1960‘s) A protein can fold reversibly and the conformation of its native state is at the global minimum of its free energy

26. The arising problemLevinthal‘s paradox There are too many possible conformation so that it is impossible to find native state by random search. conclusion For each protein there has to be a specific sequence of conformational changes that brings the denatured protein to its native state the: folding pathway

27. vast conformational space - 4 preferred phi-psiangels for each peptide bond - assuming 100 monomers 4100=1060 chain conformations the golf-ball will "never" find its goal by random search

28. folding pathway well defined sequence of changes in conformation. The pathway leads the ball to its hole

29. What causes the collapse Backbone-centric view: • Hydrogen bonds aid collapse but otherwise play little role in dictating the specific architecture • Phi-psi-propensities predict only helices or strands but no collapse Side-chain-centric view: • hydrophobic interactions are the strongest interactions among amino acids in water • the collapse is dominated by hydrophobic interaction

30. hydrophilic hydrophobic minimal model sequence folding But for detailed predictions for the native state all forces have to be considered

31. a 100 residue chains 4100 conformations free energy function plot over all degrees of freedom is called energy landscape but only are compact Smooth funnel

32. old and new view

33. more realistic funnel interaction in the folding process is about [kT] Brownian motion causes large variations during the folding process there is no specific pathway for D N no sequential but parallel events, folding is a diffusion like process

34. D N classical trajectories folding via multiples routes D D N N

35. N D I D N I intermediate and transition state possible schemes

36. uphill and downhill pathways A: nofavourable contacts are broken B: favourable contacts are broken made possible by thermal energy or chaperonin proteins

37. the bottom of the funnel smooth: only small fluctuations around N are allowed rugged: other conformations can be populated under native conditions this is important for protein function.

38. Protein Folding An Urgent Problem in the Post-Genomic Era Protein Energy Landscape

39. Model System Atomic-Detail Computer Simulation Molecular Mechanics Potential Energy Surface Exploration by Simulation..

40. bR 3 Mio years 1 year 1 month Ne Ne2 12 hours Size 10 30 100 1 000 10 000 100 000 Computing time versus molecular size – number of electronsCI/QMC-for correctly treating electron correlations  very unfavourable scaling 2 x 1020 years time ~ N6 Number of Electrons (N)

41. Protein Folding

42. Active site Hydrophobic cluster Truncation site Staphylococcal Nuclease Salt Bridge

43. Protein Folding Exploring the Folding Landscape Future: - Short-Term:Understanding Rate Limiting Steps - Long-Term:Complete Folding Simulations?

44. Unmodified Charges Charges Neutralized Here Arg – Glu Salt Bridge

45. - Free Energy Differences (Thermodynamic Integration,e.g. drug design Umbrella Sampling e.g. conformational pathway).

47. IBM PLANS SUPERCOMPUTER THAT WORKS AT SPEED OF LIFE IBM today will announce its intention to invest $100 million over the next five years to build Blue Gene, a supercomputer that will be 500 times faster than current supercomputing technology. Researchers plan to use the supercomputer to simulate the natural biological process by which amino acids fold themselves into proteins. (New York Times 12/06/99)

48. Bundeshochleistungsrechner Hitachi SR8000-F1

49. Science, 282, 440 (1998)34-residue villin headpiece subdomain

50. Safety in Numbers