HOW TO UNBOIL AN EGG

.. SOME REFLECTIONS ON LIVING THINGS.

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

Monod:

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

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

OPINIONS ON PROTEIN FOLDING. student postdoc professor Geneticist?

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

Statistical Models of a Strongly Unfolded Protein

Trichter

Protein folding funnels A lecture from Achim Besser

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)

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

The arising problem Levinthal‘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

vast conformational space the golf-ball will "never" find its goal by random search - 4 preferred phi-psiangels for each peptide bond - assuming 100 monomers =10 60 chain conformations

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

What causes the collapse  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: Backbone-centric view:  hydrophobic interactions are the strongest interactions among amino acids in water  the collapse is dominated by hydrophobic interaction

minimal model hydrophilichydrophobic folding sequence But for detailed predictions for the native state all forces have to be considered

Smooth funnel a 100 residue chains conformations but onlyare compact free energy function plot over all degrees of freedom is called energy landscape

old and new view sequential micropath view ensemble view principle language Paths, intermediates, transition states, reaction coordinates landscapes, funnels explains what exponentials do (what you see) what molecules do (how it works) main problem search problemtrap problem proposed solution sequential pathwaysfunnels intermediates milepoststraps

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

D N classical trajectoriesfolding via multiples routes D N D N

intermediate and transition state DN I DI N possible schemes

uphill and downhill pathways A: no favourable contacts are broken B: favourable contacts are broken made possible by thermal energy or chaperonin proteins

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

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

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

Computing time versus molecular size – number of electrons CI/QMC-for correctly treating electron correlations  very unfavourable scaling 2 x years Ne 2 Ne Number of Electrons (N) 3 Mio years 1 year 1 month 12 hours Size time ~ N 6 bR

Protein Folding

Hydrophob ic cluster Truncation site Active site Staphylococcal Nuclease Salt Bridge

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

Unmodified Charges Charges Neutralized Here Arg – Glu Salt Bridge

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

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) IBM PLANS SUPERCOMPUTER THAT WORKS AT SPEED OF LIFE

Bundeshochleistungsrechner Hitachi SR8000-F1

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

Safety in Numbers

“The grail had different manifestations throughout its long history, and many have claimed to possess it or its’ like” - J. Matthew, The Grail, Quest for the Eternal, (Thames and Hudson, London, 1981).