how to unboil an egg. .. some reflections on living things

HOW TO UNBOIL AN EGG

..SOME REFLECTIONS ON LIVING THINGS.

Schroedinger:

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

Monod:

Monod:

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

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

OPINIONS ON PROTEINFOLDING.

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 conformationof its native state is at the global minimum of its free energy

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

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

4100=1060 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

hydrophilic hydrophobic

folding

sequence

But for detailed predictions for the native state all forces have to be considered

Smooth funnel

a 100 residue chains4100 conformations

17100

104

ebut only are compact

),...,,( 21 nf free energy function

plot over all degrees of freedom is called energy landscape

old and new viewsequential

micropath viewensemble view

principle

languagePaths, intermediates,

transition states, reaction coordinates

landscapes, funnels

explainswhat exponentials do

(what you see)

what molecules do

(how it works)

main problem search problem trap problem

proposed solution sequential pathways funnels

intermediates mileposts traps

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 trajectories folding via multiples routes

D

N

D

N

intermediate and transition state

D N

I

D I N

possible schemes

uphill and downhill pathways

A: no favourable contacts are broken

B: favourable contacts are broken

made possible by thermal energyor

chaperonin proteins

the bottom of the funnel

rugged: other conformations can be populated under native conditionsthis is important for protein function.

smooth: only small fluctuations around N are allowed

Protein Folding

An Urgent Problem in the Post-Genomic Era

Protein EnergyLandscape

Atomic-Detail Computer SimulationModel System

Molecular Mechanics Potential

ji ij

ji

ji ij

ij

ij

ijij

impropersdihedrals

N

n

n

anglesbondsb

Dr

qq

rr

KnK

kbbkV

,,

612

20

1

20

20

4

cos1

Energy Surface Exploration by Simulation..

Computing time versus molecular size – number of electrons CI/QMC-for correctly treating electron correlations very unfavourable scaling

Computing time versus molecular size – number of electrons CI/QMC-for correctly treating electron correlations very unfavourable scaling

2 x 1020 years

Ne2Ne

Number of Electrons (N)

3 Mio years

1 year

1 month12 hours

Size30 100 00010 0001 00010010

time ~ N6

bR

Protein Folding

Hydrophobic clusterTruncation

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?

0 50 100 150 200 250 3000

5

10

15 C

Time (ps)

0

5

10

15 B

Dis

tan

ce (

Å) 0

5

10

15 A

Unmodified Charges

Charges Neutralized Here

Arg – Glu Salt Bridge

- Free Energy Differences

(Thermodynamic Integration,e.g. drug design Umbrella Sampling e.g. conformational pathway).

3 4 5 6 7 8 9-1

0

1

2

3

4

5

6

7

Free

ene

rgy

(kca

l/mol

)

Distance CZ-CD (Å)

IBM today will announce its intention to invest $100 million overthe next five years to build Blue Gene, a supercomputer that willbe 500 times faster than current supercomputing technology.Researchers plan to use the supercomputer to simulate thenatural biological process by which amino acids fold themselvesinto 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).