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

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Presentation transcript:

..

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

(SFB 653)

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

Power Stroke in Muscle Contraction. BJORN WINDSHUGEL STEFAN FISCHER KEN HOLMES

Drunk Golfer

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

Lysozyme in explicit water

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

Bundeshochleustungsrechner Hitachi SR8000-F1

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

“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).

Enzyme Reactions SONJA SCHWARZL STEFAN FISCHER

Proton Transfer Step #1 in Bacteriorhodopsin NICOLETA BONDAR MARCUS ELSTNER STEFAN FISCHER SANDOR SUHAI

Structural Changes in Proteins: The Physical Problem ENERGY LANDSCAPE: high-dimensional, rugged. Need to find PATHWAY WITH LOWEST SADDLE POINT.

Protein Hydration. Svergun et al PNAS 1998: First 3Å hydration layer around lysozyme ~10% denser than bulk water FRANCI MERZEL

EVN EVB LE EVN EVB LE Snapshots of Atomic-Detail Models of Strongly-Unfolded PGK

Time Resolved Crystallography.

Scattering of X-Rays by Protein Crystals Real Crystal = Ideal Crystal + Perturbations STÉPHANIE HÉRY DANIEL GENEST

Rigid-Body Decomposition Rigid-Body Fit (R-factor re: Full Trajectory = 5.3%) Molecular Dynamics of Lysozyme Unit Cell Experimental Full Trajectory

Fast Calculation of Absolute Binding Free Energies: Interaction of Benzamidine Analogs with Trypsin Benzamidine-like Trypsin InhibitorsEnergy Terms and Results - van der Waals protein:ligand - hydrophobic effect (surface area dependent) - electrostatic interactions (continuum approach) - translational, rotational, vibrational degrees of freedom