Biochemie IV – Struktur und Dynamik von Biomolekülen II. (Mittwochs 8-10 h, INF 230, klHS)

30.4. Jeremy Smith: Intro to Molecular Dynamics Simulation.7.5. Stefan Fischer: Molecular Modelling and Force Fields.14.5. Matthias Ullmann: Current Themes in Biomolecular Simulation.21.5. Ilme Schlichting: X-Ray Crystallography-recent advances (I).28.5. Klaus Scheffzek: X-Ray Crystallography-recent advances (II).4.6. Irmi Sinning: Case Study in Protein Structure.11.6. Michael Sattler: NMR Applications in Structural Biology.18.6. Jörg Langowski: Brownian motion basics.25.6. Jörg Langowski: Single Molecule Spectroscopy.2.7. Karsten Rippe: Scanning Force Microscopy.9.7. Jörg Langowski: Single Molecule Mechanics.16.7. Rasmus Schröder: Electron Microscopy.23.7. Jeremy Smith: Biophysics, the Future, and a Party.

Universität Heidelberg

Protein

Computational Computational Molecular BiophysicsMolecular Biophysics

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

Protein Folding

Exploring the Folding Landscape

Uses of Molecular Dynamics Simulation:

•structure•flexibility•solvent effects•chemical reactions•ion channels•thermodynamics (free energy changes, binding)•spectroscopy•NMR/crystallography

Atomic-Detail Computer Simulation

Model System

Molecular Mechanics Potential

ji ij

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ij

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ijij

impropersdihedrals

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n

anglesbondsb

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20

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20

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cos1

Energy Surface Exploration by Simulation..

Model System

•set of atoms•explicit/implicit solvent•periodic boundary conditions

Potential Function

•empirical•chemically intuitive•quick to calculate

Tradeoff: simplicity (timescale) versus accuracy

Lysozyme in explicit water

2/8MM Energy Function

l

r

qi qj

Newton’s Law:Newton’s Law:

i

ii r

VF

iii amF

Potential Function Force

Taylor expansion:

Verlet’s Method

Ensemble AverageObservable

StatisticalMechanics

1 hour here

1 hour here

Ergodic Hypothesis:MD Simulation:

Analysis of MD

ConfigurationsAveragesFluctuationsTime Correlations

Molecular dynamics:Integration timestep - 1 femtosecondSet by fastest varying force.Accessible timescale about 10 nanoseconds.

Bond vibrations - 1 fsCollective vibrations - 1 psConformational transitions - ps or longerEnzyme catalysis - microsecond/millisecondLigand Binding - micro/millisecondProtein Folding - millisecond/second

Timescales.

•SOME EXAMPLES

11 Sequences in 9 clades

• A1 LEU PRO CYS ARG ILE LYS GLN PHE ILE ASN MET TRP GLN GLU VAL +2• B1 LEU PRO CYS ARG ILE LYS GLN ILE VAL ASN MET TRP GLN GLU VAL +2• C1 ILE PRO CYS ARG ILE LYS GLN ILE ILE ASN MET TRP GLN GLU VAL +2• D2 LEU PRO CYS ARG ILE LYS PRO ILE ILE ASN MET TRP GLN GLU VAL +2• E2 LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN MET TRP GLN GLY VAL +3• E3 LEU PRO CYS LYS ILE LYS GLN ILE ILE LYS MET TRP GLN GLY VAL +4• F1 LEU LEU CYS LYS ILE LYS GLN ILE VAL ASN LEU TRP GLN GLY VAL +2• G2 LEU PRO CYS LYS ILE LYS GLN ILE VAL ARG MET TRP GLN ARG VAL +5• 1A0 LEU PRO CYS LYS ILE LYS GLN ILE VAL ASN MET TRP GLN ARG VAL +4• 2A3 LEU GLN CYS ARG ILE LYS GLN ILE VAL ASN MET TRP GLN LYS VAL +4• OC4 ILE PRO CYS LYS ILE LYS GLN VAL VAL ARG SER TRP ILE ARG GLY +5

Does CD4-binding peptide have a similar

structure in all strains of HIV-1 ?

Molecular Dynamics Simulation Setup

• Box dimensions: 53x40x40 Ǻ• Explicit water molecules (TIP3P)

(~8600 atoms)• Explicit ions

(Sodium and Chloride, 26 ions in total);physiological salt: 0.23M

• ~240 peptide atoms=> approx. 8900 atoms in total

• Uncharged system• NPT ensemble: 300K, 1atm• 5ns simulation time for each strain

=> 55ns total simulation time

Dihedral angles

Surface electrostatic properties conserved.

Detection of Individual p53-Autoantibodies in Human Sera

Cancer Biotechnology.

Rhodamine 6G

O H

N

O

O

N

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MR121

Fluorescence Quenching of Dyes by Trytophan

Dye

Quencher

Fluorescently labeled Peptide

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Analysis

r

Strategy:

Quenched Fluorescent

Results:

HealthyPersonSerum

CancerPatientSerum

Protein Folding/Unfolding

Protein Folding

Exploring the Folding Landscape

BSE cattle bovine spongiform encephalopathy scrapie sheepCWD elk chronic wasting disease TME mink transmissible mink encephalopathy

kuru human

CJD human Creutzfeldt-Jakob disease sporadic

genetic

infectious

vCJD human variant CJD

GSS human Gerstmann-Sträussler-Scheinker disease

FFI human fatal familial insomnia

Prion diseases of animal and man

Properties of the prion protein

- The natural prion protein is encoded by a single exon as a polypeptide chain of about 250 to 260 amino acid residues.

- Posttranslational modification: cleavage of a 22 (N-terminal) and 23 (C-terminal) residue signal sequence => about 210 amino acid residues

- PrP contains a single disulfide bridge.

- PrP contains 2 glycosylation sites.

- PrP inserts into the cellular plasma membrane through a glycosyl-phosphatidyl-inositol anchor at the C-terminus.

Structure of the prion protein

Superimposed PrP structures

The first image below shows the structure of part of the hamster and mouse PrPC molecules superimposed. The close similarity in the structures is obvious, as is the preponderance of alpha helical structure.

Location of human mutations

The picture shows the position of various mutations important for prion disease development in humans modelled on the hamster structure PrPC.

Many of these mutations are positioned such that they could disrupt the secondary structure of the molecule.

Mouse Prion Protein (PrPc)

NMR Structure

Structure of PrPSc

The PrPSc has a much higher -sheet content.

Bundeshochleistungsrechner Hitachi SR8000-F1

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

Safety in Numbers

Large-Scale Conformational Change

Structural Changes in Proteins:The Physical Problem

ENERGY LANDSCAPE: high-dimensional, rugged.

Need to find PATHWAY WITH LOWEST SADDLE POINT.

Conformational Pathways

Navigate energy landscape to find continuous path of lowest free energy from one end point to the other.

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Thick filament

Muscle Contraction

of Myosin and ActinSliding filaments….

Thin filament

Z disc

ATP Hydrolysis by Myosin

SONJA SCHWARZLSTEFAN FISCHER

Power Stroke in Muscle Contraction.

End ss 2003