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
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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
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Newton’s Law:Newton’s Law:
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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
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MR121
Fluorescence Quenching of Dyes by Trytophan
Dye
Quencher
Fluorescently labeled Peptide
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Analysis
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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