Biochemie IV

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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. Matthi
as 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.
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Computational Molecular Biophysics
Universität Heidelberg
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IBM PLANS SUPERCOMPUTER THAT WORKS AT SPEED OF
LIFE
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)
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Protein Folding
Exploring the Folding Landscape
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• Uses of Molecular Dynamics Simulation
• structure
• flexibility
• solvent effects
• chemical reactions
• ion channels
• thermodynamics (free energy changes, binding)
• spectroscopy
• NMR/crystallography

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Atomic-Detail Computer Simulation
Molecular Mechanics Potential
Energy Surface ? Exploration by Simulation..
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• Model System
• set of atoms
• explicit/implicit solvent
• periodic boundary conditions
• Potential Function
• empirical
• chemically intuitive
• quick to calculate

Tradeoff simplicity (timescale) versus
accuracy
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Lysozyme in explicit water
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Potential Function ? Force
Newtons Law
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Taylor expansion
Verlets Method
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1 hour here
Statistical Mechanics
Ensemble Average
Observable
1 hour here
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MD Simulation
Ergodic Hypothesis
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Analysis of MD
Configurations Averages Fluctuations Time
Correlations
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Timescales.
Bond vibrations - 1 fs Collective vibrations - 1
ps Conformational transitions - ps or
longer Enzyme catalysis - microsecond/millisecond
Ligand Binding - micro/millisecond Protein
Folding - millisecond/second
Molecular dynamics Integration timestep - 1
femtosecond Set by fastest varying
force. Accessible timescale about 10 nanoseconds.
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• SOME EXAMPLES

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Does CD4-binding peptide have a similar structure
in all strains of HIV-1 ?

• 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

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Molecular Dynamics Simulation Setup

• Box dimensions 53x40x40 ?
• Explicit water molecules (TIP3P)
• (8600 atoms)
• Explicit ions
• (Sodium and Chloride, 26 ions in total)
• physiological salt 0.23M
• 240 peptide atoms
• gt approx. 8900 atoms in total
• Uncharged system
• NPT ensemble 300K, 1atm
• 5ns simulation time for each strain
• gt 55ns total simulation time

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Dihedral angles
?
?
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Surface electrostatic properties conserved.
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Cancer Biotechnology.
Detection of Individual p53-Autoantibodies in
Human Sera
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Rhodamine 6G
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Fluorescence Quenching of Dyes by Trytophan
Quencher
MR121
Dye
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Fluorescently labeled Peptide
?
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Analysis
r
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Strategy
Quenched
Fluorescent
Results
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Protein Folding/Unfolding
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Protein Folding
Exploring the Folding Landscape
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Prion diseases of animal and man
BSE cattle bovine spongiform
encephalopathy scrapie sheep CWD
elk chronic wasting disease TME mink
transmissible mink encephalopathy kuru
human CJD human Creutzfeldt-Jakob
disease sporadic
genetic infectiousvCJD
human variant CJDGSS human Gerstmann-Sträuss
ler-Scheinker diseaseFFI human fatal
familial insomnia
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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 gt 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.

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Structure of the prion protein
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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.
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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.
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Mouse Prion Protein (PrPc) NMR Structure
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Structure of PrPSc
The PrPSc has a much higher b-sheet content.
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Bundeshochleistungsrechner Hitachi SR8000-F1
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IBM PLANS SUPERCOMPUTER THAT WORKS AT SPEED OF
LIFE
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)
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Safety in Numbers
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Large-Scale Conformational Change
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Structural Changes in ProteinsThe Physical
Problem
ENERGY LANDSCAPE high-dimensional,
rugged. Need to find PATHWAY WITH LOWEST SADDLE
POINT.
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Conformational Pathways

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

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Muscle Contraction
Thick filament
Thin filament
Z disc
of Myosin and Actin
Sliding filaments.
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ATP Hydrolysis by Myosin
SONJA SCHWARZL STEFAN FISCHER
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Power Stroke in Muscle Contraction.
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End ss 2003