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Biochemie IV – Struktur und Dynamik von Biomolekülen II. (Mittwochs 8-10 h, INF 230, klHS) 30.4. 7.5. 14.5. 21.5. 28.5. 4.6. 11.6. 18.6. 25.6. 2.7. 9.7. 16.7. 23.7. Jeremy Smith: Intro to Molecular Dynamics Simulation. Stefan Fischer: Molecular Modelling and Force Fields. Matthias Ullmann: Current Themes in Biomolecular Simulation. Ilme Schlichting: X-Ray Crystallography-recent advances (I). Klaus Scheffzek: X-Ray Crystallography-recent advances (II). Irmi Sinning: Case Study in Protein Structure. Michael Sattler: NMR Applications in Structural Biology. Jörg Langowski: Brownian motion basics. Jörg Langowski: Single Molecule Spectroscopy. Karsten Rippe: Scanning Force Microscopy. Jörg Langowski: Single Molecule Mechanics. Rasmus Schröder: Electron Microscopy. Jeremy Smith: Biophysics, the Future, and a Party. Protein Computational Molecular Biophysics Universität Heidelberg 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) 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 V k b b 2 b 0 bonds k 2 0 angles N K 1 cosn K 2 n dihedrals n 1 0 impropers 12 6 qq 4 ij ij ij i j r i , j Dr rij i, j ij ij 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 2/8 MM Energy Function l r qi qj Potential Function Force Newton’s Law: Vi Fi ri Fi mi ai Taylor expansion: Verlet’s Method 1 h o u r h e r e Statistical Mechanics Observable 1 hour here Ensemble Average MD Simulation: Ergodic Hypothesis: Analysis of MD Configurations Averages Fluctuations Time Correlations 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. •SOME EXAMPLES Does CD4-binding peptide have a similar structure in all strains of HIV-1 ? 11 Sequences in 9 clades • • • • • • • • • • • A1 B1 C1 D2 E2 E3 F1 G2 1A0 2A3 OC4 LEU PRO CYS ARG ILE LYS GLN PHE ILE ASN MET TRP GLN GLU VAL LEU PRO CYS ARG ILE LYS GLN ILE VAL ASN MET TRP GLN GLU VAL ILE PRO CYS ARG ILE LYS GLN ILE ILE ASN MET TRP GLN GLU VAL LEU PRO CYS ARG ILE LYS PRO ILE ILE ASN MET TRP GLN GLU VAL LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN MET TRP GLN GLY VAL LEU PRO CYS LYS ILE LYS GLN ILE ILE LYS MET TRP GLN GLY VAL LEU LEU CYS LYS ILE LYS GLN ILE VAL ASN LEU TRP GLN GLY VAL LEU PRO CYS LYS ILE LYS GLN ILE VAL ARG MET TRP GLN ARG VAL LEU PRO CYS LYS ILE LYS GLN ILE VAL ASN MET TRP GLN ARG VAL LEU GLN CYS ARG ILE LYS GLN ILE VAL ASN MET TRP GLN LYS VAL ILE PRO CYS LYS ILE LYS GLN VAL VAL ARG SER TRP ILE ARG GLY +2 +2 +2 +2 +3 +4 +2 +5 +4 +4 +5 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. Cancer Biotechnology. Detection of Individual p53Autoantibodies in Human Sera Rhodamine 6G Fluorescence Quenching of Dyes by Trytophan Quencher N N O OH O MR121 Dye N Fluorescently labeled Peptide ? Analysis r Strategy: Quenched Results: Healthy Person Serum Cancer Patient Serum Fluorescent Protein Folding/Unfolding Protein Folding Exploring the Folding Landscape Prion diseases of animal and man BSE scrapie CWD TME cattle sheep elk mink bovine spongiform encephalopathy chronic wasting disease transmissible mink encephalopathy kuru CJD human human Creutzfeldt-Jakob disease vCJD GSS FFI human human human variant CJD Gerstmann-Sträussler-Scheinker disease fatal familial insomnia sporadic genetic infectious 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 (Cterminal) 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 glycosylphosphatidyl-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 b-sheet content. Bundeshochleistungsrechner Hitachi SR8000-F1 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) 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. ` Muscle Contraction Thin filament Thick filament Z disc Sliding filaments…. of Myosin and Actin SONJA SCHWARZL STEFAN FISCHER ATP Hydrolysis by Myosin Power Stroke in Muscle Contraction. End ss 2003