1 / 34

Peptide Folding

Protein Physics. Structural Change. Peptide Folding. Petascale Future. Movie Time. Molecular Mechanical. Quantum Mechanical. Computer Simulation - Basic Principles. Model System. or QM/MM Potential. Molecular Mechanics Potential. Simulation - exploring the energy landscape.

kishi
Download Presentation

Peptide Folding

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Protein Physics Structural Change Peptide Folding Petascale Future Movie Time

  2. Molecular Mechanical Quantum Mechanical Computer Simulation - Basic Principles Model System or QM/MM Potential Molecular Mechanics Potential Simulation - exploring the energy landscape

  3. Product Reactant Energy Landscape

  4. ANDREEA GRUIA Halorhodopsin - Chloride Pumping at Atomic Resolution

  5. Not Enough Room

  6. Structure13 617 (2005).

  7. . Spring-loaded throttle valve helps prevent chloride leakage Valve Energy = EI = 12 kcal/mol Barrier without valve = EII = 13 kcal/mol. Sum = 25 kcal/mol = no backflow.

  8. Muscle Contraction Thin filament Thick filament

  9. SONJA SCHWARZL ATP Hydrolysis by Myosin Biochemistry 45 5830 (2006)

  10. BJORN WINDSHUEGEL Dynamics of Muscle Contraction. MSBIO - Universität Heidelberg PNAS 102 6873 (2005)

  11. FRANK NOE Large-Scale Functional Conformational Transitions product reactant s range ns range

  12. Ras p21 GTP-Bound Form (ON) GDP-Bound Form (OFF)

  13. Ras p21 GTP-Bound Form (ON)

  14. FRANK NOE Ras p21 trajectory

  15. FRANK NOE 6 product reactant 7 6 28 3 1 13 8 11 25 7 5 18 9 J. Chem. Phys. 126 155102 (2007)

  16. Sampling: Uniform Distribution

  17. Sampling:Exclusion of „Bad Structures“

  18. Sampling:Fail-Fast Minimization

  19. Sampling:Increase Density of Low-Energy Points

  20. Transition Network:Edges between Neighbours

  21. Temperature Connectivity of Network of Best Paths

  22. Ras Molecular Switch ON - state OFF - state

  23. Spallation Neutron Source Expensive Toys Cray XT4

  24. Cray XT4 One Million Atoms – Molecular Dynamics

  25. Lars Meinhold Zoe Cournia

  26. Lignocellulosic Biomass Exhibits Structural Complexity Hemicellulose Lignin Cellulose

  27. Spallation Neutron Source Cray XT4

  28. Molecular Simulation Projects Cellulose. Lignin. Lignocellulosic Biomass. Cellulase Reaction Mechanism. Cellulosomes (subsequent talk).

  29. Now 5 years ago Computer Power Improvement for Biological Molecular Dynamics Simulation • Gromacs with Reaction-Field • 5.4 million atoms, 175 atoms/core

  30. Softwood Lignin & Cellulose Cellulose Ib + 26 lignins Probe for factors that might influence recalcitrance • cellulose accessible surface area • radii of gyration of lignins Large-Scale Molecular Dynamics Simulation (1-3M atoms) using 2008 DOE INCITE award on ORNL Cray XT4.

  31. Cellulose: Benjamin Lindner Preliminary Findings

  32. Crystalline/Amorphous Crystalline 7 ns 1 ns

  33. Collaborators UT/ORNL Center for Molecular Biophysics • Maramuthu Krishnan (CMB, ORNL) • Loukas Petridis (CMB, ORNL) • Jiancong Xu (CMB, ORNL) • Roland Schulz (CMB, ORNL) • Benjamin Lindner (CMB, ORNL) External • Nicoleta Bondar (U. Cal Irvine) • Lars Meinhold, Ahmed Zewail (Caltech) • Kei Moritsugu (RIKEN) • Akio Kitao (U. Tokyo) • Stefan Fischer, Isabella Daidone (U. Heidelberg) • Torsten Becker (U. Bayreuth) • Frank Noe (Free University of Berlin). • Vandana Kurkal-Siebert (BASF, Ludwigshafen). • Franci Merzel (U. Ljubljana) • John Finney (U. London) • Roy Daniel (U. Waikato) • Andrea Amadei, Alfredo Di Nola (U. Rome “La Sapienza”)

More Related