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Simulating Protein Folding

This presentation discusses innovative methods for simulating protein folding, utilizing Molecular Dynamics and Wang-Landau techniques to analyze complex trajectories. We explore strategies for constructing transition matrices that reveal transition states and patterns within protein folding processes. By studying a tripeptide system through GROMACS, we investigate the probabilities of state transitions and analyze the resulting Ramachandran Plot for insights into protein conformations. This work aims to bridge molecular simulations with statistical analysis to enhance our understanding of protein behavior.

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Simulating Protein Folding

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  1. Simulating Protein Folding - Some Ideas Christian Hedegaard Jensen Dmitry Nerukh

  2. Outline • Introduction • Transition Matrix • Wang-Landau

  3. Outline • Introduction • Transition Matrix • Wang-Landau

  4. Introduction • We are simulation protein folding using Molecular Dynamics, and understanding using complexity analysis. • Try to do statistics on trajectories, to see if there are any patterns in where they go. (Transition Matrix) • Try and look at the paths that a protein can take when it folds. (Wang-Landau)

  5. Outline • Introduction • Transition Matrix • Wang-Landau

  6. Transition Matrix • Find states in trajectory • Find transitions between states in trajectory • Write up transition matrix for system • Possibly include some memory into the system.

  7. Transition Matrix

  8. Transition Matrix

  9. Transition Matrix • We have a molecular dynamics simulation of a tripeptide. • Trianaline • 300 K, 1 atm • 12 ps (2fs) • OPLSAA-2001 force field • GROMACS

  10. Transition Matrix Ramachandran Plot

  11. Transition Matrix

  12. Transition Matrix

  13. Transition Matrix • Gives useful information about what is going on in the system. • Find out where we end and with what probabilities. • Look at transitions between clusters of states.

  14. Outline • Introduction • Transition Matrix • Wang-Landau

  15. Wang-Landau • Wang-Landau simulations, using a combination of Molecular Dynamics and Monte Carlo.

  16. Wang-Landau • Wang-Landau gives the (relative) density of states. • The dos of a simple protein was obtained, d(E). • Try to calculate d(,E) or d(, ,E) .

  17. dos q 0 2p Wang-Landau

  18. Wang-Landau • Define reaction coordinates • Sample as function of these coordinates • Method does not say what the system does, but is says what is possible.

  19. Wang-Landau • Matlab

  20. Thank you!

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