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Elastic models of conformational transitions in macromolecules

Elastic models of conformational transitions in macromolecules. Moon K. Kim, Gregory S. Chirikjian, Robert L. Jernigan Presented by: Amit Jain. Outline. Introduction Problem Statement Related Work Elastic Model Approach Results Conclusion. Introduction. What are Macromolecules ?

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Elastic models of conformational transitions in macromolecules

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  1. Elastic models of conformational transitions in macromolecules Moon K. Kim, Gregory S. Chirikjian, Robert L. Jernigan Presented by: Amit Jain NUS CS5247

  2. Outline • Introduction • Problem Statement • Related Work • Elastic Model • Approach • Results • Conclusion NUS CS5247

  3. Introduction • What are Macromolecules ? • Carbohydrates • Proteins • Nucleic Acids • Why are conformational transitions important ? • Understanding functional relationship NUS CS5247

  4. Problem Statement Input: Two conformation x, χ Output: List of realistic displacements δ NUS CS5247

  5. Related Work • Interpolation • Linear interpolation in cartesian space • Linear interpolation in bond lengths and bond angles • Molecular Dynamics • Coarse models • Simple • Unrealistic bond lengths and bond angles • Solves the unrealistic bond lengths and angles • Can still get impossible paths NUS CS5247

  6. Outline • Introduction • Problem Statement • Related Work • Elastic Model • Approach • Results • Conclusion NUS CS5247

  7. Elastic Model • Key Enabler • Discrete model for small conformational changes about an equilibrium position for macromolecules • Model • Alpha carbons • Inter carbon force interactions NUS CS5247

  8. Elastic Model • Potential Energy function • Can be reduced to NUS CS5247

  9. Elastic Model Substituting, We get, NUS CS5247

  10. Elastic Model Analytical equation for motion where M is diagonal matrix NUS CS5247

  11. Approach • Interpolate conformation • Find the displacement(δ) which minimizes cost • Increment alpha • Calculate new • Use new conformation to find new displacement NUS CS5247

  12. Approach Cost can be simplified to, Hence, minimizing for δ NUS CS5247

  13. Approach • Issue: • Position and orientation of final conformation does not match • Solution: • Superposition • RMS Superposition • Incremental Rotation NUS CS5247

  14. Outline • Introduction • Problem Statement • Related Work • Elastic Model • Approach • Results • Conclusion NUS CS5247

  15. Results NUS CS5247

  16. Results NUS CS5247

  17. Results: Comparison with NMA Consistent with NMA analysis NUS CS5247

  18. Conclusion Elastic network model has been introduced • Benefits • Efficient and realistic simulation of macromolecules transitions • Faster NMA analysis (Coarse grained) NUS CS5247

  19. Questions NUS CS5247

  20. Thank You NUS CS5247

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