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1. Introduction
2. Content
3. Methods - molecular mechanics force field
4. Methods - molecular dynamics (MD)
5. Native protein dynamics and function
6. Dynamics is important for protein behavior
7. Why molecular dynamics?
8. Starting a molecular dynamics simulation
9. Wild-type MD simulation 25 degrees c
10. Mutants construction tests whether cleft forms
11. Construction of cyt c - cyt b5 complexes
12. Monitored changes in chemical shift of cyt b5
13. Cleft allows electron transfer through a channel
14. Native protein dynamics
15. Protein unfolding
16. Unfolding pathway of En-HD in water
17. En-HD unfolding in C-alpha-RMSD space
18. En-HD TS independent of T
19. En-HD unfolds on same timescale
20. Experiment and simulation for the TS of En-HD
21. All 3 helices formed in intermediate
22. X-ray scattering support U-shaped intermediate
23. Protein unfolding
24. Protein unfolding and disease
25. Conformational changes lead to prion diseases
26. Objectives for MD simulations
27. Loose beta-structure forms at low pH
28. Improvement of sheet packing
29. Conversion of ShaPrP D147N
30. Building a prion protofibril
31. Interface forms continuous beta-sheet
32. Addition of diglycosylated subunits
33. Imaging of residues 141-176
34. Imaging of the helices and sugars
35. Unfolding and disease: prion protein
36. Recap
37. References for the studies presented (1)
38. References for the studies presented (2)
39. References for the studies presented (3)

Topics Covered

• Molecular mechanics force fields and starting structures
• Molecular dynamics (MD) simulations
• Native protein dynamics
• Protein unfolding
• Unfolding pathways of En-HD
• Protein unfolding and disease
• Objectives for MD simulations

Links

Series:

• Protein Folding, Aggregation and Design

Categories:

• Biochemistry
• Methods

Talk Citation

Daggett, V. (2007, October 1). Molecular dynamics simulations of protein dynamics, unfolding and misfolding [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved December 3, 2024, from https://doi.org/10.69645/WUAN4092.
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Publication History

• Published on October 1, 2007

Financial Disclosures

• Prof. Valerie Daggett has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.