• Introduction to Protein Folding and Misfolding
• 69 min
  1. Protein folding and misfolding: from theory to therapy

  • Prof. Christopher Dobson
• Stability and Kinetics of Protein Folding
• 55 min
  2. Mechanisms of protein folding reactions

  • Prof. Thomas Kiefhaber
• Protein Folding Theory
• 53 min
  3. Mapping disordered proteins with single-molecule FRET

  • Dr. Hagen Hofmann
• Protein Folding Simulations
• 36 min
  4. Protein folding

  • Prof. Eugene Shakhnovich
• 42 min
  5. Simulating protein folding with full atomistic detail

  • Prof. Vijay Pande
• 58 min
  6. Molecular dynamics simulations of protein dynamics, unfolding and misfolding

  • Prof. Valerie Daggett
• Protein Folding Inside the Cell: Chaperones
• 42 min
  7. Protein folding Inside the cell: macromolecular crowding and protein aggregation

  • Prof. Emeritus R. John Ellis
• 34 min
  8. Chaperone mechanisms in cellular protein folding

  • Prof. Dr. F. Ulrich Hartl
• 60 min
  9. Quality control of proteins mislocalized to the cytosol

  • Dr. Ramanujan Hegde
• Protein Misfolding and Disease
• 44 min
  10. Protein aggregation, metals and oxidative stress in neurodegenerative diseases

  • Prof. David Allsop
• Protein Design
• 33 min
  11. Designing proteins with life sustaining activities 1

  • Prof. Michael Hecht
• 24 min
  12. Designing proteins with life sustaining activities 2

  • Prof. Michael Hecht
• 48 min
  13. Folding and design of helical repeat proteins

  • Prof. Lynne Regan
• 44 min
  14. Design and engineering of zinc-finger domains

  • Prof. Jacqui Matthews
• 47 min
  15. Prediction and design of protein structures and interactions

  • Prof. David Baker
• Amyloid Fibrils: Structure, Formation and Nanotechnology
• 39 min
  16. Amyloid fibrils as functional nanomaterials

  • Prof. Juliet Gerrard
• 37 min
  17. Functional amyloid fibrils from fungi and viruses

  • Prof. Margaret Sunde
• Intrinsically disordered Proteins
• 40 min
  18. Fuzzy protein theory for disordered proteins

  • Prof. Monika Fuxreiter
• Intersection of RNA, translation and protein aggregation.
• 47 min
  19. Expanding roles of RNA-binding proteins in neurodegenerative diseases

  • Prof. Aaron D. Gitler
• Proteostasis
• 49 min
  20. Adapting proteostasis to ameliorate aggregation-associated amyloid diseases

  • Dr. Jeffery W. Kelly
• Archived Lectures *These may not cover the latest advances in the field
• 60 min
  21. Amyloidosis: disease caused by amyloid

  • Prof. Mark Pepys
• 34 min
  22. Protein folding and dynamics from single molecule spectroscopy

  • Prof. Dr. Benjamin Schuler
• 41 min
  23. Prion diseases

  • Prof. Fred Cohen
• 31 min
  24. Basic studies of protein folding and stability: the folding of related protein families

  • Dr. Jane Clarke
• 38 min
  25. Titin I27: a protein with a complex folding landscape

  • Dr. Jane Clarke
• 49 min
  26. Novel proteins from designed combinatorial libraries

  • Prof. Michael Hecht
• 47 min
  27. Fast folding dynamics of small proteins: placing limits on diffusional limits

  • Dr. Stephen Hagen
• 35 min
  28. The sequence determinants of amyloid fibril formation

  • Prof. Fabrizio Chiti

Printable Handouts

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Navigable Slide Index

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

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.