Protein folding pathways and kinetics: Molecular dynamics simulations of β-strand motifs

Biophysical Journal

Volumn 83, Issue 2, 2002, Pages 819-835

  Jang, Hyunbum ^a   Hall, Carol K ^a   Zhou, Yaoqi ^b  

^a North Carolina State University   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION; BIOPHYSICS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; KINETICS; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STATISTICAL MODEL; TEMPERATURE;

PROTEIN;

AMINO ACID MOTIFS; BIOPHYSICS; KINETICS; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE; TEMPERATURE;

EID: 0035997013     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75211-9     Document Type: Article

References (89)

1. Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations
2. Studies in molecular dynamics. I. General method
3. A surprising simplicity to protein folding
4. Propagating structure of Alzheimer's β-amyloid(10-35) is parallel β-sheet with residues in exact register
5. Two-dimensional structure of β-amyloid(10-35) fibrils
6. Formation and stability of β-hairpin structures in polypeptides
7. C-terminal PEG blocks the irreversible step in β-amyloid(10-35) fibrillogenesis
8. Folding free energy surface of a three-stranded β-sheet protein
9. Kinetic studies of β-sheet protein folding
10. Transition states and folding dynamics of proteins and heteropolymers
11. Phase separation inhibitors and prevention of selenite cataract
12. Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
13. Conformation of twisted β-pleated sheets in proteins
14. De novo design of a monomeric three-stranded antiparallel β-sheet
15. Principles of protein folding: A perspective from simple exact models
16. From Levinthal to pathways to funnels
17. Understanding β-hairpin formation
18. The fundamentals of protein folding: Bring together theory and experiment
19. Discrete molecular dynamics studies of the folding of a protein-like model
20. Identifying the protein folding nucleus using molecular dynamics
21. Searching for "downhill scenarios" in protein folding
22. Sickle cell hemoglobin polymerization
23. Activation barriers to structural transition determine deposition rates of Alzheimer's disease Aβ amyloid
24. In vitro growth of Alzheimer's disease β-amyloid plaques displays first-order kinetics
25. Folding simulations of a three-stranded antiparallel β-sheet peptide
26. Light chain cardiomyopathy: Structural analysis of the light chain tissue deposits
27. Exploring the energy landscape of a β-hairpin in explicit solvent
28. Respective roles of short range and long range interactions in protein folding
29. Studies on protein folding, unfolding and fluctuations by computer simulation. IV. Hydrophobic interactions
30. Mechanisms of protein folding
31. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction
32. Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein
33. Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
34. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
35. Effect of solvent conditions upon refolding pathways and intermediates for a simple lattice protein
36. Effect of denaturant and protein concentrations upon protein refolding and aggregation: A simple lattice model
37. Folding thermodynamics of model four-strand antiparallel β-sheet proteins
38. Theoretical studies of protein folding and unfolding
39. Diffusion-collision model for protein folding
40. Protein folding dynamics: The diffusion-collision model and experimental data
41. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding?
42. Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism
43. WW: An isolated three-stranded antiparallel β-sheet domain that unfolds and refolds reversibly: Evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state
44. Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model
45. Computer design of idealized β-motifs
46. Dynamics and thermodynamics of β-hairpin assembly: Insights from various simulation techniques
47. Design of a 20-amino acid, three-stranded β-sheet protein
48. A lattice statistical mechanics model of the conformational and sequence spaces of protein
49. "New view" of protein folding reconciled with the old through multiple unfolding simulations
50. Amyloid fibrils may be assembled from β-helical protofibrils
51. Understanding β-hairpin formation by molecular dynamics simulations of unfolding
52. Betabellins 15D and 16D, de novo designed β-sandwich proteins that have amyloidogenic properties
53. Review: Model peptides and the physicochemical approach to β-amyloids
54. Folding kinetics of proteins and copolymers
55. Transgenic analysis of prion diseases
56. A simple model for calculating the kinetics of protein folding from three-dimensional structures
57. Folding dynamics and mechanism of β-hairpin formation
58. Folding funnels and frustration in off-lattice minimalist protein landscapes
59. Is the molten globule a third phase of proteins?
60. Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G
61. Configurations of polypeptide chains with favored orientations around single bonds - 2 New pleated sheets
62. Contact order, transition state placement and the refolding rates of single domain proteins
63. Molten globule and protein folding
64. De novo design and structural analysis of a model β-hairpin peptide system
65. Molecular dynamics simulation of polymer chains with excluded volume
66. Observation of strange kinetics in protein folding
67. How does a protein fold?
68. Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
69. Alzheimer's disease: A central role for amyloid
70. Modeling protein folding: The beauty and power of simplicity
71. Energetic frustration and the nature of the transition state in protein folding
72. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation
73. Transient aggregates in protein folding are easily mistaken for folding intermediates
74. Secondary structure of amyloid β peptide correlates with neurotoxic activity in vitro
75. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics
76. Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein
77. Molecular dynamic study of entangled hard-chain fluids
78. Common core structure of amyloid fibrils by synchrotron x-ray diffraction
79. Studies on protein folding, unfolding and fluctuations by computer simulation: The effect of specific amino acid sequence represented by specific inter-unit interactions
80. Studies on protein folding, unfolding and fluctuations by computer simulation. II. A three-dimensional lattice model of lysozyme
81. β-hairpin folding simulations in atomistic detail using an implicit solvent model
82. The Alzheimer's peptide Aβ adopts a collapsed coil structure in water
83. The free energy landscape for β-hairpin folding in explicit water
84. Role of hydrophilic and hydrophobic contacts in folding of the second β-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model
85. Folding thermodynamics of a model three-helix bundle protein
86. Interpreting the folding kinetics of helical proteins
87. Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis
88. Folding rate prediction using total contact distance