The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation

Journal of Molecular Biology

Volumn 308, Issue 1, 2001, Pages 79-95

  Shimada, Jun ^a   Kussell, Edo L ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

All atom simulations; Crambin; Monte Carlo; Nucleation condensation; Protein folding

Indexed keywords

CRAMBIN; PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; SYSTEM ANALYSIS; THERMODYNAMICS;

EID: 0035917318     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4586     Document Type: Article

References (63)

1. Free energy landscape for protein folding kinetics: Intermediates, traps and multiple pathways in theory and lattice model simulations
2. Specific nucleus as the transition state for protein folding: Evidence from the lattice model
3. Absence of a stable intermediate on the folding pathway of protein A
4. A surprising simplicity to protein folding
5. Cooperativity and stability in a langevin model of proteinlike folding
6. Funnels, pathways, and the energy landscape of protein folding: A synthesis
7. Spin glasses and the statistical mechanics of folding
8. 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
9. Molecular dynamics simulations of helix denaturation
10. Folding-unfolding thermodynamics of a beta-hepta-peptide from equilibrium simulations
11. Principles of protein folding - A perspective from simple exact models
12. Is protein unfolding the reverse of protein folding? A lattice simulation analysis
13. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
14. New Monte Carlo technique for studying phase transitions
15. Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications
16. Rate of beta-structure formation in polypeptides
17. Can protein unfolding simulate protein folding?
18. Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation
19. Folding dynamics of the src SH3 domain
20. Evolution-like selection of fast-folding model proteins
21. Theory of two-state cooperative folding of proteins
22. Analysis of Monte Carlo results on the kinetics of lattice polymer chains with excluded volume
23. The nature of folded states of globular proteins
24. Conformational diffusion and helix formation kinetics
25. Helix nucleation kinetics from molecular dynamics simulations in explicit solvent
26. How do small single-domain proteins fold?
27. Folding of chymotrypsin inhibitor-2.1. Evidence for a two-state transition
28. Protein folding dynamics
29. A criterion which determines foldability of proteins
30. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin
31. "New view" of protein folding reconciled with the old through multiple unfolding simulations
32. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 using molecular dynamics simulations
33. Equation of state calculations by fast computing machines
34. Elucidating the folding problem of helical peptides using empirical parameters
35. Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence
36. Folding dynamics and mechanism of beta-hairpin formation
37. Theory of protein folding: The energy landscape perspective
38. Folding pathway of a lattice model for proteins
39. Pathways for protein folding: Is a "new view" needed?
40. Heteropolymer freezing and design: Towards physical models of protein folding
41. Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing
42. Contact order, transition state placement and the refolding rates of single domain proteins
43. Statistical mechanics of proteins with "evolutionary selected" sequences
44. Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins
45. An analysis of packing in the protein folding problem
46. How does a protein fold?
47. The mechanism of α-helix formation by peptides
48. Theoretical studies of protein-folding thermodynamics and kinetics
49. Engineering of stable and fast-folding sequences of model proteins
50. Molecular collapse: The rate-limiting step in two-state cytochrome c folding
51. Atomic resolution crystal structure of the hydrophobic protein crambin at 130 K
52. Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a "kinetic zipper" model
53. The packing density in proteins: Standard radii and volumes
54. Monte Carlo studies of lattice-model polymer chains. 3. Relaxation of Rouse coordinates
55. Automated 2D NOESY assignment and structure calculation of crambin (S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs
56. A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices
57. Interpreting the folding kinetics of helical proteins
58. Theory of the phase transition between helix and random coil in polypeptide chains