Characterization of the folding kinetics of a three-helix bundle protein via a minimalist langevin model

Journal of Molecular Biology

Volumn 310, Issue 3, 2001, Pages 673-685

  Berriz, Gabriel F ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

B domain; Minimalist models; Protein folding: Langevin dynamics; Staphylococcus aureus; Three helix bundle

Indexed keywords

PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; KINETICS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION; THERMODYNAMICS; THERMOSTABILITY;

STAPHYLOCOCCUS AUREUS;

EID: 0035854476     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4792     Document Type: Article

References (41)

1. Principles that govern the folding of protein chains
2. Is protein folding hierarchic? I. Local structure and peptide folding
3. Is protein folding hierarchic? II. Folding intermediates and transition states
4. Protein folding dynamics: The diffusion-collision model and experimental data
5. Nucleation mechanisms in protein folding
6. Theoretical studies of protein folding thermodynamics and kinetics
7. How do small single-domain proteins fold?
8. From Levinthal to pathways to funnels
9. The Levinthal paradox: Yesterday and today
10. Pathways for protein folding: Is a new view needed?
11. Protein folding: Nucleation and compact intermediates
12. Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
13. The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
14. Fast kinetics and mechanisms in protein folding
15. Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
16. Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
17. Folding nuclei in proteins
18. A method for predicting protein structure from sequence
19. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
20. Folding thermodynamics of a model three-helix-bundle protein
21. Exploring the folding free energy surface of a three-helix bundle
22. Interpreting the folding kinetics of helical proteins
23. Absence of a stable intermediate in the folding pathway of protein A
24. The stability and unfolding of an IgG binding protein based on the B domain of protein A from Staphylococcus aureus probed by tryptophan substitution and fluorescence spectroscopy
25. First-principles calculation of the folding free energy of a three-helix bundle protein
26. Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains
27. Cooperativity and stability in a Langevin model of proteinlike folding
28. Energetics of protein structure
29. Theory of the phase transition between helix and random coil in polypeptide chains
30. The energy landscape of a fast-folding protein mapped by ala → gly substitutions
31. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
32. Mechanisms and kinetics of β-hairpin formation
33. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
34. Experiment and theory highlight role of native state topology in SH3 folding
35. Functional rapidly folding proteins from simplified amino acid sequences
36. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
37. On the convergence of the SHAKE algorithm
38. Conformation of polypeptides and proteins
39. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
40. Relationship between protein structure and geometrical constraints