Different circular permutations produced different folding nuclei in proteins: A computational study

Journal of Molecular Biology

Volumn 306, Issue 1, 2001, Pages 121-132

  Li, Lewyn ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Circular permutation; Computer simulation; Folding nucleus; Protein folding

Indexed keywords

BETA LACTOGLOBULIN; CHYMOTRYPSIN INHIBITOR; FODRIN;

ARTICLE; MATHEMATICAL ANALYSIS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; SEQUENCE ANALYSIS;

EID: 0035830487     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.4375     Document Type: Article

References (46)

1. Specific nucleus as the transition state for protein folding: Evidence from lattice model
2. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
3. Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity
4. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
5. Differential stabilization of two hydrophobic cores in the transition state of the villin 14T folding reaction
6. De novo protein design: Fully automated sequence selection
7. β-sheet proteins with nearly identical structures have different folding intermediates
8. Identification of kinetically hot residues in proteins
9. De novo design of the hydrophobic cores of proteins
10. A metastable state in folding simulations of a protein model
11. Protein folding: A perspective from theory and experiment
12. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
13. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
14. Is folding of β-lactoglobulin non-hierarchic? Intermediate with native-like β-sheet and non-native α-helix
15. Mapping the interactions present in the transition state for unfolding/folding of FKBP12
16. A theoretical search for folding/unfolding nuclei in three-dimensional protein native structures
17. Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition
18. Non-native α-helical intermediate in the refolding of β-lactoglobulin, a predominantly β-sheet protein
19. An essential intermediate in the folding of dihydrofolate reductase
20. Random circular permutation of DsbA reveals segments that are essential for protein folding and stability
21. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
22. Systematic circular permutation of an entire protein reveals essential folding elements
23. How do small single-domain proteins fold?
24. Packing interactions in the apomyoglobin folding intermediate
25. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues
26. A breakdown of symmetry in the folding transition state of protein L
27. Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism
28. Designing the hydrophobic core of Thermus flavus malate dehydrogenase based on side-chain packing
29. "New view" of protein folding reconciled with the old through multiple unfolding simulations
30. Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate
31. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
32. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2
33. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
34. The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure
35. Critical role of β-hairpin formation in protein G folding
36. Equation of state calculations by fast computing machines
37. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
38. Folding of circular and permuted chymotrypsin inhibitor 2: Retention of the folding nucleus
39. Contact order, transition state placement and the refolding rates of single domain proteins
40. Confirmation of the hierarchical folding of RNase H: A protein engineering study
41. Experiment and theory highlight role of native state topology in SH3 folding
42. Protein folding mechanisms and the multidimensional folding funnel
43. Different folding transition states may result in the same native structure
44. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
45. Three-state model for lysozyme folding: Triangular folding mechanism with an energetically trapped intermediate
46. Folding intermediates in cytochrome c