Similarities between the spectrin SH3 domain denatured state and its folding transition state

Journal of Molecular Biology

Volumn 297, Issue 5, 2000, Pages 1217-1229

  Kortemme, Tanja ^a   Kelly, Mark J S ^a,b   Kay, Lewis E ^c   Forman Kay, Julie ^d,e   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^c UNIVERSITY OF TORONTO   (Canada)

^d HOSPITAL FOR SICK CHILDREN   (Canada)

^e UNIVERSITY OF TORONTO   (Canada)

Author keywords

Denatured state ensemble; Deuteration; NMR; Protein folding; Transition state

Indexed keywords

FODRIN; SPECTRIN;

ALPHA HELIX; ARTICLE; CHEMICAL REACTION KINETICS; CHICKEN; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN DOMAIN; PROTEIN FOLDING; REACTION ANALYSIS; STRUCTURE ANALYSIS;

EID: 0034646562     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3618     Document Type: Article

References (50)

1. Structure and dynamics of a denatured 131-residue fragment of staphylococcal nuclease: A heteronuclear NMR study
2. Matching theory and experiment in protein folding
3. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
4. 15N NMR assignment and solution structure of the SH3 domain of spectrin: Comparison of unrefined and refined structure sets with the crystal structure
5. High populations of non-native structures in the denatured state are compatible with the formation of the native folded state
6. Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway
7. Funnels, pathways, and the energy landscape of protein folding: A synthesis
8. Acceleration of the folding of acylphosphatase by stabilization of local secondary structure
9. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
10. Protein folding: An unfolding story
11. Conformational pathway of the polypeptide chain of chymotrypsin inhibitor-2 growing from its N terminus in vitro. Parallels with the protein folding pathway
12. NMRPipe: A multidimensional spectral processing system based on UNIX pipes
13. The fundamentals of protein folding: Bringing together theory and experiment
14. Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications
15. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
16. HMQC-NOESY-HMQC, a three-dimensional NMR experiment which allows detection of nuclear Overhauser effects with protons between overlapping signals
17. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
18. Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels
19. Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures
20. 15N NMR spectroscopy
21. Detection of nuclear Overhauser effects between degenerate amide resonances by heteronuclear three-dimensional nuclear magnetic resonance spectroscopy
22. How do small single-domain proteins fold?
23. NMRView: A computer program for the visualization and analysis of NMR data
24. X-ray solution scattering studies of protein folding
25. 2H] enriched protein
26. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
27. Obligatory steps in protein folding and the conformational diversity of the transition state
28. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions
29. Crystal structure of a Src-homology 3 (SH3) domain
30. Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments
31. The effect of selective deuteration on magnetization transfer in larger proteins
32. Non-native local interactions in protein folding and stability: Introducing a helical tendency in the all beta-sheet alpha-spectrin SH3 domain
33. The burst phase in ribonuclease A folding and solvent dependence of the unfolded state
34. Experiment and theory highlight role of native state topology in SH3 folding
35. Exploring structures in protein folding funnels with free energy functionals: The denatured ensemble
36. The denatured state (the other half of the folding equation) and its role in protein stability
37. Analysis of long-range interactions in a model denatured state of staphylococcal nuclease based on correlated changes in backbone dynamics
38. The concept of a random coil. Residual structure in peptides and denatured proteins
39. Molecular collapse: The rate-limiting step in two-state cytochrome c folding
40. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
41. Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain
42. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition
43. Different folding transition states may result in the same native structure
44. 15N chemical shift referencing in biomolecular NMR
45. NMR assignments as a basis for structural characterization of denatured states of proteins
46. Structural characterization of folded and unfolded states of an SH3 domain in equilibrium in aqueous buffer
47. NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions
48. Triple-resonance NOESY-based experiments with improved spectral resolution: Applications to structural characterization of unfolded, partially folded and folded proteins
49. Comprehensive NOE characterization of a partially folded large fragment of staphylococcal nuclease Δ131Δ, using NMR methods with improved resolution
50. Two-dimensional linear prediction for signals truncated in both dimensions