Calculation of ensembles of structures representing the unfolded state of an SH3 domain

Journal of Molecular Biology

Volumn 308, Issue 5, 2001, Pages 1011-1032

  Choy, Wing Yiu ^a   Forman Kay, Julie D ^a,b  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

NMR; SH3 domain; Structure calculations; Unfolded state ensemble

Indexed keywords

INSECT PROTEIN;

ALGORITHM; ARTICLE; CALCULATION; CARBON NUCLEAR MAGNETIC RESONANCE; FLUORESCENCE ANALYSIS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 0035906650     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4750     Document Type: Article

References (58)

1. Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
2. Structural analysis of nonnative states of proteins by NMR methods
3. Similarities between the spectrin SH3 domain denatured state and its folding transition state
4. Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding
5. Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels
6. 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
7. Characterisation of protein unfolding by NMR diffusion measurements
8. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions
9. Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques
10. 13C dipole-dipole cross-correlated spin relaxation as a probe of dynamics in unfolded proteins: Application to the DrkN SH3 domain
11. NMR determination of residual structure in a urea-denatured protein, the 434-repressor
12. Where U and I meet
13. Structural characterization of folded and unfolded states of an SH3 domain in equilibrium in aqueous buffer
14. 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium
15. 15N resonance assignments of the N-terminal SH3 domain of drk in folded and unfolded states using enhanced-sensitivity pulsed field gradient NMR techniques
16. Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer
17. Characterization of the backbone dynamics of folded and denatured states of an SH3 domain
18. NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions
19. Triple-resonance NOESY-based experiments with improved spectral resolution: Applications to structural characterization of unfolded, partially folded and folded proteins
20. 13C cross-correlation NMR experiments: Application to the N-terminal SH3 domain from drk
21. Refinement of the NMR structures for acyl carrier protein with scalar coupling data
22. Structure refinement using time-averaged J-coupling constant restraints
23. Time- and ensemble-averaged direct NOE restraints
24. Conformational variability of solution nuclear magnetic resonance structures
25. Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble
26. FINGAR: A new genetic algorithm-based method for fitting NMR data
27. The effect of motional averaging on the calculation of NMR-derived structural properties
28. Elucidation of solution structures by conformer population analysis of NOE data
29. Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?
30. Conformations of the dermenkephalin backbone in DMSO solution by a new approach to the solution conformations of flexible peptides
31. Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformational analysis anf NMR spectroscopy
32. A fast method to sample real protein conformational space
33. Comparison between the φ distribution of the amino acids in the protein database and NMR data indicates that amino acids have various φ propensities in the random coil conformation
34. Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations
35. Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements
36. Protein chemical shift analysis: A practical guide
37. 13C nuclear magnetic resonance chemical shifts
38. Hydration of denatured and molten globule proteins
39. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure
40. Dimensions of portein random coils
41. Energetics of protein structure
42. Theory for the folding and stability of globular proteins
43. Modeling the effects of mutations on the denatured states of proteins
44. Contact order, transition state placement and the refolding rates of single domain proteins
45. Environment of tryptophan side chains in proteins
46. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
47. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
48. PROCHECK: Program to check the stereochemical quality of protein structures
49. Prediction and structural characterization of an independently folding substructure in the src SH3 domain
50. Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states
51. Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability
52. Crystallography & NMR system: A new software system for macromolecular structure determination
53. 15N-enriched proteins
54. Protein backbone angle restraints from searching a database for chemical shift and sequence homology
55. Stereochemical quality of protein structure coordinates
56. A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix-coil transitions
57. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
58. MOLMOL: A program for display and analysis of macromolecular structures