Denatured state thermodynamics: Residual structure, chain stiffness and scaling factors

Journal of Molecular Biology

Volumn 311, Issue 5, 2001, Pages 1091-1104

  Hammack, Barbara N ^a   Smith, Christopher R ^a   Bowler, Bruce E ^a  

^a UNIVERSITY OF DENVER   (United States)

Author keywords

Cytochrome c; Denatured state; Guanidine hydrochloride; Protein folding; Random coil

Indexed keywords

CYTOCHROME C; GUANIDINE; HEME; HISTIDINE; MONOMER;

ACETYLATION; ARTICLE; CONFORMATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE; RIGIDITY; SACCHAROMYCES CEREVISIAE; THERMODYNAMICS;

EID: 0035979801     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4909     Document Type: Article

References (80)

1. Protein folding mechanism: New methods and emerging ideas
2. Kinetic role of early intermediates in protein folding
3. Fast kinetics and mechanisms in protein folding
4. Protein folding intermediates and pathways studied by hydrogen exchange
5. Denatured states of proteins and their roles in folding and stability
6. The denatured state (the other half of the folding equation) and its role in protein stability
7. Structural analysis of non-native states of proteins by NMR methods
8. NMR determination of residual structure in a urea-denatured protein, the 434-repressor
9. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions
10. Similarities between the spectrin SH3 domain denatured states and its folding transition state
11. NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions
12. Protein folding: Assignment of the energetic changes of reversible chemical modifications to the folded or unfolded states
13. Partitioning the effects of changes in a protein to the folded or unfolded forms by using a thermodynamic cycle: A change in Escherichia coli thioredoxin does not affect the unfolded state
14. Interactions in nonnative and truncated forms of staphylococcal nuclease as indicated by mutational free energy changes
15. Rapid formation of the native 14-38 disulfide bond in the early stages of BPTI folding
16. Thermodynamic cycles as probes of structure in unfolded proteins
17. A histidine variant of yeast iso-1-cytochrome c that strongly affects the energetics of the denatured state
18. Measuring denatured state energetics: Deviations from random coil behavior and implications for the folding of iso-1-cytochrome c
19. Measuring the rate of intramolecular contact formation in polypeprides
20. The speed limit for protein folding measured by triplet-triplet energy transfer
21. Protein redesign
22. Using loop length variants to dissect the folding pathway of a four-helix-bundle protein
23. Reinterpretation of GCN4-N1 folding kinetics: Partial helix formation precedes dimerization in coiled coil folding
24. Protein folding dynamics: Quantitative comparison between theory and experiments
25. Contact order, transition state placement and the refolding rates of single domain proteins
26. 553, a small heme protein that lacks misligation in its unfolded state, folds with rapid two-state kinetics
27. Macrocyclization equilibria of polypeprides
28. Theoretical predictions of folding pathways using the proximity rule, with application to bovine pancreatic trypsin inhibitor
29. Time scales for the formation of the most probable tertiary contact in proteins with application to cytochrome c
30. The existence of heme-protein coordinate-covalent bonds in denaturant solvents
31. Cytochrome c folding traps are not due solely to histidine-heme ligation: Direct demonstration of a role for N-terminal amino group-heme ligation
32. 2-terminal residues by transamination
33. − strains deficient in the major N-terminal acetyl transferase of the yeast saccharomyces cerevisaie
34. α-acetyltransferase in the yeast Saccharomyces cerevisiae
35. Oxidation state-dependent conformational changes in cytochrome c
36. Denatured states of proteins
37. Staphylococcal nuclease: A showcase of m-value effects
38. The stability of globular proteins
39. Thermodynamics of denaturation of staphylococcal nuclease mutants: An intermediate state in protein folding
40. A lysine 73 → histidine variant of yeast iso-1-cytochrome c: Evidence for a native-like intermediate in the unfolding pathway and implications for m value effects
41. Effect of pH on formation of a nativelike intermediate on the unfolding pathway of a Lys73 → His variant of yeast iso-1-cytochrome c
42. Rational design of a more stable yeast iso-1-cytochrome c
43. NMR investigation of ferricytochrome c unfolding: Detection of an equilibrium unfolding intermediate and residual structure in the denatured state
44. The role of histidines 26 and 33 in the structural stabilization of cytochrome c
45. Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cyochrome c
46. The conformation of eukaryotic cytochrome c around residues 39, 57, 59 and 74
47. Helix stabilizing propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
48. The magnitude of changes in guanidine-HCl m-values in the protein, iso-1-cytochrome c, depends upon the substructure containing the mutation
49. Coupled kinetic traps in cytochrome c folding: His-heme misligation and proline isomerization
50. Disulfide bonds and the stability of globular proteins
51. Synthetic heme-peptide complexes
52. Hydrophobic interactions in metalloporphyrin-peptide complexes
53. Aromatic side-chain-porphyrin interactions in designed hemoproteins
54. Protein denaturation
55. Intrachain loops in polymers: Effects of excluded volume
56. Distribution functions in the interior of polymer chains
57. Conformational stability and activity of ribonuclease T1 with zero, one and two intact disulfide bonds
58. An inverse correlation between loop length and stability in a four helix bundle
59. Dissecting the disulphide-coupled folding pathway of bovine pancreatic trypsin inhibitor: Forming the first disulphide bonds in analogues of the reduced protein
60. Moments and distribution functions for polypeptide chains. Poly-L-alanine
61. Identification of the predominant non-native histidine ligand in unfolded cytochrome c
62. Random coil configurations of polypeptide copolymers
63. Structural characterization of folding intermediates in cytochrome c by H-exchange labeling and proton NMR
64. Site-directed replacement of the invariant lysine 73 of Saccharomyces cerevisiae iso-1-cytochrome c with all ribosomally encoded amino acids
65. An improved filamentous helper phage for generating single-stranded plasmid DNA
66. Inhibition of restriction endonuclease NciI cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis
67. Site-directed mutagenesis of virtually any plasmid by eliminating a unique site
68. 35S label as an aid to rapid DNA sequence determination
69. Deletion mapping of sequences essential for in vivo transcription of the iso-1-cytochrome c gene
70. Transformation of intact yeast cells treated with alkali cations
71. Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: Implications for the denatured state
72. Recovery of plasmids from yeast into Escherichia coli: Shuttle vectors
73. Characterization of the guanidine-HCl denatured state of iso-1-cytochrome c by infrared spectroscopy
74. Determination and analysis of urea and guanidine hydrochloride denaturation curves
75. The effects of hydrophilic to hydrophobic surface mutations on the denatured state of iso-1-cytochrome c: Investigation of aliphatic residues
76. Solvent denaturation
77. The specificities of yeast methionine aminopeptidase and acetylation of amino-terminal methionine in vivo