Mapping the folding pathway of an immunoglobulin domain: Structural detail from phi value analysis and movement of the transition state

Structure

Volumn 9, Issue 5, 2001, Pages 355-366

  Fowler, S B ^a   Clarke, J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Beta sheet; Homologous proteins; Immunoglobulin; Protein folding; Topology

Indexed keywords

ALANINE; CONNECTIN; CORE PROTEIN; CYSTEINE; FIBRONECTIN; GLUTAMIC ACID; GLYCINE; HISTIDINE; IMMUNOGLOBULIN; ISOLEUCINE; LEUCINE; METHIONINE; MUTANT PROTEIN; PHENYLALANINE; PROTEIN; PROTEIN TI 127; SERINE; SOLVENT; UNCLASSIFIED DRUG; VALINE;

AMINO TERMINAL SEQUENCE; ARTICLE; COMPARATIVE STUDY; GENETIC ENGINEERING; IMMUNOGLOBULIN STRUCTURE; PEPTIDE MAPPING; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY;

HUMANS; IMMUNOGLOBULINS; KINETICS; MUSCLE PROTEINS; MUTAGENESIS; PEPTIDE MAPPING; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN KINASES; PROTEIN STRUCTURE, TERTIARY;

EID: 0034984382     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(01)00596-2     Document Type: Article

References (69)

1. Conserved residues and the mechanism of protein folding
2. Protein folding and protein evolution: Common folding nucleus in different subfamilies of c-type cytochromes?
3. Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
4. Sequence evolution and the mechanism of protein folding
5. Evolutionary conservation in protein folding kinetics
6. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
7. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
8. Different folding transition states may result in the same native structure
9. Folding mechanism of three structurally similar beta-sheet proteins
10. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9
11. Beta-sheet proteins with nearly identical structures have different folding intermediates
12. Conservation of folding pathways in evolutionarily distant globin sequences
13. A surprising simplicity to protein folding
14. Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability and the extended nucleus mechanism
15. Topology, stability, sequence and length: Defining the determinants of two-state protein folding kinetics
16. The immunoglobulin fold. Structural classification, sequence patterns and common core
17. Folding studies of Ig-like beta-sandwich proteins suggest a common folding pathway
18. Population statistics of protein structures: Lessons from structural classifications
19. The Pfam protein families database
20. Structure and stability of an immunoglobulin superfamily domain from twitchin, a muscle protein of the nematode Caenorhabditis elegans
21. The effect of boundary selection on the stability and folding of the third fibronectin domain from human tenascin
22. Folding of beta-sandwich proteins: Three-state transition of a fibronectin type III module
23. Two proteins with the same structure respond very differently to mutation- the role of plasticity in protein stability
24. Conservation of folding and stability within a protein family: A tyrosine corner as a structural cul-de-sac
25. The folding of an immunoglobulin-like greek key protein is defined by a common core nucleus and regions constrained by topology
26. The folding nucleus of a fibronectin type III domain is composed of core residues of the conserved immunoglobulin-like fold
27. Effects of core mutations on the folding of a beta-sheet protein: Implications for backbone organization in the I-state
28. The assembly of immunoglobulin-like modules in titin: Implications for muscle elasticity
29. Mechanical and chemical unfolding of a single protein: A comparison
30. Atomic force microscopy reveals the mechanical design of a modular protein
31. Immunoglobulin-type domains of titin: Same fold, different stability?
32. The folding and stability of titin immunoglobulin-like modules with implications for the mechanism of elasticity
33. Immunoglobulin-like modules from titin I-band: Extensible components of muscle elasticity
34. The elastic I-band region of titin is assembled in a "modular" fashion by weakly interacting Ig-like domains
35. Acquisition of native beta-strand topology during the rapid collapse phase of protein folding
36. Module-module interactions in the cell binding region of fibronectin: Stability, flexibility and specificity
37. Folding kinetics of the SH3 domain of PI3 kinase by real-time NMR combined with optical spectroscopy
38. The folding kinetics and thermodynamics of the Fyn-SH3 domain
39. Experiment and theory highlight role of native state topology in SH3 folding
40. Capping and alpha-helix stability
41. Structural factors contributing to the hydrophobic effect: The partly exposed hydrophobic minicore in chymotrypsin inhibitor 2
42. Context dependent nature of destabilising mutants on the stability of FKBP12
43. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
44. Characterizing transition states in protein folding: An essential step in the puzzle
45. Movement of the position of the transition state in protein folding
46. The changing nature of the protein folding transition state: Implications for the shape of the free-energy profile for folding
47. Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots
48. The energy landscape of a fast-folding protein mapped by Ala→Gly substitutions
49. A correlation of reaction rates
50. Application of physical-organic chemistry to engineered mutants of proteins: Hammond postulate behaviour in the transitional state of protein folding
51. 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
52. Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: Observation of Hammond behavior for the gross structure of the transition state and anti-Hammond behavior for structural elements for unfolding/folding of barnase
53. From snapshot to movie: phi analysis of protein folding transition states taken one step further
54. Movement of the intermediate and rate determining transition state of barnase on the energy landscape with changing temperature
55. Combined molecular dynamics and phi value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects
56. How evolution makes proteins fold quickly
57. Conserved residues and their role in the structure, function, and stability of acyl-coenzyme A binding protein
58. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition
59. Folding dynamics of the src SH3 domain
60. Functional rapidly folding proteins from simplified amino acid sequences
61. A breakdown of symmetry in the folding transition state of protein L.
62. Critical role of beta-hairpin formation in protein G
63. Determination and analysis of urea and guanidinium hydrochloride denaturation curves
64. Engineered dilsulfide bonds as probes of the folding pathway of barnase: Increasing the stability of proteins against the rate of denaturation
65. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
66. Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains
67. MolScript, a program to produce both detailed and schematic plots of protein structures