Structural examination of Φ-value analysis in protein folding

Biochemistry

Volumn 43, Issue 45, 2004, Pages 14325-14331

  Feng, Hanqiao ^a   Vu, Ngoc Diep ^a   Zhou, Zheng ^a   Bai, Yawen ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CONFORMATIONS; HYDROPHOBICITY; MOLECULAR STRUCTURE; MUTAGENESIS;

MUTATIONS; PROTEIN FOLDING;

PROTEINS;

CYTOCHROME; MUTANT PROTEIN; PROTEIN RD APOCYTOCHROME; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL REACTION KINETICS; ENERGY TRANSFER; HYDROPHOBICITY; MUTATION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALANINE; AMINO ACID SUBSTITUTION; APOENZYMES; CYTOCHROME B GROUP; DEUTERIUM EXCHANGE MEASUREMENT; ESCHERICHIA COLI PROTEINS; HYDROPHOBICITY; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHENYLALANINE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 8544268672     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048126m     Document Type: Article

References (33)

1. Goldenberg, D. P. (1999) Finding the right fold, Nat. Struct. Biol. 6, 987-990.
2. Matouschek, A., Serrano, L., and Fersht, A. R. (1992) The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure, J. Mol. Biol. 224, 819-835.
3. Raschke, T. M., Kho, J., and Marqusee, S. (1999) Confirmation of the hierarchical folding of RNase H: a protein engineering study, Nat. Struct. Biol. 6, 825-831.
4. Bulaj, G., and Goldenberg, D. P. (2001) Φ-values for BPTI folding intermediates and implications for transition state analysis, Nat. Struct. Biol. 8, 326-330.
5. Matthews, C. R., and Hurle, M. R. (1987) Mutant sequences as probes of protein folding mechanisms, BioEssays 6, 254-257.
6. Fersht, A. R., Matouschek, A., and Serrano, L. (1992) The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding, J. Mol. Biol. 224, 771-782.
7. Li, A., and Daggett, V. (1994) Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2, Proc. Natl. Acad. Sci. U.S.A. 91, 10430-10434.
8. Vendruscolo, M., Paci, E., Dobson, C. M., and Karplus, M. (2001) Three key residues form a critical contact network in a protein folding transition state, Nature 409, 641-645.
9. Hubner, I. A., Shimada, J., and Shakhnovich, E. E. (2004) Commitment and nucleation in the protein G transition state, J. Mol. Biol. 336, 745-761.
10. Bai, Y., Sosnick, T. R., Mayne, L., and Englander, S. W. (1995) Protein folding intermediates: native-state hydrogen exchange, Science 269, 192-197.
11. Chu, R. A., Pei, W. H., Takei, J., and Bai, Y. (2002) Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein, Biochemistry 41, 7998-8003.
12. Feng, H., Takei, J., Lipsitz, R., Tjandra, N., and Bai, Y. (2003) Specific non-native hydrophobic interactions in a hidden intermediate: implications for protien folding, Biochemistry 42, 12461-12465.
13. Takei, J., Pei, W., Vu, D., and Bai, Y. (2002) Populating partially unfolded forms by hydrogen exchange-directed protein engineering, Biochemistry 41, 12308-12312.
14. Pace, C. N. (1986) Determination and analysis of urea and guanidinium hydrochloride denaturation curves, Methods Enzymol. 131, 266-280.
15. Minor, D. L., Jr., and Kim, P. S. (1994) Measurement of the β-sheet-forming propensities of amino acids, Nature 367, 660-663.
16. Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX Pipes, J. Biomol. NMR 6, 277-293.
17. Johnson, B. A., and Blevins, R. A. (1994) NMRview: a computer program for the visualization and analysis of NMR data, J. Biomol. NMR 4, 603-614.
18. Santoro, M. M., and Bolen, D. M. (1992) A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range, Biochemistry 31, 4901-4907.
19. 15N-enriched proteins, J. Am. Chem. Soc. 115, 7772-7777.
20. Schwieters, C. D., Kuszewski, J. J., Tjandra, N., and Clore, G. M. (2003) The Xplor-NIH NMR Molecular Structure Determination Package, J. Magn. Reson. 160, 65-73.
21. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
22. 562 selected by phage-display and proteolysis, Proteins 56, 426-429.
23. Sanchez, I., and Kiefhaber, T. (2003) Origin of unusual Φ-values in protein folding, J. Mol. Biol. 334, 1077-1085.
24. 562 examined by the dependence of hydrogen exchange on hydrostatic pressure, Biochemistry 37, 9877-9883.
25. Bai, Y., Milne, J. S., Mayne, L., and Englander, S. W. (1994) Protein stability parameters measured by hydrogen exchange, Proteins 20, 4-14.
26. Huyghues-Despointes, B. M., Scholtz, J. M., and Pace, C. N. (1999) Protein conformational stabilities can be determined from hydrogen exchange rates, Nat. Struct. Biol. 6, 910-912.
27. Kim, D. E., Fisher, C., and Baker, D. (2000) A breakdown of symmetry in the folding transition state of protein L, J. Mol. Biol. 298, 971-984.
28. Itzhaki, L. S., Otzen, D. E., and Fersht, A. R. (1995) 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, J. Mol. Biol. 254, 260-288.
29. Li, L., Mirny, L. A., and Shakhnovich, E. I. (2000) Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus, Nat. Struct. Biol. 7, 336-342.
30. Krantz, B. A., Dothager, R. S., and Sosnick, T. R. (2004) Discerning the structure and energy of multiple transition states in protein folding using Φ-analysis, J. Mol. Biol. 337, 463-475.
31. Crane, J. C., Koepf, E. K., Kelly, J. W., and Gruebele, M. (2000) Mapping the transition state of the WW domain β-sheet, J. Mol. Biol. 298, 283-292.
32. Ozkan, S. B., Bahar, I., and Dill, K. A. (2001) Transition states and the meaning of Φ-values in the protein folding kinetics, Nat. Struct. Biol. 8, 765-769.
33. Onuchic, J., and Wolynes, P. G. (2004) Theory of protein folding, Curr. Opin. Struct. Biol. 14, 70-75.