Communication of stabilizing energy between substructures of a protein

Biochemistry

Volumn 44, Issue 7, 2005, Pages 2349-2359

  Kristinsson, Richard ^a   Bowler, Bruce E ^a  

^a UNIVERSITY OF DENVER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALKALINITY; BIOCHEMISTRY; MUTAGENESIS; PH EFFECTS; THERMODYNAMICS;

CYTOCHROMES; MUTATIONS; STABILIZING ENERGY; THERMODYNAMIC COMMUNICATION;

PROTEINS;

CYTOCHROME C; GUANIDINE; HISTIDINE; ISOCYTOCHROME C1; LEUCINE; LYSINE; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; ENERGY; MUTATION; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMODYNAMICS;

AMINO ACID SUBSTITUTION; ASPARAGINE; CYTOCHROMES C; ENZYME STABILITY; GUANIDINE; HYDROGEN-ION CONCENTRATION; ISOENZYMES; LEUCINE; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE PROTEINS; TEMPERATURE; THERMODYNAMICS; VARIATION (GENETICS);

EID: 14044257270     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048141r     Document Type: Article

References (47)

1. Dill, K. A. (1990) Dominant forces in protein folding, Biochemistry 29, 7133-7155.
2. Pace, C. N., Shirley, B. A., McNutt, M., and Gajiwala, K. (1996) Forces contributing to the conformational stability of proteins, FASEB J. 10, 75-83.
3. Suel, G. M., Lockless, S. W., Wall, M. A., and Ranganathan, R. (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins, Nat. Struct. Biol. 10, 59-69.
4. Englander, S. W., Mayne, L., and Rumbley, J. N. (2002) Submolecular cooperativity produces multi-state protein unfolding and refolding, Biophys. Chem. 101-102, 57-65.
5. Chamberlain, A. K., and Marqusee, S. (2000) Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms, Adv. Protein Chem. 53, 283-328.
6. Bai, Y., Sosnick, T. R., Mayne, L., and Englander, S. W. (1995) Protein folding intermediates: Native-state hydrogen exchange, Science 269, 192-197.
7. Xu, Y., Mayne, L., and Englander, S. W. (1998) Evidence for an unfolding and refolding pathway in cytochrome c, Nat. Struct. Biol. 5, 774-778.
8. Milne, J. S., Xu, Y., Mayne, L. C., and Englander, S. W. (1999) Experimental study of the protein folding landscape: Unfolding reactions in Cytochrome c, J. Mol. Biol. 290, 811-822.
9. Hoang, L., Bédard, S., Krishna, M. M. G., Lin, Y., and Englander, S. W. (2002) Cytochrome c folding pathway: Kinetic native state hydrogen exchange. Proc. Natl. Acad. Sci. U.S.A. 99, 12173-12178.
10. Krishna, M. M. G., Lin, Y., Rumbley, J. N., and Englander, S. W. (2003) Cooperative omega loops in cytochrome c: Role in folding and function, J. Mol. Biol. 331, 29-36.
11. Krishna, M. M. G., Lin, Y., Mayne, L., and Englander, S. W. (2003) Intimate view of a kinetic protein folding intermediate: Residue-resolved structure, interaction, stability, folding and unfolding rates, homogeneity, J. Mol. Biol. 334, 501-513.
12. 15N]-labeled oxidized and reduced iso-1-cytochrome c, Biochemistry 38, 4493-4503.
13. 15N relaxation measurements for oxidized and reduced iso-1-cytochrome c, Biochemistry 38, 4480-4492.
14. Marmorino, J. L., Auld, D. S., Betz, S. F., Doyle, D. F., Young, G. B., and Pielak, G. J. (1993) Amide proton exchange rates of oxidized and reduced Saccharomyces cerevisiae iso-1-cytochrome c, Protein Sci. 2, 1966-1974.
15. Goedken, E. R., and Marqusee, S. (2001) Native-state energetics of a thermostabilized variant of Ribonuclease HI, J. Mol. Biol. 314, 863-871.
16. Spudich, G., Lorenz, S., and Marqusee, S. (2002) Propagation of a single destabilizing mutation throughout the Escherichia coli ribonuclease HI native state, Protein Sci. 11, 522-528.
17. Luque, I., Leavitt, S. A., and Freire, E. (2002) The linkage between protein folding and functional cooperativity: Two sides of the same coin, Annu. Rev. Biophys. Biomol. Struct. 31, 235-256.
18. Godbole, S., Dong, A., Garbin, K., and Bowler, B. E. (1997) 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, Biochemistry 36, 119-126.
19. Godbole, S., and Bowler, B. E. (1999) Effect of pH on formation of a nativelike intermediate on the unfolding pathway of a Lys 73 → His variant of yeast iso-1-cytochrome c, Biochemistry 38, 487-495.
20. Nelson, C. J., and Bowler, B. E. (2000) pH dependence of formation of a partially unfolded state of a Lys 73 → His variant of iso-1-cytochrome c: Implications for the alkaline conformational transition of cytochrome c, Biochemistry 39, 13584-13594.
21. Nelson, C. J., LaConte, M. J., and Bowler, B. E. (2001) Direct detection of heat and cold denaturation for partial unfolding of a protein, J. Am. Chem. Soc. 123, 7453-7454.
22. Rosell, F. I., Ferrer, J. C., and Mauk, A. G. (1998) Proton-linked protein conformational switching: Definition of the alkaline conformational transition of yeast iso-1-ferricytochrome c, J. Am. Chem. Soc. 120, 11234-11245.
23. Martinez, R. M., and Bowler, B. E. (2004) Proton-mediated dynamics of the alkaline conformational transition of yeast iso-1-cytochrome c, J. Am. Chem. Soc. 126, 6751-6758.
24. Wilson, M. T., and Greenwood, C. (1996) The alkaline transition in ferricytochrome c, in Cytochrome c: A Multidisciplinary Approach (Scott, R. A., and Mauk, A. G., Eds) pp 611-634, University Science Books, Sausalito, CA.
25. Hoang, L., Maity, H., Krishna, M. M. G., Lin, Y., and Englander, S. W. (2003) Folding units govern the cytochrome c alkaline transition, J. Mol. Biol. 331, 37-43.
26. Das, G., Hickey, D. R., McLendon, D., McLendon, G., and Sherman, F. (1989) Dramatic thermostabilization of yeast iso-1-cytochrome c by an asparagine → isoleucine replacement at position 57, Proc. Natl. Acad. Sci. U.S.A. 86, 496-499.
27. Hickey, D. R., Berghuis, A. M., Lafond, G., Jaeger, J. A., Cardillo, T. S., McLendon, D., Das, G., Sherman, F., Brayer, G. D., and McLendon, G. (1991) Enhanced thermodynamic stabilities of yeast iso-1-cytochromes c with amino acid replacements at positions 52 and 102, J. Biol. Chem. 266, 11686-11694.
28. Linske-O'Connell, L. I., Sherman, F., and McLendon, G. (1995) Stabilizing amino acid replacements at position 52 in yeast iso-1-cytochrome c: In vivo and in vitro effects. Biochemistry 34, 7094-7102.
29. Berghuis, A. M., and Brayer, G. D. (1992) Oxidation state-dependent conformational changes in cytochrome c, J. Mol. Biol. 223, 959-976.
30. Sobolev, V., Sorokine, A., Lusky, J., and Abola, E. E. (1999) Automated analysis of interatomic contacts in proteins, Bioinformatics 15, 327-332.
31. Smith, C. R., Mateljevic, N., and Bowler, B. E. (2002) Effects of topology and excluded volume on protein denatured state conformational properties, Biochemistry 41, 10173-10181.
32. Deng, W. P. D., and Nickoloff, J. A. (1992) Site-directed mutagenesis of virtually any plasmid by eliminating a unique site, Anal. Biochem. 200, 81-88.
33. Ito, H., Fukada, Y., Murata, K., and Kimura, K. (1983) Transformation of intact yeast cells treated with alkali cations, J. Bacteriol. 153, 163-168.
34. Bowler, B. E., May, K., Zaragoza, T., York, P., Dong, A., and Caughey, W. S. (1993) Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: Implications for the denatured state, Biochemistry 32, 183-190.
35. Strathern, J. N., and Higgins, D. R. (1991) Recovery of plasmids from yeast into Escherichia coli: shuttle vectors, Methods Enzymol. 194, 319-329.
36. Bowler, B. E., Dong, A., and Caughey, W. S. (1994) Characterization of the guanidine hydrochloride-denatured state of iso-1-cytochrome c by infrared spectroscopy, Biochemistry 33, 2402-2408.
37. Pace, C. N. (1986) Determination and analysis of urea and guanidine hydrochloride denaturation curves, Methods Enzymol. 26, 266-280.
38. Herrmann, L., Bowler, B. E., Dong, A., and Caughey, W. S. (1995) The effects of hydrophilic to hydrophobic surface mutations on the denatured state of iso-1-cytochrome c: Investigation of aliphatic residues, Biochemistry 34, 3040-3047.
39. Godbole, S., Hammack, B., and Bowler, B. E. (2000) Measuring denatured state energetics: Deviations from random coil behavior and implications for the folding of iso-1-cytochrome c, J. Mol. Biol. 296, 217-228.
40. Santoro, M. M., and Bolen, D. W. (1988) Unfolding free energy determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants, Biochemistry 27, 8063-8068.
41. Moore, G. R., and Pettigrew, G. (1990) Cytochrome c: Evolutionary, Structural and Physicochemical Aspects, pp 69-70, Springer-Verlag, New York.
42. Zhang, M.-M., Ford, C. D., and Bowler, B. E. (2004) Estimation of the compaction of the denatured state by a protein variant involved in a reverse hydrophobic effect, Protein J. 23, 119-126.
43. Pace, C. N. (1975) The stability of globular proteins, CRC Crit. Rev. Biochem. 3, 1-43.
44. Nozaki, Y., and Tanford, C. (1967) Acid-base titrations in concentrated guanidine hydrochloride. Dissociation constants of the guanidinium ion and of some amino acids, J. Am. Chem. Soc. 89, 736-742.
45. Wandschneider, E., and Bowler, B. E. (2004) Conformational properties of the iso-1-cytochrome c denatured state: Dependence on guanidine hydrochloride concentration, J. Mol. Biol. 339, 185-197.
46. Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding, Protein Sci. 4, 2138-2148.
47. Assfalg, M., Bertini, I., Dolfi, A., Turano, P., Mauk, A. G., Rosell, F. I., and Gray, H. B. (2003) Structural model for an alkaline form of ferricytochrome c, J. Am. Chem. Soc. 125, 2913-2922.