Partially formed native tertiary interactions in the A-state of cytochrome c

Journal of Molecular Biology

Volumn 289, Issue 3, 1999, Pages 639-644

  Hostetter, Daniel R ^a   Weatherly, Gresham T ^a   Beasley, James R ^a   Bortone, Kara ^a   Cohen, David S ^b   Finger, Shelly A ^a   Hardwidge, Philip ^a   Kakouras, Dionysios S ^a   Saunders, Aleister J ^b   Trojak, Sonja K ^a   Waldner, Jennifer C ^a   Pielak, Gary J ^a  

^a University of North Carolina at Chapel Hill   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

A state; Cytochrome c; Molten globule model; Saturation mutagenesis; Tertiary structure

Indexed keywords

CYTOCHROME C; ISOPROTEIN; LEUCINE;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; ENERGY; EUKARYOTE; MOLECULAR INTERACTION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; YEAST;

EUKARYOTA;

EID: 0033546385     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2764     Document Type: Article

References (43)

1. Allen, D. L. & Pielak, G. J. (1998). Baseline length and automated fitting of denaturation data. Protein Sci. 7, 1262-1263.
2. Beasley, J. R. (1995). Genetic and Thermodynamic Studies of Saccharomyces Cerevisiae Iso-1-cytochrome C with Substitutions at the Interface between the N- and C- Terminal Helices. Doctoral dissertation, The University of North Carolina, Chapel Hill, NC.
3. Beasley, J. R. & Pielak, G. J. (1996). Requirements for perpendicular helix pairing. Proteins: Struct. Funct. Genet. 26, 95-107.
4. Becktel, W. J. & Schellman, J. A. (1987). Protein stability curves. Biopolymers, 26, 1859-1877.
5. Berghuis, A. M. & Brayer, G. D. (1992). Oxidation state-dependent conformational changes in cytochrome c. J. Mol. Biol. 223, 959-976.
6. Betz, S. F. & Pielak, G. J. (1992). Introduction of a disulfide bond into cytochrome c stabilizes a compact denatured state. Biochemistry, 31, 12337-12344.
7. Brayer, G. D. & Murphy, M. E. P. (1996). Structural studies of eukaryotic cytochromes c. In Cytochrome C: A Multidisciplinary Approach (Scott, R. A. & Mauk, A. G., eds), pp. 103-166, University Science Books, Sausalito, CA.
8. Brems, D. N. & Stellwagen, E. (1983). Conformational transitions of a cytochrome c having a single thioether bridge. J. Biol. Chem. 258, 10919-10923.
9. Chothia, C. (1975). Structural invariants in protein folding. Nature, 254, 304-308.
10. Cohen, D. S. & Pielak, G. J. (1994). Stability of yeast iso-1-ferricytochrome c as a function of pH and temperature. Protein Sci. 3, 1253-1260.
11. Colón, W. & Roder, H. (1996). Kinetic intermediates in the formation of the cytochrome c molten globule. Nature Struct. Biol. 3, 1019-1025.
12. Colón, W., Elöve, G. A., Wakem, L. P., Sherman, F. & Roder, H. (1996). Side chain packing of the N- And C-terminal helices plays a critical role in the kinetics of cytochrome c folding. Biochemistry, 35, 5538-5549.
13. Cutler, R. L., Pielak, G. J., Mauk, A. G. & Smith, M. (1987). Replacement of cysteine-107 of Saccharomyces cerevisiae iso-1-cytochrome c with threonine: Improved stability of the mutant protein. Protein Eng. 1, 95-99.
14. Elöve, G. A., Bhuyan, A. K. & Roder, H. (1994). Kinetic mechanism of cytochrome c folding: Involvement of the heme and its ligands. Biochemistry, 33, 6925-6935.
15. Gao, Y., Boyd, J., Pielak, G. J. & Williams, R. J. P. (1991). Proton nuclear magnetic resonance as a probe of differences in structure between the C102T and F82S,C102T variants of iso-1-cytochrome c from the yeast Saccharomyces cerevisiae. Biochemistry, 30, 7033-7040.
16. Gietz, D., St. Jean, A., Woods, R. A. & Schiestl, R. H. (1992). Improved method for high efficiency transformation of intact yeast cells. Nucl. Acids Res. 20, 1425-.
17. Goto, Y., Calciano, L. J. & Fink, A. L. (1990). Acid-induced folding of proteins. Proc. Natl Acad. Sci. USA, 87, 573-577.
18. Hampsey, D. M., Das, G. & Sherman, F. (1986). Amino acid replacements in yeast iso-1-cytochrome c. J. Biol. Chem. 261, 3259-3271.
19. Hanahan, D., Jessee, J. & Bloom, F. R. (1983). Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166, 557-580.
20. Hanahan, D. (1995). Techniques for transformation of E. coli. In DNA Cloning: A Practical Approach (Glover, D. M. & Hames, B. D., eds), vol. 1, pp. 1-36, IRL Press, Oxford.
21. Hill, J., Donald, K. A., Griffiths, D. E. & Donald, K. (1991). DMSO-enhanced whole cell yeast transformation. Nucl. Acids Res. 19, 5791-.
22. Holzschu, D., Principio, L., Conklin, K. T., Hickey, D. R., Short, J., Rao, R., McLendon, G. & Sherman, F. (1987). Replacement of the invariant lysine 77 by arginine in yeast iso-1-cytochrome c results in enhanced and normal activities in vitro and in vivo. J. Biol. Chem. 262, 7125-7131.
23. Ito, H., Fukuda, Y., Murata, K. & Kimura, A. (1983). Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153, 163-168.
24. Jeng, M. F., Englander, S. W., Elöve, G. A., Wand, A. J. & Roder, H. (1990). Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry, 29, 10433-10437.
25. Kataoka, M., Hagihara, Y., Mihara, K. & Goto, Y. (1993). Molten globule of cytochrome c studied by small angle X-ray scattering. J. Mol. Biol. 229, 591-596.
26. Kunkel, T. A., Roberts, J. D. & Zakour, R. A. (1987). Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154, 367-382.
27. Margoliash, E. & Frohwirt, N. (1959). Spectrum of horse-heart cytochrome c. Biochem. J. 71, 570-572.
28. Marmorino, J. L. & Pielak, G. J. (1995). A native tertiary interaction stabilizes the A state of cytochrome c. Biochemistry, 34, 3140-3143.
29. Marmorino, J. L., Lehti, M. & Pielak, G. J. (1998). Native tertiary structure in an A-state. J. Mol. Biol. 275, 379-388.
30. Moore, G. R. & Pettigrew, G. W. (1990). Cytochromes C: Evolutionary, Structural and Physicochemical Aspects, Springer-Verlag, Berlin.
31. Myers, J. K., Pace, C. N. & Scholtz, J. M. (1997). Helix propensities are identical in proteins and peptides. Biochemistry, 36, 10923-10929.
32. Ner, S. S., Goodin, D. B., Pielak, G. J. & Smith, M. (1988). A rapid droplet method for Sanger dideoxy sequencing. Biotechniques, 6, 408-.
33. Pielak, G. J., Auld, D. S., Beasley, J. R., Betz, S. F., Cohen, D. S., Doyle, D. F., Finger, S. A., Fredericks, Z. L., Hilgen-Willis, S., Saunders, A. J. & Trojak, S. K. (1995). Protein thermal denaturation, side-chain models, and evolution: Amino acid substitutions at a conserved helix-helix interface. BiochemIstry, 34, 3268-3276.
34. Ptitsyn, O. (1996). How molten is the molten globule?. Nature Struct. Biol. 3, 488-490.
35. Radzicka, A. & Wolfenden, R. (1998). Comparing the polarities of the amino acids: Side-chain distribution coefficients between the polar and vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry, 27, 1664-1670.
36. Robinson, J. R. Jr, Strottman, J. M. & Stellwagen, E. (1983). A globular high spin form of ferricytochrome c. J. Biol. Chem. 258, 6772-6776.
37. Roder, H., Elöve, G. A. & Englander, S. W. (1988). Structural characterization of folding intermediates in cytochrome c by H-exchange labeling and proton NMR. Nature, 335, 700-704.
38. Rose, M. D. (1987). Isolation of genes by complementation in yeast. Methods Enzymol. 152, 481-504.
39. Schiestl, R. H. & Gietz, R. D. (1989). High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr. Genet. 16, 339-346.
40. Shastry, M. C. R. & Roder, H. (1998). Evidence for barrier-limited protein folding kinetics on the micro-second time scale. Nature Struct. Biol. 4, 385-392.
41. Sherman, F., Stewart, J. W., Parker, J. H., Inhaber, E., Shipman, N. A., Putterman, G. J., Gardisky, R. L. & Margoliash, E. (1968). The mutational alteration of the primary structure of yeast iso-1-cytochrome c. J. Biol. Chem. 243, 5446-5456.
42. Woods, A. C., Guilemette, J. G., Parrish, J. C., Smith, M. & Wallace, C. J. A. (1996). Synergy in protein engineering. J. Biol. Chem. 271, 32008-32015.
43. Zoller, M. J. & Smith, M. (1983). Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol. 100, 468-500.