Protein hydrogen exchange mechanism: Local fluctuations

Protein Science

Volumn 12, Issue 1, 2003, Pages 153-160

  Maity, Haripada ^a   Lim, Woon Ki ^a,b   Rumbley, Jon N ^a   Englander, S Walter ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b Pusan National University   (South Korea)

Author keywords

Cytochrome c; Glycine mutations; Hydrogen exchange; Local fluctuation

Indexed keywords

CYTOCHROME C; GLYCINE; HYDROGEN; LEUCINE; LYSINE; PROTEIN; SOLVENT;

ARTICLE; CATALYST; MUTATION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN HYDROGEN EXCHANGE; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN TRANSPORT; PROTON TRANSPORT; STRUCTURE ANALYSIS;

AMIDES; AMINO ACID SUBSTITUTION; ANIMALS; CYTOCHROME C GROUP; DEUTERIUM; GLYCINE; HORSES; HYDROGEN; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; LYSINE; MOTION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTONS; RECOMBINANT PROTEINS; SOLVENTS; THERMODYNAMICS;

EID: 0037214137     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0225803     Document Type: Article

References (60)

1. Bai, Y., Milne, J.S., Mayne, L., and Englander, S. W. 1993. Primary structure effects on peptide group hydrogen exchange. Proteins Struct. Funct. Genet. 17: 75-86.
2. -, 1994. Protein stability parameters measured by hydrogen exchange. Proteins Struct. Funct. Genet. 20: 4-14.
3. Bai, Y., Sosnick, T.R., Mayne, L., and Englander, S.W. 1995. Protein folding intermediates: Native-state hydrogen exchange. Science 269: 192-197.
4. Barksdale, A.D. and Rosenberg, A. 1982. Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. In Methods of Biochemical Analysis (ed. D. Glick), p. 113. John Wiley & Sons, New York, NY.
5. Berger, A. and Linderstrøm-Lang, K. 1957. Deuterium exchange of poly-D,L-alanine in aqueous solution. Arch. Biochem. Biophys. 69: 106-118.
6. Bhuyan, A.K. and Udgaonkar, J.B. 1998. Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange. Proteins Struct. Funct. Genet. 30: 295-308.
7. Bryan, W.D. 1970. The mechanism of hydrogen exchange in proteins. Recent Prog. Surf. Sci. 3: 101-120.
8. Buck, M., Radford, S.E., and Dobson, C.M. 1994. Amide hydrogen exchange in a highly denatured state. Hen egg-white lysozyme in urea. J. Mol. Biol. 237: 247-254.
9. Chamberlain, A.K. and Marqusee, S. 1997. Touring the landscapes: Partially folded proteins examined by hydrogen exchange. Structure 5: 859-863.
10. Chamberlain, A.K., Handel, T.M., and Marqusee, S. 1996. Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat. Struct. Biol. 3: 782-787.
11. Chu, R., Pei, W., 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. Connelly, G.P., Bai, Y., Jeng, M.F., and Englander, S.W. 1993. Isotope effects in peptide group hydrogen exchange. Proteins Struct. Funct. Genet. 17: 87-92.
13. Eigen, M. 1964. Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Angew. Chem. Int. Ed. Eng. 3: 1-19.
14. Englander, S.W. and Kallenbach, N.R. 1983. Hydrogen exchange and structural dynamics of proteins and nucleic-acids. Q. Rev. Biophys. 16: 521-655.
15. Englander, S.W., Mayne. L., and Rumbley, J. 2002. Submolecular cooperativity produces multi-state protein unfolding and refolding. Biophys. Chem. (in press).
16. Fuentes, E.J. and Wand, A.J. 1998. Local stability and dynamics of apocytochrome b562 examined by the dependence of hydrogen exchange on hydrostatic pressure. Biochemistry 37: 9877-9883.
17. Haslam, J.L. and Eyring, E.M. 1967. Deuterium oxide solvent isotope effects on N-H...O, O-H...N, and N-H...N intramolecular hydrogen bonds. J. Phys. Chem. 71: 4470-4475.
18. Hiller, R., Zhou, Z.H., Adams, M.W., and Englander, S.W. 1997. Stability and dynamics in a hyperthermophilic protein with melting temperature close to 200°C. Proc. Natl. Acad. Sci. 94: 11329-11332.
19. Hilser, V.J. and Freire, E. 1996. Structure-based calculation of the equilibrium folding pathway of proteins: Correlation with hydrogen-exchange protection factors. J. Mol. Biol. 262: 756-772.
20. Hilton, B.D., Trudeau, K., and Woodward, C.K. 1981. Hydrogen exchange rates in pancreatic trypsin inhibitor are not correlated to thermal stability in urea. Biochemistry 20: 4697-4703.
21. 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. 99: 12173-12178.
22. Huyghues-Despointes, B.M., Pace, C.N., Englander, S.W., and Scholtz, J.M. 2001. Measuring the conformational stability of a protein by hydrogen exchange. Methods Mol. Biol. 168: 69-92.
23. Hvidt, A. and Nielsen, S.O. 1966. Hydrogen exchange in proteins. Adv. Protein Chem. 21: 287-386.
24. Jeng, M.-F. and Englander, S.W. 1991. Stable submolecular folding units in a non-compact form of cytochrome c. J. Mol. Biol. 221: 1045-1061.
25. Kim, K.S. and Woodward, C. 1993. Protein internal flexibility and global stability: Effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor. Biochemistry 32: 9609-9613.
26. Krantz, B.A., Mayne, L., Rumbley, J.N., Englander, S.W., and Sosnick, T.R. 2002. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J. Mol. Biol. (in press).
27. Linderstrøm-Lang, K.U. 1958. Deuterium exchange and protein structure. In: Symposium on Protein Structure (ed. A. Neuberger). London: Methuen.
28. Llinas, M., Gillespie, B., Dahlquist F.W., and Marqusee, S. 1999. The energetics of T4 lysozyme reveal a hierarchy of conformations. Nat. Struct. Biol. 6: 1072-1078.
29. Lumry, R. and Rosenberg, A. 1975. The mobile defect hypothesis of protein function. Col. Int. C.N.R.S. L'Eau Syst. Biol. 246: 55-63.
30. Luo, P. and Baldwin, R.L. 1997. Mechanism of helix induction by trifluoroethanol: A framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry 36: 8413-8421.
31. Marcus, Y. 1994. A simple empirical model describing the thermodynamics of hydration of ions of widely varying charges, sizes, and shapes. Biophys. Chem. 51: 111-127.
32. Mayne, L. and Englander, S.W. 2000. Two-state vs. multistate protein unfolding studied by optical melting and hydrogen exchange. Protein Sci. 9: 1873-1877.
33. Mayo, S.L. and Baldwin, R.L. 1993. Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A. Science 262: 873-876.
34. Miller, D.W. and Dill, K.A. 1995. A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci. 4: 1860-1873.
35. Milne, J.S., Mayne, L., Roder, H., Wand, A.J., and Englander, S.W. 1998. Determinants of protein hydrogen exchange studied in equine cytochrome c. Protein Sci. 7: 739-745.
36. 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.
37. Molday, R.S., Englander, S.W., and Kallen, R.G. 1972. Primary structure effects on peptide group hydrogen exchange. Biochemistry 11: 150-158.
38. Nakanishi, M., Tsuboi, M., and Ikegami, A. 1973. Fluctuation of the lysozyme structure. II. Effects of temperature and binding of inhibitors. J. Mol. Biol. 75: 673-682.
39. Nozaki, Y. 1972. The preparation of guanidinium chloride. Methods Enzymol. 26: 43-50.
40. Pace, C.N. 1975, The stability of globular proteins. CRC Crit. Rev. Biochem. 3: 1-43.
41. Parker, M.J., Dempsey, C.E., Lorch, M., and Clarke, A.R. 1997. Acquisition of native beta-strand topology during the rapid collapse phase of protein folding. Biochemistry 36: 13396-13405.
42. Richards, F.M. 1979. Packing defects, cavities, volume fluctuations, and access to the interior of proteins, including some general comments on surface area and protein structure. Carlsberg Res. Commun. 44: 47-63.
43. Robertson, A.D. and Baldwin, R.L. 1991. Hydrogen exchange in thermally denatured ribonuclease A. Biochemistry 30: 9907-9914.
44. Roder, H., Wagner, G., and Wuthrich, K. 1985. Individual amide proton exchange rates in thermally unfolded basic pancreatic trypsin inhibitor. Biochemistry 24: 7407-7411.
45. Rose, M.C. and Stuehr, J. 1968. Kinetics of proton transfer reactions in aqueous solutions: Rates of internally hydrogen bonded systems. J. Am. Chem. Soc. 90: 7205-7209.
46. Rosenberg, A. and Enberg, J. 1969. Studies of hydrogen exchange in proteins. II. The reversible thermal unfolding of chymotrypsinogen A as studied by exchange kinetics. J. Biol. Chem. 244: 6153-6159.
47. Rumbley, J.N., Hoang, L., Mayne, L., and Englander, S.W. 2001. An amino acid code for protein folding. Proc. Natl. Acad. Sci. 98: 105-112.
48. Rumbley, J.N., Hoang, L., and Englander, S.W. 2002. Recombinant equine cytochrome c in E. coli: High level expression, characterization, and folding and assembly mutants. Biochemistry (in press).
49. Salemme, F.R. 1981. Conformational and geometrical properties of beta-sheets in proteins. 3. Isotropically stressed configurations. J. Mol. Biol. 146: 143-156.
50. Scholtz, J.M. and Robertson, A.D. 1995. Hydrogen exchange techniques. Methods Mol. Biol. 40: 291-311.
51. Serrano, L., Neira, J.L., Sancho, J., and Fersht, A.R. 1992. Effect of alanine versus glycine in alpha-helices on protein stability. Nature 356: 453-455.
52. Srivastava, A.K., and Sauer, R.T. 2000. Evidence for partial secondary structure formation in the transition state for arc repressor refolding and dimerization. Biochemistry 39: 8308-8314.
53. Tsuboi, M. and Nakanishi, M. 1979. Overall and localized fluctuation in the structure of a protein molecule. Adv. Biophys. 12: 101-130.
54. Wagner, G. and Wuthrich, K. 1982. Amide proton exchange and surface conformation of BPTI in solution: Studies with 2D NMR. J. Mol. Biol. 160: 343-361.
55. Wand, A.J. and Englander, S.W. 1996. Protein complexes studied by NMR spectroscopy. Curr. Opin. Biotechnol. 7: 403-408.
56. Wishart, D.S. and Case, D.A. 2001. Use of chemical shifts in macromolecular structure determination. Methods Enzymol. 338: 3-34.
57. Woodward, C.K. 1994. Hydrogen exchange rates and protein folding. Curr. Opin. Struct. Biol. 4: 112-116.
58. Woodward, C.K. and Hilton, B.D. 1979. Hydrogen exchange kinetics and internal motions in proteins and nucleic acids. Annu. Rev. Biophys. Bioeng. 8: 99-127.
59. Wooll, J.O., Wrabl, J.O., and Hilser, V.J. 2000. Ensemble modulation as an origin of denaturant-independent hydrogen exchange in proteins. J. Mol. Biol. 301: 247-256.
60. 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.