Mechanisms and uses of hydrogen exchange

Current Opinion in Structural Biology

Volumn 6, Issue 1, 1996, Pages 18-23

  Englander, S Walter ^a   Sosnick, Tobin R ^a   Englander, Joan J ^a   Mayne, Leland ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN; PROTEIN;

ENERGY TRANSFER; MACROMOLECULE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTON TRANSPORT; REVIEW; THERMODYNAMICS;

EID: 0029911695     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80090-X     Document Type: Article

References (92)

1. Linderstrøm-Lang KU: Deuterium exchange and protein structure. In Symposium on Protein Structure. Edited by Neuberger A. London: Methuen; 1958:23-34.
2. Hvidt A, Nielsen SO: Hydrogen exchange in proteins. Adv Protein Chem 1966, 21:287-386.
3. Englander SW, Kallenbach NR: Hydrogen exchange and structural dynamics of proteins and nucleic acids. O Rev Biophys 1984, 16:521-655.
4. Woodward CK, Simon I, Tuchsen E: Hydrogen exchange and the dynamic structure of proteins. Mol Cell Biochem 1982, 48:135-160.
5. Eigen M: Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Angew Chem 1964, 3:1-19.
6. Molday RS, Englander SW, Kallen RG: Primary structure effects on peptide group hydrogen exchange. Biochemistry 1972, 11:150-158.
7. Bai Y, Milne JS, Mayne L, Englander SW: Primary structure effects on peptide group hydrogen exchange. Proteins 1993, 17:75-86.
8. Henry GD, Sykes BD: Determination of the rotational dynamics and pH dependence of the hydrogen exchange rates of the arginine guanidino group using NMR spectroscopy. J Biomol NMR 1995, 6:59-66.
9. Liepinsh E, Otting G, Wüthrich K: NMR spectroscopy of hydroxyl protons in aqueous solutions of peptides and proteins. J Biomol NMR 1992, 2:447-465.
10. Gueron M, Leroy JL: Base pair opening in double stranded nucleic acids. In Nucleic Acids and Molecular Biology. Edited by Eckstein F, Lilley DMJ. Berlin: Springer-Verlag; 1992:1-22.
11. Teitelbaum H, Englander SW: Open states in native polynucleotides. Hydrogen exchange study of cytosine containing double helices. J Mol Biol 1975, 92:79-92.
12. Teitelbaum H, Englander SW: Open states in native polynucleotides. Hydrogen exchange study of adenine containing double helices. J Mol Biol 1975, 92:55-78.
13. Connelly GP, Bai Y, Jeng MF, Englander SW: Isotope effects in peptide group hydrogen exchange. Proteins 1993, 17:87-92.
14. Englander JJ, Rogero JR, Englander SW: Protein hydrogen exchange studied by the fragment separation method. Anal Biochem 1985, 147:234-244.
15. Zhang Y, Paterson Y, Roder H: Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR. Protein Sci 1995, 4:804-814.
16. Robertson AD, Baldwin RL: Hydrogen exchange in thermally denatured ribonuclease A. Biochemistry 1991, 30:9907-9914.
17. Buck M, Radford SE, Dobson CM: Amide hydrogen exchange in a highly denatured state. Hen egg-white lysozyme in urea. J Mol Biol 1994, 237:247-254.
18. Mandal C, Kallenbach NR, Englander, SW: Base pair opening and closing reactions in the double helix. J Mol Biol 1979, 135:391-411.
19. Englander JJ, Kallenbach NR, Englander SW: Hydrogen exchange study of some polynucleotides and transfer RNA. J Mol Biol 1972, 63:153-169.
20. Englander SW: Measurement of structural and free energy changes in hemoglobin by hydrogen exchange methods. Ann NY Acad Sci 1975, 244:10-27.
21. Kossiakoff AA: Protein dynamics investigated by the neutron diffraction-hydrogen exchange technique. Nature 1982, 296:713-721.
22. Miller DW, Dill KA: A statistical-mechanical model for hydrogen exchange in globular proteins. Protein Sci 1995, 4:1860-1873.
23. Richards FM: 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 1979, 44:47-63.
24. Bai Y, Sosnick T, Mayne L, Englander SW: Protein folding intermediates studied by native-state hydrogen exchange. Science 1995, 269:192-197. The methods used in [27*] are extended to identify partially unfolded forms of cyt c, measure their free-energy levels, and define the cooperative units of structure that comprise the molecule. These forms may represent the major intermediates in kinetic folding.
25. Roder H, Wagner G, Wüthrich K: Amide protein exchange in proteins by EX1 kinetics: studies of BPTI at variable pD and temperature. Biochemistry 1985, 24:7396-7407.
26. Pedersen TG, Thomson NK, Andersen KV, Madsen JC, Poulsen FM: Determination of the rate constants k1 and k2 of the Linderstrom-Lang model for protein amide hydrogen exchange. A study of the individual amides in hen egg-white lysozyme. J Mol Biol 1993, 230:651-660.
27. Bai Y, Milne JS, Mayne L, Englander SW: Protein stability parameters measured by hydrogen exchange. Proteins 1994, 20:4-14. Following the denaturant-dependent approach of Mayo and Baldwin [34], this paper demonstrates that the most protected hydrogens in cyt c and ribonuclease A exchange by way of transient global unfolding under native conditions, and shows how to handle the quantitative data and a number of the qualitative issues. See also [28,29*,30,35].
28. Loh SN, Prehoda KE, Wang J, Markley JL: Hydrogen exchange in unligated and ligated staphylococcal nuclease. Biochemistry 1993, 32:11022-11028.
29. Perrett S, Clarke J, Hounslow AM, Fersht AR: Relationship between equilibrium amide proton exchange behavior and the folding pathway of barnase. Biochemistry 1995, 34:9288-9298. A detailed study of transient unfolding reactions in barnase and various mutants by site-resolved HX, and their possible relationship to the kinetic folding pathway.
30. Swint-Kruse L, Robertson AD: Temperature and pH dependences of hydrogen exchange for ovomucoid third domain. Biochemistry 1995, in press.
31. Wagner G, Wüthrich K: Observation of internal motility of proteins by nuclear magnetic resonance in solution. Methods Enzymol 1986, 131:307-326.
32. Wagner G: Characterization of the distribution of internal motions in BPTI using a large number of internal NMR probes. Q Rev Biophys 1983, 16:1-57.
33. Kiefhaber T, Baldwin RL: Kinetics of hydrogen bond breakage in the process of unfolding of ribonuclease A measured by pulsed hydrogen exchange. Proc Natl Acad Sci USA 1995, 92:2657-2661.
34. Mayo SL, Baldwin RL: Guanidinium chloride induction of partial unfolding in amide proton exchange in ribonuclease A. Science 1993, 262:873-876.
35. Orban J, Alexander P, Bryan P: Hydrogen-deuterium exchange in the free and immunoglobin G-bound protein G B-domain. Biochemistry 1994, 33:5702-5710.
36. Englander SW, Englander JJ: Structure and energy change in hemoglobin by hydrogen exchange labeling. Methods Enzymol 1994, 232:26-42.
37. Englander SW, Englander JJ, McKinnie RE, Ackers GK, Turner GJ, Westrick JA, Gill SJ: Hydrogen exchange measurement of the free energy of structural and allosteric change in hemoglobin. Science 1992, 256:1684-1687.
38. Zhou HX, Hull LA, Kallenbach NR, Mayne L, Bai Y, Englander SW: Quantitative evaluation of stabilizing interactions in a prenucleated alpha-helix by hydrogen exchange. J Am Chem Soc 1994, 116:6482-6483.
39. 2-amide. Biochemistry 1995, 34:2348-2361.
40. De Jongh HH, Goormaghtigh E, Ruysschaert JM: Tertiary stability of native and methionine-80 modified cytochrome c detected by proton-deuterium exchange using on-line Fourier transform infrared spectroscopy. Biochemistry 1995, 34:172-179.
41. Hildebrandt P, Vanhecke F, Heibel G, Mauk AG: Structural changes in cytochrome c upon Hydrogen-deuterium exchange. Biochemistry 1993, 32:14158-14164.
42. Englander JJ, Calhoun DB, Englander SW: Measurement and calibration of peptide group hydrogen-deuterium exchange by UV spectrophotometry. Anal Biochem 1979, 92:517-524.
43. Kaminsky SM, Richards FM: Differences in hydrogen exchange behavior between the oxidized and reduced forms of E. coli thioredoxin. Protein Sci 1992, 1:10-21.
44. Bai Y, Englander JJ, Mayne L, Milne JS, Englander SW: Thermodynamic parameters from hydrogen exchange measurements. Methods Enzymol 1995, 259:344-356.
45. Thevenon-Emeric G, Kozlowski J, Zhang Z, Smith DL: Determination of amide hydrogen exchange rates in peptides by mass spectrometry. Anal Chem 1992, 64:2456-2458.
46. Zhang Z, Smith DL: Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 1993, 2:522-531.
47. Katta V, Chait BT: Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry. Rapid Commun Mass Spectrom 1991, 5:214-217.
48. Anderegg RJ, Wagner DS: Mass-spectrometric characterization of a protein ligand interaction. J Am Chem Soc 1995, 117:1374-1377.
49. Eyles SJ, Radford SE, Robinson CV, Dobson CM: Kinetic consequences of the removal of a disulfide bridge on the folding of hen lysozyme. Biochemistry 1994, 33:13038-13048.
50. Miranker A, Robinson CV, Radford SE, Aplin RT, Dobson CM: Detection of transient protein folding populations by mass spectrometry. Science 1993, 262:896-900.
51. Robinson CV, Gross M, Eyles SJ, Ewbank JJ, Mayhew M, Hartl FU, Dobson CM, Radford SE: Conformation of GroEL-bound alpha-lactalbumin probed by mass spectrometry. Nature 1994, 372:646-651. An elegant application of mass spectrometry together with HX to study the structural condition of a protein while it is bound to the exceedingly large GroEL chaperonin.
52. 15N-labeled helical peptides measured by isotope-edited NMR. Biochemistry 1994, 33:7760-7767. A nice demonstration of the use of HX to obtain site-resolved bond free energies in a helical host (see also [38]).
53. 3amide. J Am Chem Soc 1994, 116:8288-8293.
54. Englander SW, Mayne L: Protein folding studied by hydrogen-exchange labeling and two-dimensional NMR. Annu Rev Biophys Biomol Struc 1992, 21:243-265.
55. Chyan CL, Wormald C, Dobson CM, Evans PA, Baum J: Structure and stability of the molten globule state of Guinea-pig alpha-lactalbumin: a hydrogen exchange study. Biochemistry 1993, 32:5681-5691.
56. Alexandrescu AT, Evans PA, Pitkeathly M, Baum J, Dobson CM: Structure and dynamics of the acid-denatured molten globule state of alpha-lactalbumin: a two-dimension NMR Study. Biochemistry 1993, 32:1707-1718.
57. Jeng M, Englander SW, Elöve GA, Wand AJ, Roder H: Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry 1990, 29:10433-10437.
58. Jeng MF, Englander SW: Stable submolecular folding units in a non-compact form of cytochrome c. J Mol Biol 1991, 221:1045-1061.
59. Pan Y, Briggs MS: Hydrogen exchange in native and alcohol forms of ubiquitin. Biochemistry 1992, 31:11405-11412.
60. Fart P, Bracken C, Baum J: Structural characterization of monellin in the alcohol denatured state by NMR: evidence for beta-sheet to alpha helix conversion. Biochemistry 1993, 32:1573-1582.
61. Hughson FM, Wright PE, Baldwin RL: Structural characterization of a partly folded apomyoglobin intermediate. Science 1990, 249:1544-1548.
62. Kuroda Y, Kidokoro S, Wada A: Thermodynamic characterization of cytochrome c at low pH: observation of the molten globule state and of the cold denaturation process. J Mol Biol 1992, 223:1139-1153.
63. Chyan CL, Wormald C, Dobson CM, Evans PA, Baum J: Structure and stability of the molten globule state of guinea pig alpha-lactalbumin: a hydrogen exchange study. Biochemistry 1993, 32:5681-5691.
64. Wu J, Gorenstein DG: Structure and dynamics of cytochrome c in nonaqueous solvents by 2D NH exchange NMR spectroscopy. J Am Chem Soc 1993, 115:6843-6850.
65. Dempsey CE: Hydrogen-bond stabilities in the isolated alamethicin helix: pH-dependent amide exchange measurements in methanol. J Am Chem Soc 1995, 117:7526-7534.
66. Desai UR, Klibanov AM: Assessing the structural integrity of a lyophilized protein in organic solvents. J Am Chem Soc 1995, 117:3940-3945.
67. Desai UR, Osterhout JJ, Klibanov AM: Protein structure in the lyophilized state: a hydrogen isotope exchange NMR study with bovine pancreatic trypsin-inhibitor. J Am Chem Soc 1994, 116:9420-9422.
68. 562. Nature Struct Biol 1994, 1:30-35.
69. Redfield C, Smith RAG, Dobson CM: Structural characterization of a highly ordered 'molten globule' at low pH. Nature Struct Biol 1994, 1:23-29.
70. Paterson Y, Englander SW, Roder H: An antibody binding site on a protein antigen defined by hydrogen exchange and two-dimensional NMR. Science 1990, 249:755-759.
71. Yi Q, Erman JE, Satterlee JD: Studies of protein-protein association between yeast cytochrome c peroxidase and yeast iso-1 ferricytochrome c by hydrogen-deuterium exchange labeling and proton NMR spectroscopy. Biochemistry 1994, 33:12032-12041.
72. Jeng M, Englander SW, Pardue K, Rogalskyj JS, McLendon G: Structural dynamics in an electron transfer complex. Nature Struct Biol 1994, 1:234-238.
73. Mayne L, Paterson Y, Cerasoli D, Englander SW: Effect of antibody binding on protein motions studied by hydrogen exchange labeling and two-dimensional NMR. Biochemistry 1992, 31:10678-10685.
74. Benjamin DC, Williams DC, Smith-Gill SJ, Rule GS: Longrange changes in a protein antigen due to antigen-antibody interaction. Biochemistry 1992, 31:9539-9545.
75. Werner MH, Wemmer DE: Identification of a protein-binding surface by differential amide hydrogen-exchange measurements. Application to Bowman-Birk serine-protease inhibitor. J Mol Biol 1992, 225:873-889.
76. Jones DN, Bycroft M, Lubienski MJ, Fersht AR: Identification of the Barstar binding site of barnase by NMR spectroscopy and hydrogen-deuterium exchange. FEBS Lett 1993, 331:165-172.
77. Zahn R, Spitzfaden C, Ottiger M, Wüthrich K, Pluckthun A: Destabilization of the complete protein secondary structure on binding to the chaperone GroEL. Nature 1994, 368:261-265.
78. Okazaki A, Ikura T, Nikaido K, Kuwajima K: The chaperonin GroEL does not recognize apo-alpha-lactalbumin in the molten globule state. Nature Struct Biol 1994, 7:439-445.
79. 1H NMR. FEBS Lett 1993, 317:128-130.
80. Thornton K, Gorenstein DG: Structure of glucagon-like peptide (7-36) amide in a dodecylphosphocholine micelle as determined by 2D NMR. Biochemistry 1994, 33:3532-3539.
81. Gallagher W, Tao F, Woodward CK: Comparison of hydrogen exchange rates for bovine pancreatic trypsin inhibitor in crystals and in solution. Biochemistry 1992, 31:4673-4680.
82. Pedersen TG, Sigurskjold BW, Andersen KV, Kjaer M, Poulsen FM, Dobson CM, Redfield C: A nuclear magnetic resonance study of the hydrogen exchange behaviour of lysozyme in crystals and solution. J Mol Biol 1991, 218:413-426.
83. Ehrhardt MR, Urbauer JL, Wand AJ: The energetics and dynamics of molecular recognition by calmodulin. Biochemistry 1995, 34:2731-2738. An elegant application of multiple NMR methods to measure site-resolved HX of a calmodulin-bound target peptide in situ, and thus determine its structure, its dynamic unfolding fluctuations, and its probable binding and folding sequence.
84. Gryk MR, Finucane MD, Zheng Z, Jardetzky O: Solution dynamics of the trp repressor: a study of amide proton exchange by T1 relaxation. J Mol Biol 1995, 246:618-627.
85. Udgaonkar JB, Baldwin RL: NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature 1988, 335:694-699.
86. Roder H, Elöve GA, Englander SW: Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature 1988, 335:700-704.
87. Baldwin RL: Pulsed H/D-exchange studies of folding intermediates. Curr Opin Struct Biol 1993, 3:84-91.
88. Woodward CK: Hydrogen exchange rates and protein folding. Curr Opin Struct Biol 1994, 4:112-116.
89. Dobson CM: Protein folding. Solid evidence for molten globules. Curr Biol 1994, 4:636-640.
90. Roder H, Elöve GA: Early stages in protein folding. In Mechanisms in Protein Folding. Edited by Pain RH. Oxford: Oxford University Press; 1994:26-54.
91. Matouschek A, Serrano L, Meiering EM, Bycroft M, Fersht AR: The folding of an enzyme V. 1H/2H exchange-nuclear magnetic resonance studies on the folding pathway of barnase: complementarity to and agreement with protein engineering studies. J Mol Biol 1992, 224:837-845.
92. Rodgers ME, Englander JJ, Englander SW, Harrington WF: The measurement of protein structure change in active muscle. Biophys Chem 1995, in press.