Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange

Proteins: Structure, Function and Genetics

Volumn 30, Issue 3, 1998, Pages 295-308

  Bhuyan, Abani K ^a   Udgaonkar, Jayant B ^a,b  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

^b INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Denaturants; Hydrogen exchange mechanism

Indexed keywords

ARTICLE; CALCULATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTON TRANSPORT;

AMIDES; BACILLUS; BACTERIAL PROTEINS; CIRCULAR DICHROISM; DEUTERIUM; FLUORESCENCE; GUANIDINE; HYDROGEN; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 0032519738     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980215)30:3<295::AID-PROT9>3.0.CO;2-J     Document Type: Article

References (56)

1. Englander, S.W., Kallenbach, N.R. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16:521-655, 1984.
2. Udgaonkar, J.B., Baldwin, R.L. NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature 335:694-699, 1988.
3. Roder, H., Elöve, G.A., Englander, S.W. Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature 335:700-704, 1988.
4. Englander, S.W., Mayne, L. Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu. Rev. Biophys. Biomol. Struct. 21:243-265, 1992.
5. Baum, J., Dobson, C., Evans, P., Hanley, C. Characterization of a partly folded protein by NMR methods: Studies on the molten globule state of guinea pig α-lactalbumin. Biochemistry 28:7-13, 1989.
6. Englander, S.W., Englander, J.J., McKinnie, R., Ackers, G.K., Turner, G.J., Westrick, J.A., Gill, S.J. Hydrogen exchange measurement of the free energy of structural and allosteric change in hemoglobin. Science 256:1684-1687, 1992.
7. Kim, K.-S., Fuchs, J.A., Woodward, C.K. Hydrogen exchange identifies native-state motional dynamics important in protein folding. Biochemistry 32:9600-9608, 1993.
8. Kim, K.-S., Woodward, C. Protein internal flexibility and global stability: Effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor. Biochemistry 32: 9609-9613, 1993.
9. Bai, Y., Sosnick, T.R., Mayne, L., Englander, S.W. Protein folding intermediates: Native state hydrogen exchange. Science 269:192-196, 1995.
10. Eriksson, M.A.L., Härd, T., Nilsson, L. On the pH dependence of amide proton exchange rates in proteins. Biophys. J. 69:329-339, 1995.
11. Perrett, S., Clarke, J., Hounslow, A.M., Fersht, A.R. Relationship between equilibrium amide proton exchange behavior and the folding pathway of barnase. Biochemistry 34:9288-9298, 1995.
12. Christoffersen, M., Bolvig, S., Tüchsen, E. Salt effects on the amide hydrogen exchange of bovine pancreatic trypsin inhibitor. Biochemistry 35:2309-2315, 1996.
13. Loh, S.N., Rohl, C.A., Kiefhaber, T., Baldwin, R.L. A general two-process model describes the hydrogen exchange behavior of RNase A in unfolding conditions. Proc. Natl. Acad. Sci. U.S.A. 93:1982-1987, 1996.
14. Mayo, S.L., Baldwin, R.L. Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A. Science 262:873-876, 1993.
15. Bai, Y., Milne, J.S., Mayne, L., Englander, S.W. Protein stability parameters measured by hydrogen exchange. Proteins 20:4-14, 1994.
16. Chamberlain, A.K., Handel, T.M., Marqusee, S. Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nature Struct. Biol. 3:782-787, 1996.
17. Clarke, J., Fersht, A.R. An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway. Folding Design 1:243-254, 1996.
18. Hartley, R.W. Barnase and barstar. Expression of its cloned inhibitor permits expression of a cloned ribonuclease. J. Mol. Biol. 202:913-915, 1988.
19. Nath, U., Udgaonkar, J.B. How do proteins fold? Curr. Sci. 72:180-191, 1997.
20. 15N NMR resonance and secondary structure characterization of barstar. FEBS Lett. 332:81-87, 1993.
21. 13C assignments of barstar using nuclear magnetic resonance spectroscopy. Biochemistry 33:8866-8877, 1994.
22. Khurana, R., Udgaonkar, J.B. Equilibrium unfolding studies of barstar: Evidence for an alternative conformation which resembles a molten globule. Biochemistry 33:106-115, 1994.
23. Woodward, C.K., Rosenberg, A. Studies of hydrogen exchange in proteins. VI. Urea effects on ribonuclease exchange kinetics leading to a general model for hydrogen exchange from folded proteins. J. Biol. Chem. 246:4114-4121, 1971.
24. Woodward, C.K., Hilton, B.D. Hydrogen isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor. Biophys. J. 32:561-575, 1980.
25. Bai, Y., Milne, J.S., Mayne, L., Englander, S.W. Primary structure effects on peptide group hydrogen exchange. Proteins 17:75-86, 1993.
26. Hvidt, A. A discussion of the pH dependence of the hydrogen-deuterium exchange of proteins. C. R. Trav. Lab. Carlsberg 34:299-317, 1964.
27. Pace, C.N. The stability of globular proteins. CRC Crit. Rev. Biochem. 3:1-43, 1975.
28. Myers, J.K., Pace, C.N., Scholtz, J.M. Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4:2138-2148, 1995.
29. Agashe, V.R., Udgaonkar, J.B. Thermodynamics of denaturation of barstar: Evidence for cold denaturation and evaluation of the interaction with guanidine hydrochloride. Biochemistry 34:3286-3299, 1995.
30. Qian, H., Mayo, S.L., Morton, A. Protein hydrogen exchange in denaturant: Quantitative analysis by a two-process model. Biochemistry 33:8167-8171, 1994.
31. Khurana, R., Hate, A.T., Nath, U., Udgaonkar, J.B. pH dependence of the stability of barstar to chemical and thermal denaturation. Protein Sci. 4:1133-1144, 1995.
32. Wintrode, P.L., Griko, Y.V., Privalov, P.L. Structural energetics of barstar studied by differential scanning microcalorimetry. Protein Sci. 4:1528-1534, 1995.
33. Elöve, G.A., Bhuyan, A.K., Roder, H. Kinetic mechanism of cytochrome c folding: Involvement of the heme and its ligands. Biochemistry 33:6925-6935, 1994.
34. Wlodawer, E., Sjölin, L. Hydrogen exchange in RNase: Neutron diffraction study. Proc. Natl. Acad. Sci. U.S.A. 79:1418-1422, 1982.
35. Gregory, R.B., Rosenberg, A. Proteinconformational dynamics measured by hydrogen isotope exchange techniques. Methods Enzymol. 131:448-508, 1986.
36. Tüchsen, E., Woodward, C. Hydrogen kinetics of peptide amide protons at the bovine pancreatic trypsin inhibitor protein-solvent interface. J. Mol. Biol. 185:405-419, 1985.
37. Tüchsen, E., Woodward, C. Mechanism of surface peptide proton exchange in bovine pancreatic trypsin inhibitor: Salt effects and O-protonation. J. Mol. Biol. 185:421-430, 1985.
38. Ramachandran, S., Udgaonkar, J.B. Stabilization of barstar by chemical modification of the buried cysteines. Biochemistry 35:8776-8785, 1996.
39. Woodward, C., Simon, I., Tüchsen, E. Hydrogen exchange and the dynamic structure of proteins. Mol. Cell. Biochem. 48:135-160, 1982.
40. Bai, Y., Englander, S.W. Future directions in folding: The multi-state nature of protein structure. Proteins 24:145-151, 1996.
41. Miller, D.W., Dill, K.A. A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci. 4: 1860-1873, 1996.
42. Bryngelson, J.D., Wolynes, P.G. Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. U.S.A. 84:7524-7528, 1987.
43. Bryngelson, J.D., Wolynes, P.G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93:6902-6915, 1989.
44. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D., Chan, H.S. Principles of protein folding: A perspective from simple exact models. Protein Sci. 4:561-602, 1995.
45. Wolynes, P.G., Onuchic, J.N., Thirumalai, D. Navigating the folding routes. Science 267:5204-5205, 1995.
46. Leeson, D.T., Wiersma, D.A. Looking into the energy landscape of myoglobin. Nature Struct. Biol. 2:848-851, 1995.
47. Nölting, B., Golbik, R., Fersht, A.R. Submillisecond events in protein folding. Proc. Natl. Acad. Sci. U.S.A. 92:10668-10672, 1997.
48. Nath, U., Udgaonkar, J.B. Folding of trypsin mutant of barstar: Evidence for an initial hydrophobic collapse on the folding pathway. Biochemistry 36:8602-8610, 1997.
49. Shastry, M.C.R., Udgaonkar, J.B. The folding mechanism of barstar: Evidence for multiple pathways and multiple intermediates. J. Mol. Biol. 247:1013-1027, 1995.
50. Shastry, M.C.R., Agashe, V.R., Udgaonkar, J.B. Quantitative analysis of the kinetics of denaturation and renaturation of barstar in the folding transition zone. Protein Sci. 3:1409-1417, 1994.
51. Schreiber, G., Fersht, A.R. The refolding of cis-and trans7 peptidylprolyl isomers of barstar. Biochemistry 32:11195-11203, 1993.
52. Nath, U., Agashe, V.R., Udgaonkar, J.B. Initial loss of secondary structure in the unfolding of barstar. Nature Struct. Biol. 3:920-923, 1996.
53. Garel, J.-R., Baldwin, R.L. Both the fast and the slow refolding reactions of ribonuclease A yield native enzyme. Proc. Natl. Acad. Sci. U.S.A. 70:3347-3350, 1973.
54. Schmid, F.X. Proline isomerization in unfolded ribonuclease A. Eur. J. Biochem. 128:77-80, 1982.
55. Nall, B. Proline isomerization and protein folding. Mol. Cell Biophys. 3:123-143, 1985.
56. Kraulis, P.J. (1991) "MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures." J. Appl. Crystallogr. 24:946-950, 1991.