Defining protein ensembles with native-state NH exchange: Kinetics of interconversion and cooperative units from combined NMR and MS analysis

Journal of Molecular Biology

Volumn 285, Issue 3, 1999, Pages 1265-1275

  Arrington, Cammon B ^b   Teesch, Lynn M ^a   Robertson, Andrew D ^b  

^a UNIVERSITY OF IOWA   (United States)

^b NONE

Author keywords

Electrospray mass spectrometry; Ensembles; Hydrogen atom exchange; Ovomucoid third domain; Protein unfolding

Indexed keywords

HYDROGEN; OVOMUCOID; PEPTIDE; PROTEIN;

ARTICLE; HYPOTHESIS; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; SIMULATION;

EID: 0033593247     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2338     Document Type: Article

References (31)

1. Arrington C. B., Robertson A. D. Microsecond protein folding kinetics from native-state hydrogen exchange. Biochemistry. 36:1997;8686-8691.
2. Bahar I., Wallqvist A., Covell D. G., Jernigan R. L. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry. 37:1998;1067-1075.
3. Bai Y., Milne J. S., Mayne L., Englander S. W. Primary structure effects on peptide group hydrogen exchange. Proteins: Struct. Funct. Genet. 17:1993;75-86.
4. Bevington P. R., Robinson D. K. Data Reduction and Error Analysis for the Physical Sciences. 1992;McGraw-Hill Inc. New York.
5. Bhuyan A. K., Udgaonkar J. B. Multiple kinetic intermediates accumulate during the unfolding of horse cytochrome c in the oxidized state. Biochemistry. 37:1998;9147-9155.
6. Bode W., Epp O., Huber R., Laskowski M., Ardelt W. The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3). Eur. J. Biochem. 147:1985;387-395.
7. Brandts J. F. Conformational transitions of proteins in water and in aqueous mixtures. Timasheff S. N., Fasman G. D. Structure and Stability of Biological Molecules. 1969;213-290 Marcel Dekker Inc. New York.
8. Brooks C. L. III. Simulations of protein folding and unfolding. Curr. Opin. Struct. Biol. 8:1998;222-226.
9. Bryngelson J. D., Onuchic J. N., Socci N. D., Wolynes P. G. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins: Struct. Funct. Genet. 21:1995;167-195.
10. Chung E. W., Nettleton E. J., Morgan C. J., Groß M., Miranker A., Radford S. E., Dobson C. M., Robinson C. A. Hydrogen exchange properties of proteins in native and denatured states monitored by mass spectrometry and NMR. Protein Sci. 6:1997;1316-1324.
11. Clarke J., Fersht A. R. An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway. Folding and Design. 1:1996;243-254.
12. Dill K. A., Chan H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4:1997;10-19.
13. Hilser V. J., Freire E. Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J. Mol. Biol. 262:1996;756-772.
14. Hop C. E. C. A. Generation of high molecular weight cluster ions by electrospray ionization; implications for mass calibration. J. Mass Spect. 31:1996;1314-1316.
15. Hvidt A. Discussion of the pH dependence of the hydrogen-deuterium exchange of proteins. C. R. Trav. Lab. Carlsberg. 34:1964;299-317.
16. Hvidt A., Nielsen S. O. Hydrogen exchange in proteins. Advan. Protein Chem. 21:1966;287-386.
17. Johnson M. L., Faunt L. M. Parameter estimation by least-squares methods. Methods Enzymol. 210:1992;1-37.
18. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
19. Lazaridis T., Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1997;1928-1931.
20. Li A., Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 257:1996;412-429.
21. Li A., Daggett V. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J. Mol. Biol. 275:1998;677-694.
22. Miranker A., Robinson C. V., Radford S. E., Aplin R. T., Dobson C. M. Detection of transient protein folding populations by mass spectrometry. Science. 262:1993;896-900.
23. Miranker A., Robinson C. V., Radford S. E., Dobson C. M. Investigation of protein folding by mass spectrometry. FASEB J. 10:1996;93-101.
24. Muñoz V., Henry E. R., Hofrichter J., Eaton W. A. A statistical mechanical model for β-hairpin kinetics. Proc. Natl Acad. Sci. USA. 95:1998;5872-5879.
25. Smith D. L., Deng Y., Zhang Z. Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry. J. Mass Spect. 32:1997;135-146.
26. Swint L., Robertson A. D. Thermodynamics of unfolding for turkey ovomucoid third domain: thermal and chemical denaturation. Protein Sci. 2:1993;2037-2049.
27. Swint-Kruse L., Robertson A. D. Temperature and pH dependences of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry. 35:1996;171-180.
28. Yi Q., Baker D. Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. Protein Sci. 5:1996;1060-1066.
29. Zaidi F. N., Nath U., Udgaonkar J. B. Multiple intermediates and transition states during protein unfolding. Nature Struct. Biol. 4:1997;1016-1024.
30. Zhang Z., Smith D. L. Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 2:1993;522-531.
31. Zhang Z., Post C. B., Smith D. L. Amide hydrogen exchange determined by mass spectrometry: application to rabbit muscle aldolase. Biochemistry. 35:1996;779-791.