A New H/D Exchange- and Mass Spectrometry-Based Method for Thermodynamic Analysis of Protein-DNA Interactions

Chemistry and Biology

Volumn 10, Issue 12, 2003, Pages 1205-1213

  Ma, Liyuan ^a   Fitzgerald, Michael C ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 0348229029     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2003.11.017     Document Type: Article

References (29)

1. Winzor D.J., Sawyer W.H. Quantitative Characterization of Ligand Binding. 1995;Wiley-Liss, New York.
2. Hill J.J., Royer C.A. Fluorescence approaches to study of protein-nucleic acid complexation. Methods Enzymol. 278:1997;390-416.
3. Carey J. Gel retardation. Methods Enzymol. 208:1991;103-117.
4. Powell K.D., Ghaemmaghami S., Wang M.Z., Ma L., Oas T.G., Fitzgerald M.C. A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution. J. Am. Chem. Soc. 124:2002;10256-10257.
5. Ghaemmaghami S., Fitzgerald M.C., Oas T.G. A quantitative, high-throughput screen for protein stability. Proc. Natl. Acad. Sci. USA. 97:2000;8296-8301.
6. Powell K.D., Wales T.E., Fitzgerald M.C. Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based method. Protein Sci. 11:2002;841-851.
7. Powell K.D., Fitzgerald M.C. Accuracy and precision of a new H/D exchange- and mass spectrometry-based technique for measuring the thermodynamic properties of protein-peptide complexes. Biochemistry. 42:2003;4962-4970.
8. Ghaemmaghami S., Oas T.G. Quantitative protein stability measurement in vivo. Nat. Struct. Biol. 8:2001;879-882.
9. 1H NMR spectrometry. Biochemistry. 28:1989;9826-9833.
10. Raumann B.E., Rould M.A., Pabo C.O., Sauer R.T. DNA recognition by β-sheets in the Arc repressor-operator crystal structure. Nature. 367:1994;754-757.
11. Vershon A.K., Youderian P., Susskind M.M., Sauer R.T. The bacteriophage P22 arc and mnt repressors. overproduction, purification, and properties J. Biol. Chem. 260:1985;12124-12129.
12. Brown B.M., Sauer R.T. Assembly of the Arc repressor-operator complex. cooperative interactions between DNA-bound dimers Biochemistry. 32:1993;1354-1363.
13. Brown B.M., Bowie J.U., Sauer R.T. Arc repressor is tetrameric when bound to operator DNA. Biochemistry. 29:1990;11189-11195.
14. Del Solar G.H., Perez-Martin J., Espinosa M. Plasmid pLSI-encoded RepA protein regulates transcription from repAB promoter by binding to a DNA sequence containing a 13-base pair symmetric element. J. Biol. Chem. 265:1990;12569-12575.
15. Del Solar G., Albericio F., Eritja R., Espinosa M. Chemical synthesis of a fully active transcriptional repressor protein. Proc. Natl. Acad. Sci. USA. 91:1994;5178-5182.
16. Milla M.E., Sauer R.T. Arc repressor. folding kinetics of a single-domain, dimeric protein Biochemistry. 33:1994;1125-1133.
17. Oas T.G., Toone E.J. Thermodynamic solvent isotope effects and molecular hydrophobicity. Adv. Biophys. Chem. 6:1997;1-52.
18. Krantz B.A., Moran L.B., Kentsis A., Sosnick T.R. D/H amide kinetic isopote effects reveal when hydrogen bonds form during protein folding. Nat. Struct. Biol. 7:2000;62-71.
19. Gomis-Ruth F.X., Sola M., Acebo P., Parraga A., Guasch A., Eritja R., Gonzalez A., Espinosa M., Del Solar G., Coll M. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J. 17:1998;7404-7415.
20. Pace C.N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131:1986;266-280.
21. Glasoe P.K., Long F.A. Use of glass electrodes to measure acidities in deuterium oxide. J. Phys. Chem. 64:1960;188-190.
22. Wales T.E., Fitzgerald M.C. The energetic contribution of backbone-backbone hydrogen bonds to the thermodynamic stability of a hyperstable P22 arc repressor mutant. J. Am. Chem. Soc. 123:2001;7709-7710.
23. Schnolzer M., Alewood P., Jones A., Alewood D., Kent S.B.H. Highly optimized solid phase peptide synthesis protocols for Boc-chemistry. Int. J. Pept. Protein Res. 40:1992;180-193.
24. 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. 4:1995;2138-2148.
25. Zhang, Y.-Z. (1995). Structural biology and molecular biophysics, thesis, University of Pennsylvania, Philadelphia, Pennsylvania.
26. Bai Y., Milne L., Englander S.W. Primary structure effects on peptide group hydrogen exchange. Proteins. 17:1993;75-76.
27. Schellman J. Macromolecular binding. Biopolymers. 14:1975;999-1018.
28. Pace C.N., McGrath T. Substrate stabilization of lysozyme to thermal and guanidine hydrochloride denaturation. J. Biol. Chem. 255:1980;3862-3865.
29. Segel I.H. Enzyme Kinetics. 1975;John Wiley & Sons, New York.