Mapping protein-ligand interactions by footprinting, a radical idea

Structure

Volumn 6, Issue 6, 1998, Pages 691-695

  Loizos, Nick ^a   Darst, Seth A ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FOOTPRINTING; MAPPING; PROTEIN LIGAND INTERACTION;

EID: 0032526687     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00071-9     Document Type: Article

References (27)

1. Galas, D.J. & Schmitz, B. (1978). DNA footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157-3170.
2. Jue, R.A. & Doolittle, R.F. (1985). Determination of the relative positions of amino acids by partial specific cleavages of end-labeled proteins. Biochemistry 24, 162-170.
3. Li, B.-L., Langer, J., Schwartz, B. & Pestka, S. (1989). Creation of phosphorylation sites in proteins: construction of a phosphorylatable human interferon alpha. Proc. Natl Acad. Sci. USA 86, 558-562.
4. Schagger, H. & von Jagow, G. (1987). Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 166, 368-379.
5. Heyduk, E. & Heyduk, T. (1994). Mapping protein domains involved in macromolecular interactions: a novel protein footprinting approach. Biochemistry 33, 9643-9650.
6. Heyduk, T., Heyduk, E., Severinov, K., Tang, H. & Ebright, R.H. (1996). Rapid epitope mapping by hydroxyl-radical protein footprinting: determinants of RNA polymerase alpha subunit for interaction with beta, beta', and sigma subunits. Proc. Natl Acad. Sci. USA 93, 10162-10166.
7. Wang, Y., et al., & Darst, S.A. (1997). Determinants for Escherichia coli RNA polymerase assembly within the β subunit. J. Mol. Biol. 270, 648-662.
8. Baichoo, N. & Heyduk, T. (1997). Mapping conformational changes in a protein: application of a protein footprinting technique to cAMP-induced conformational changes in cAMP receptor protein. Biochemistry 36, 10830-10836.
9. Mossessova, E., Gulbis, J.M. & Goldberg, J. (1998). Structure of the guanine nucleotide exchange factor Sec7 domain of human Arno and analysis of the interaction with ARF GTPase. Cell 92, 415-423.
10. 6-tag and hemagglutinin epitope. Gene 166, 177-178.
11. 32P labeled protein, applied to HIV-1 Gag and Rev. Gene 162, 235-237.
12. Muzzin, O., Campbell, E.A., Xia, L., Severinova, E., Darst, S.A. & Severinov, K. (1998). Disruption of Escherichia coli HepA, an RNA polymerase associated protein, causes UV sensitivity. J. Biol. Chem., in press.
13. Tullius, T.D. & Dombroski, B.A. (1986). Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda represser and Cro protein. Proc. Natl Acad. Sci. USA 83, 5469-5473.
14. Rana, T.M. & Meares, C.F. (1990). Specific cleavage of a protein by an attached iron chelate. J. Am. Chem. Soc. 112, 2457-2458.
15. Schepartz, A. & Cuenoud, B. (1990). Site-specific cleavage of the protein calmodulin using a trifluoperazine-based affinity reagent. J. Am. Chem. Soc. 112, 3247-3249.
16. Rana, T.M. & Meares, C.F. (1991). Transfer of oxygen from an artificial protease to peptide carbon during proteolysis. Proc. Natl Acad. Sci. USA 88, 10578-10582.
17. Platis, I.E., Ermacora, M.R. & Fox, R.O. (1993). Oxidative polypeptide cleavage mediated by EDTA-Fe covalently linked to cysteine residues. Biochemistry 32, 12761-12767.
18. Ermacora, M.R., Ledman, D.W., Hellinga, H.W, Hsu, G.W. & Fox, R.O. (1994). Mapping staphylococcal nuclease conformation using an EDTA-Fe derivative attached to genetically engineered cysteine residues. Biochemistry 33, 13625-13641.
19. Ermacora, M.I.R., Ledman, D.W. & Fox, R.O. (1996). Mapping the structure of a non-native state of staphylococcal nuclease. Nat. Struct. Biol. 3, 59-66.
20. Zaychikov, E, et al., & Mustaev, A. (1996). Mapping of catalytic residues in the RNA polymerase active center. Science 273, 107-109.
21. Amor, J.C, Harrison, D.H., Kahn, R.A. & Ringe, D. (1994). Structure of the human ADP-ribosylation factor 1 complexed with GDP. Nature 372, 704-708.
22. Brenowitz, M., Senear, D.F, Shea, M.A. & Ackers, G.A. (1986). Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol. 130, 132-181.
23. Borukhov, S., Lee, J. & Goldfarb, A. (1991). Mapping of a contact for the RNA 3′ terminus in the largest subunit of RNA polymerase. J. Biol. Chem. 266, 23932-23935.
24. Chait, B.T. & Kent, S.B. (1992). Weighing naked proteins: practical, high-accuracy mass measurement of peptides and proteins. Science 257, 1885-1894.
25. Sclavi, B., Woodson, S, Sullivan, M., Chance, M.R. & Brenowitz, M. (1997). Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. J. Mol. Biol. 266, 144-159.
26. Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M. & Woodson, S.A. (1998). RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279, 1940-1943.
27. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 1104-1112.