Chapter 7: Protein Interactions Captured by Chemical Cross-linking—References

Alaedini A. and Day R.A. 1999. Identification of two penicillin-binding multienzyme complexes in Haemophilus influenzae. Biochem. Biophys. Res. Commun. 264: 191–195.

Alley S.C., Ishmael F.T., Jones A.D., and Benkovic S.J. 2000. Mapping protein–protein interactions in the bacteriophage T4 DNA polymerase holoenzyme using a novel trifunctional photo-cross-linking and affinity reagent. J. Am. Chem. Soc. 122: 6126–6127.

Back J.W., de Jong L., Muijsers A.O., and de Koster C.G. 2003. Chemical cross-linking and mass spectrometry for protein structural modeling. J. Mol. Biol. 331: 303–313.

Back J.W., Notenboom V., de Koning L.J., Muijsers A.O., Sixma T.K., de Koster C.G., and de Jong L. 2002. Identification of cross-linked peptides for protein interaction studies using mass spectrometry and ¹⁸O labeling. Anal. Chem. 74: 4417–4422.

Ballmer-Hofer K., Schlup V., Burn P., and Burger M.M. 1982. Isolation of in situ crosslinked ligand-receptor complexes using an anticrosslinker specific antibody. Anal. Biochem. 126: 246–250.

Benesch R.E. and Kwong S. 1991. Hemoglobin tetramers stabilized by a single intramolecular cross-link. J. Protein Chem. 10: 503–510.

Bennett K.L., Matthiesen T., and Roepstorff P. 2000. Probing protein surface topology by chemical surface labeling, crosslinking, and mass spectrometry. In Mass spectrometry of proteins and peptides (ed. J.R. Chapman), pp. 113–131. Humana Press, Totowa, New Jersey.

Binz P.-A., Muller M., Walther D., Bienvenut W.V., Gras R., Hoogland C., Bouchet G., Gasteiger, E., Fabbretti R., Gay S., et al. 1999. A molecular scanner to automate proteomic research and to display proteome images. Anal. Chem. 71: 4981–4988.

Chen T., Jaffe J.D., and Church G. M. 2001. Algorithms for identifying protein cross-links via tandem mass spectrometry. J. Comput. Biol. 8: 571–583.

Chen X., Chen Y.H., and Anderson V.E. 1999. Protein cross-links: Universal isolation and characterization by isotopic derivatization and electrospray ionization mass spectrometry. Anal. Biochem. 273: 192–203.

de Gunzburg J., Riehl R., and Weinberg R.A. 1989. Identification of a protein associated with p21^ras by chemical crosslinking. Proc. Natl. Acad. Sci. 86: 4007–4011.

Dey D., Bochkariov D.E., Jokhadze G.G., and Traut R.R. 1998. Cross-linking of selected residues in the N- and C-terminal domains of Escherichia coli protein L7/L12 to other ribosomal proteins and the effect of elongation factor Tu. J. Biol. Chem. 273: 1670–1676.

Dukan S., Turlin E., Biville F., Bolbach G., Touati D., Tabet J.C., and Blais J.C. 1998. Coupling 2D SDS-PAGE with CNBr cleavage and MALDI-TOFMS: A strategy applied to the identification of proteins induced by a hypochlorous acid stress in Escherichia coli. Anal. Chem. 70: 4433–4440.

Fancy D.A. 2000. Elucidation of protein–protein interactions using chemical cross-linking or label transfer techniques. Curr. Opin. Chem. Biol. 4: 28–33.

Fischer K.D., Helms J.B., Zhao L., and Wieland F.T. 2000. Site-specific photocrosslinking to probe interactions of Arf1 with proteins involved in budding of COPI vesicles. Methods 20: 455–464.

Fraker P.J. and Speck J.C., Jr. 1978. Protein and cell membrane iodinations with a sparingly soluble chloroamide, 1,3,4,6-tetrachloro-3a, 6a-diphenylglycoluril. Biochem. Biophys. Res. Commun. 80: 849–857.

Gaffney B.J., Willingham G.L., and Schepp R.S. 1983. Synthesis and membrane interactions of spin-label bifunctional reagents. Biochemistry 22: 881–892.

Green N.S., Reisler E., and Houk K.N. 2001. Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers. Protein Sci. 10: 1293–1304.

Hajdu J., Wyss S.R., and Aebi H. 1977. Properties of human erythrocyte catalases after crosslinking with bifunctional reagents. Symmetry of the quaternary structure. Eur. J. Biochem. 80: 199–207.

Hartman F.C. and Wold F. 1967. Cross-linking of bovine pancreatic ribonuclease A with dimethyl adipimidate. Biochemistry 6: 2439–2448.

Hermanson G.T. 1996. Bioconjugate techniques. Academic Press, San Diego, California.

Heymann E. and Mentlein R. 1980. Cross-linking experiments for the elucidation of the quaternary structure of carboxylesterase in the microsomal membrane. Biochem. Biophys. Res. Commun. 95: 577–582.

House H.O. 1972. Modern synthetic reactions, 2nd edition (ed. R. Breslow), pp. 655–660. Benjamin Cummings, Menlo Park, California.

Hurst G.B., Lankford T.K., and Kennel S.J. 2004. Mass spectrometric detection of affinity purified crosslinked peptides. J. Am. Soc. Mass. Spectrom. 15: 832–839.

Jackson V. 1987. Deposition of newly synthesized histones: New histones H2A and H2B do not deposit in the same nucleosome with new histones H3 and H4. Biochemistry 26: 2315–2325.

Jackson V. 1999. Formaldehyde cross-linking for studying nucleosomal dynamics. Methods 17: 125–139.

Jentoft N. and Dearborn D.G. 1983. Protein labeling by reductive alkylation. Methods Enzymol. 91: 570–579.

Ji T.H. 1977. A novel approach to the identification of surface receptors. The use of photosensitive hetero-bifunctional cross-linking reagent. J. Biol. Chem. 252: 1566–1570.

Keough T., Lacey M.P., and Youngquist R.S. 2000. Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 14: 2348–2356.

Koch T., Suenson E., Korsholm B., Henriksen U., and Buchardt O. 1994. Pitfalls in characterization of protein interactions using radioiodinated crosslinking reagents. Preparation and testing of a novel photochemical ¹²⁵I-label transfer reagent. Bioconjug. Chem. 5: 205–212.

Kosaka T., Takazawa T., and Nakamura T. 2000. Identification and C-terminal characterization of proteins from two-dimensional polyacrylamide gels by a combination of isotopic labeling and nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 72: 1179–1185.

Kosower E.M. and Kosower N.S. 1995. Bromobimane probes for thiols. Methods Enzymol. 251: 133–148.

Lambert J.M., Boileau G., Cover J.A., and Traut R.R. 1983. Cross-links between ribosomal proteins of 30S subunits in 70S tight couples and in 30S subunits. Biochemistry 22: 3913–3920.

Li Y.-Z., Kirby J.P., George M.W., Poliakoff M., and Schuster G.B. 1988. 1,2-Didehydroazepines from the photolysis of substituted aryl azides: Analysis of their chemical and physical properties by time-resolved spectroscopic methods. J. Am. Chem. Soc. 110: 8092–8098.

Nadeau O.W., Sacks D.B., and Carlson G.M. 1997a. Differential affinity cross-linking of phosphorylase kinase conformers by the geometric isomers of phenylenedimaleimide. J. Biol. Chem. 272: 26196–26201.

Nadeau O.W., Sacks D.B., and Carlson G.M. 1997b. The structural effects of endogenous and exogenous Ca²⁺/calmodulin on phosphorylase kinase. J. Biol. Chem. 272: 26202–26209.

Nadeau O.W., Traxler K.W., Fee L.R., Baldwin B.A., and Carlson G.M. 1999a. Activators of phosphorylase kinase alter the cross-linking of its catalytic subunit to the C-terminal one-sixth of its regulatory α subunit. Biochemistry 38: 2551–2559.

Nadeau O.W., Domanski P., Usacheva A., Uddin S., Platanias L.C., Pitha P., Raz R., Levy D., Majchrzak B., Fish E., and Colamonici O.R. 1999b. The proximal tyrosines of the cytoplasmic domain of the β chain of the Type I interferon receptor are essential for signal transducer and activator of transcription (Stat) 2 activation. J. Biol. Chem. 274: 4045–4052.

Reynolds K.J., Yao X., and Fenselau C. 2002. Proteolytic ¹⁸O-labeling for comparative proteomics: Evaluation of endoprotease Glu-C as the catalytic agent. J. Proteome Res. 1: 27–33.

Rice N.A., Nadeau O.W., Yang Q., and Carlson G.M. 2002. The calmodulin binding domain of the catalytic γ subunit of phosphorylase kinase interacts with its inhibitory α subunit. J. Biol. Chem. 277: 14681–14687.

Sanders S.L., Whitfield K.M., Vogel J.P., Rose M.D., and Schekman R.W. 1992. Sec61p and BiP directly facilitate polypeptide translocation into the ER. Cell 69: 353–365.

Schmitt-Ulms G., Hansen K., Jialing L., Cowdrey C., Yang J., DeArmond S.J., Cohen F.E., Prusiner S.B., and Baldwin M.A. 2004. Time controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues. Nat. Biotechnol. 22: 724–731.

Schulz D.M., Ihling C., Clore G.M., and Sinz A. 2004. Mapping the topology and determination of a low-resolution three-dimensional structure of the calmodulin-melittin complex by chemical cross-linking and high-resolution FTICRMS: Direct demonstration of multiple binding modes. Biochemistry 43: 4703–4715.

Sechi S. and Chait B.T. 1998. Modification of cysteine residues by alkylation. A tool in peptide mapping and protein identification. Anal. Chem. 70: 5150–5158.

Sigrist H., Allegrini P.R., Kempf C., Schnippering C., and Zahler P. 1982. 5-Isothiocyanato-1-naphthalene azide and p-azidophenylisothiocyanate: Synthesis and application in hydrophobic heterobifunctional photoactive cross-linking of membrane proteins. Eur. J. Biochem. 125: 197–201.

Simon M.J. and Day R.A. 2000. Improved resolution of hydrophobic penicillin-binding proteins and their covalently linked complexes on a modified C18 reversed phase column. Anal. Lett. 33: 861–867.

Traut R.R., Casiano C., and Zecherle N. 1989. Cross-linking of protein subunits and ligands by the introduction of disulphide bonds. In Protein function: A functional approach (ed. T.E. Creighton), pp. 101–133. IRL Press, Oxford.

Valentine W.M., Graham D.G., and Anthony D.C. 1993. Covalent cross-linking of erythrocyte spectrin by carbon disulfide in vivo. Toxicol. Appl. Pharmacol. 121: 71–77.

Watt D.S., Kawada K., Leyva E., and Platz M.S. 1989. Exploratory photochemistry of iodinated aromatic azides. Tetrahedron Lett. 30: 899–902.

Wedekind F., Baer-Pontzen K., Bala-Mohan S., Choli D., Zahn H., and Brandenburg D. 1989. Hormone binding site of the insulin receptor: Analysis using photoaffinity-mediated avidin complexing. Biol. Chem. Hoppe-Seyler 370: 251–258.

Wong S.S. 1993. Chemistry of protein conjugation and cross-linking. CRC Press, Boca Raton, Florida.

<<< Chapter 6 References            Chapter 8 References >>>