Abstract
One of the most fundamental problems of enzymology is the elucidation of the molecular mechanisms by which enzymes work. The determination of the way in which such complex structures act to bring about efficient, specific catalytic reactions is a very interesting but difficult problem which can only be solved by the assembly of evidence from many different lines of research. Many factors contribute to the extraordinary catalytic properties of enzymes, including the precise juxtapositions of functional groups and particularly favourable micro-environments at active sites which enable specific reactions to occur. Precisely these factors influence the reactivity of functional groups in chemical modification and affinity labelling studies of enzymes.
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References
Adams, M. J. (1970). Structure of lactate dehydrogenase at 2.8Å resolution. Nature, Lond., 227, 1098
Anderson, S. R. and Weber, G. (1965). Multiplicity of binding of lactate dehydrogenases. Biochemistry, 4, 1948
Barden, R. E., Darke, P. L., Deems, R. A. and Dennis, E. A. (1980). Interaction of phospholipase A2 from cobra venom with Cibacron Blue F3G-A. Biochemistry, 19, 1621
Barker, D. G. and Winter, G. (1982). Conserved cysteine and histidine residues in the structures of the tyrosyl and methionyl-tRNA synthetases. FEBS Lett., 145, 191
Beissner, R., Quiocho, F. A. and Rudolph, F. B. (1979). Dinucleotide fold proteins. J. Molec. Biol., 134, 847
Biellmann, J.-F., Samama, J.-P., Brändén, C. I. and Eklund, H. (1979). X-Ray studies of the binding of Cibacron Blue F3G-A to liver alcohol dehydrogenase. Eur. J. Biochem., 102, 107
Blow, D. M., Bhat, T. N., Metcalf, A., Risler, J. N., Brunnie, S. and Zelwer, C. (1983). Structural homology in the amino-terminal domains of two aminoacyl tRNA-synthetases. J. Molec. Biol., 171, 571
Blow, D. M., Birktoft, J. J. and Hartley, B. S. (1969). Role of a buried acid group in the mechanism of action of chymotrypsin. Nature, Lond., 221, 337
Bond, J. S., Francis, S. H. and Park, J. H. (1970). An essential histidine in the catalytic activities of 3-phosphoglyceraldehyde dehydrogenase. J. Biol. Chem., 245, 1041
Bosshard, H. R., Koch, G. L. E. and Hartley, B. S. (1978). The aminoacyl-tRNA synthetase-tRNA complex: detection by differential labelling of lysine residues involved in complex formation. J. Molec. Biol., 119, 377
Bruton, C. J. and Atkinson, T. (1979). The binding of aminoacyl-tRNA synthetases to triazine dye conjugates. Nucleic Acids Res., 7, 1579
Buehner, M., Ford, G. C., Moras, D., Olsen, K. W. and Rossmann, M. G. (1973). D-Glyceraldehyde-3-phosphate dehydrogenase: three-dimensional structure and evolutionary significance. Proc. Natl Acad. Sci. USA, 70, 3052
Carter, C. W., Jr., and Carter, C. W. (1979). Protein crystallization using incomplete factorial experiments. J. Biol. Chem., 254, 12219
Clonis, Y. D., Goldfinch, M. J. and Lowe, C. R. (1981). The interaction of yeast hexokinase with Procion Green H-4G. Biochem. J., 197, 203
Davidson, W. S. and Flynn, T. G. (1979). A functional arginine residue in NADPH-dependent aldehyde reductase from pig kidney. J. Biol. Chem., 245, 3724
Disabato, G. and Ottesen, M. (1965). Effect of coenzymes on the hydrogen-deuterium exchange of chicken heart lactic dehydrogenase as measured by infrared spectrophotometry. Biochemistry, 4, 422
Edman, P. and Begg, G. R. (1967). A protein sequenator. Eur. J. Biochem., 1, 80
Eklund, H., Brändén, C. I. and Journvall, H. (1976a). Structural comparisons of mammalian, yeast and bacillar alcohol dehydrogenases. J. Molec. Biol., 102, 61
Eklund, H., Nordstrom, B., Zeppezauer, E., Sonderlund, G., Ohlsson, I., Boiwe, T., Sonderberg, B. O., Tapia, O., Brändén, C. I. and Akeson, A. (1976b). Three dimensional structure of horse liver alcohol dehydrogenase at 2.4Å resolution. J. Molec. Biol., 102, 27
Gilleland, M, J. and Shore, J. D. (1969). Inhibition of horse liver alcohol dehydrogenase by l-3,3–,5-triiodothyronine. J. Biol. Chem., 224, 5357
Glazer, A. N. (1967). The specific binding of Biebrick Scarlet to the active site of a-chymotrypsin. J. Biol. Chem., 247, 4528
Glazer, A. N. (1970). On the prevalence of ‘non-specific’ binding at the specific binding sites of globular proteins. Proc. Natl Acad. Sci. USA, 65, 1057
Gray, W., Jr. (1967). Dansyl chloride procedure. In Methods in Enzymology (ed. C. W. H. Hirs), Vol. XI, pp. 139–151, Academic Press, New York
Hartley, B. S. (1964). The structure and activity of chymotrypsin. In Structure and Activity of Enzymes (ed. T. W. Goodwin, J. J. Harris and B. S. Hartley), pp. 47–60, Academic Press, New York
Hartley, B. S. (1974). The active centres of serine proteinases. Ann. N. Y. Acad. Sci., 227, 438
Hill, R. L. and Smith, E. L. (1957). Leucine aminopeptidase. VI. Inhibition by alcohols and other compounds. J. Biol. Chem., 224, 209
Houndtondji, C. and Blanquet, S. (1985). Methionyl-tRNA synthetase from Escherichia coli: primary structure at the binding site for the 3–-end of tRNA. Methods Biochem., 24, 1175
Hughes, G. J. (1983). High performance liquid chromatography: analytical and preparative applications in protein structure determination. In Methods in Biochemical Analysis (ed. D. Glick), pp. 59–139
Hughes, P., Sherwood, R. F. and Lowe, C. R. (1984). Studies on the nature of transition-metal-ion-mediated binding of triazine dyes to enzymes. Eur. J. Biochem., 144, 135
Hunkapillar, M. W. and Hood, L. E. (1983). In Methods in Enzymology (ed. C. H. W. Hirs and S. N. Timasheff), Vol. 91, pp. 486–494, Academic Press, New York
Issaly, I., Poiret, M., Tanc, P., Thiry, L. and Herve, G. (1982). Interactions of Cibacron Blue F3G-A and nucleotides with E. coli aspartate carbamoyltransferase and its subunits. Biochemistry, 21, 1612
Jacobsberg, L. B., Kautrowitz, E. R. and Lipscomb, W.N. (1975). Interaction of tetraiodofluorescein with aspartate transcarbamylase and its isolated catalytic and regulatory sub-unit. J. Biol. Chem., 250, 9238
Jacobsberg, L. B., Kautrowitz, E. R., McMurray, C. H. and Lipscomb, W. N. (1973). The interaction of tetraiodofluorescein with aspartate transcarbamylase. Biochem. Biophys. Res. Commun., 55, 1255
Journvall, H. (1970). Horse liver alcohol dehydrogenase. The primary structure of the protein chain of the ethanol-active isoenzyme. Eur. J. Biochem., 16, 25
Journvall, H., Woenckhaus, C. and Johnscher, G. (1975). Modification of alcohol dehydrogenase with a reactive coenzyme analogue. Eur. J. Biochem., 53, 71
Kimmel, M. T. and Plummer, T. H. (1972). Identification of a glutamic acid at the active centre of bovine carboxypeptidase. J. Biol. Chem., 247, 7864
Kitz, R. and Wilson, I. B. (1962). Esters of methanesulfonic acid as irreversible inhibitors of acetylcholinesterase. J. Biol. Chem., 237, 3245
Lee, R. T. and McElroy, W. O. (1971). Isolation and partial characterization of a peptide derived from the luciferin binding site of firefly luciferase. Arch. Biochem. Biophys., 146, 551
Loftfield, R. B. (1972). The mechanism of aminoacylation of transfer RNA. Progr. Nucleic Acid Res. Molec. Biol., 12, 87
McArdell, J. E. C., Atkinson, T. and Bruton, C. J. (1982). The interaction of tryptophanyl-tRNA synthetase with the triazine dye Brown MX-5BR. Eur. J. Biochem., 125, 361
McArdell, J. E. C., Atkinson, T. and Bruton, C. J. (1987a). The isolation of a peptide from the catalytic domain of Bacillus stearothermophilus tryptophanyl-tRNA synthetase. The interaction of Brown MX-5BR with tyrosyl-tRNA synthetase. Biochem. J., 243, 701
McArdell, J. E. C., Atkinson, T. and Bruton, C. J. (1987b). Probing the substrate binding sites of aminoacyl-tRNA synthetases with the Procion dye Green HE-4BD and its reactive derivative Bis-dichloro-Green 4BD (in preparation)
McCarthy, K., Lovenber, W. and Sjoerdsma, A. (1968). The mechanism of inhibition of horse liver alcohol dehydrogenase by thyroxine and related compounds. J. Biol. Chem., 243, 2754
Moe, J. G. and Piszkiewicz, D. (1979). Isoleucyl transfer ribonucleic acid synthetase. Competitive inhibition with respect to transfer ribonucleic acid by Blue Dextran. Biochemistry, 18, 2810
Morris, H. R. (1974). Peptide sequence determination by mass spectrometry. Biochem. Soc. Trans., 2, 806
Murdock, A. L., Grist, K. L. and Hirs, C. H. W. (1966). On the dinitrophenylation of bovine pancreatic ribonuclease A. Arch. Biochem. Biophys., 114, 375
Petra, P. H., Bradshaw, R. A., Walsh, K. A. and Neurath, H. (1969). Identification of the amino acid replacements characterizing the allotypic forms of bovine carboxypeptidase A. Biochemistry, 8, 2762
Polgar, L. and Halasz, P. (1982). Review article: Current problems in mechanistic studies of serine and cysteine proteinases. Biochem. J., 207, 1
Pompon, D., Guiard, B. and Lederer, F. (1980). Binding of Cibacron Blue to the flavin and NADH sites in cytochrome b5 reductase. Eur. J. Biochem., 110, 565
Rao, S. T. and Rossman, M. G. (1973). Comparison of super-secondary structures in proteins. J. Molec. Biol., 76, 241
Rippa, M., Picco, C. and Pontremoli, S. (1970). Rose Bengal as a specific photosensitizer for a histidine residue at the triphosphopyridine nucleotide binding site of 6-phosphogluconate dehydrogenase. J. Biol. Chem., 245, 4977
Santi, D. V. and Cunnion, S. O. (1974). Macromolecular affinity labelling agents. Reaction of N-bromoacetylisoleucyl transfer ribonucleic acid with isoleucyl transfer ribonucleic acid synthetase. Biochemistry, 13, 481
Small, D. A. P., Lowe, C. R., Atkinson, T. and Bruton, C. J. (1982). Affinity labelling of enzymes with triazine dyes: isolation of a peptide from the catalytic domain of horse liver alcohol dehydrogenase using Procion Blue MX-R as a structural probe. Eur. J. Biochem., 128, 119
Steitz, T. A., Henderson, R. and Blow, D. M. (1969). Structure of crystalline α-chymotrypsin. J. Molec. Biol., 46, 337
Subramanian, S. and Kaufman, B. T. (1980). Dihydrofolate reductase from chicken liver and Lactobacillus casei bind Cibacron Blue F3G-A in different modes and at different sites. J. Biol. Chem., 225, 10587
Thompson, S. T., Cass, K. H. and Stellwagen, E. (1975). Blue Dextran Sepharose: an affinity column for the dinucleotide fold in proteins. Proc. Natl Acad. Sci. USA, 72, 669
Wasserman, P. M. and Lentz, P. J., Jr. (1971). The interaction of tetraiodo-fluorescein with dogfish muscle lactate dehydrogenase: a chemical and X-ray crystallographic study. J. Molec. Biol., 60, 509
Wilson, J. E. (1976). Applications of Blue Dextran and Cibacron Blue F3G-A in purification and structural studies of nucleotide requiring enzymes. Biochem. Biophys. Res. Commun., 72, 816
Witt, J. J. and Roskoski, R., Jr. (1980). Adenosine cyclic 3–,5–-monophosphate dependent protein kinase: active site directed inhibition by Cibacron Blue F3G-A. Biochemistry, 19, 143
Zelwer, C., Risler, J. L. and Brunie, S. (1982). Crystal structure of Escherichia coli methionyl tRNA-synthetase at 2.5Å resolution. J. Molec. Biol., 155, 63
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McArdell, J.E.C., Bruton, C.J. (1987). The Use of Organic Dyes in the Elucidation of Enzyme Structures and Mechanisms. In: Clonis, Y.D., Atkinson, T., Bruton, C.J., Lowe, C.R. (eds) Reactive Dyes in Protein and Enzyme Technology. Palgrave, London. https://doi.org/10.1007/978-1-349-06582-0_8
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DOI: https://doi.org/10.1007/978-1-349-06582-0_8
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