Chemical topography of sidechains in enzymes
Information concerning the structure and the structural flexibility, the motility, of polypeptide chains in an enzyme may be obtained by use of the method of sidechain modification. Evaluation of such information requires a rigorous kinetic analysis of the chemical modification process. The need to restrict the study to a single residue is emphasized and illustrated with examples. It is shown that the reaction of the second reactive SH group of triosephosphatedehydrogenase with an appropriate reagent is the result of the fluctuation of the polypeptide chain in the native enzyme. A similar reaction due to the same cause is described for the reaction of the buried SH group of pancreatic amylase. The complex analysis of the carboxymethylation of aldolase, using correlated kinetic, enzymological and sequence studies, has established in the author's laboratory, the relation of a less reactive SH group to the active site. Similar considerations have been applied to the study of SH groups involved in subunit interaction within lactate dehydrogenase. In the lifetime of a generation the chemistry of proteins has made a full turn from the ignoramus et ignorabimus of the early 'twenties to the complete amino acid sequences and detailed three-dimensional models deduced from x-ray crystallography. During the development of these modern methods, chemical topography or surface chemistry of enzymes has contributed a great deal to our knowledge of the biologically important functional groups of enzymes. The rapid progress in enzyme chemistry has led to the belief that knowledge of the nature and position of all atoms in the enzyme molecule is enough to explain its biological function. Such reductionism is, in my view, not warranted. In our laboratory in Budapest we have collected in the past few years some data on the location of sidechains and on their role in biological activity. These results I should like to use to illustrate the potentialities of the method of sidechain modification in order to show in which respects chemical topography may contribute to the understanding of the biological function. Chemical modification of sidechains, and some physicochemical methods specific for one kind of sidechain, have long been used to determine which of these sidechains might be on the surface of the protein and again which of them might be involved in the mechanism of enzyme action. The scattered data obtained in this way have been the only evidence available for a long time. With