Warum sind Enzyme Makromoleküle?

Abstract

The paper is devoted to the question wheter the macromolecular structure is really essential for the chemical and biological qualities of enzymes. Recognizing that high molecular weight compounds are relevant both in nature and in modern technology, the question is first approached by considering whether there are some common and quite general properties intrinsic to long chains which may explain the overall success of a polymer. It is pointed out that in the process of building polymers from low molecular weight monomers so many structural parameters (copolymerisation, branching, cross-linking, stereoisomerism, grafting, compounding, etc.) can be utilized and regulated, that the physical and chemical properties of the final products can be modulated almost at will. For functional proteins, the two most important of such structural parameters are the copolymerization (from twenty different amino acid residues) and the resultant rigid folding in solution. One cannot, however, easily dispell the doubt that enzymes are oversized, particularly if one considers the principles by which enzymes develop in the evolutionary process. Indeed, the products synthesized by nature do not correspond to the optimal structural efficiency; on the contrary, structures are built at random without a prefixed finality, and they assume a function that depends on the circumstances. As a consequence of this “molecular tinkering” all enzymes may be mostly oversized, at least in principle.
To analyze the question of whether the large structure of enzymes is really necessary or whether it is an unnecessary amount of molecular tinkering and fossil sequences, an enzyme can be ideally depicted as having three regions: the active site region, its overall folding, and the region in contact with its environment. Concerning the active site region, it is argued that the main structural feature is an ordered high atomic packing density (the meaning of the term order is also briefly discussed). This is a prerequisite for catalysis also in other types of chemistry, e.g. in inorganic catalysis by zeolites or other inorganic crystalline solids. In the case of enzymes the high molecular packing density is expressed in four main phenomenological properties: a good binding energy for the substrate, the stereochemical complementary of the active concavity, the obliged proximity of active amino acid residues, and the physical microenvironment of the site where the reaction has to take place. It is shown that a long chain fulfills in the best way the chemical pre-requisites for providing these four properties.
After the active site region, the conformational properties of enzymes are discussed. It is argued that they are based on a compromise between two seemingly contadictory qualities, i.e. the conformational rigidity on the one hand, and the ability of undergoing conformational changes on the other. A few examples are discussed. It is shown that a long chain is the best and perhaps the only way to accomodate both conformational rigidity (via long series of intramolecular interactions) and flexibility upon ligand binding. This can give rise both to local conformational changes, very often quite important for catalysis, as well as to long-range channelled conformational changes, very often quite relevant for allostery and other biologically important mechanisms.
Concerning the external surface of the enzyme, it is recognized that a long chain permits a best fitting with the environment (e. g. solubilizing, with the help of hydrophilic residues, a largely insoluble water-active site region). But the macromolecular chain is also valuable for permitting the enzyme to go from one environment to another by selective conformational changes: in this way the enzyme body behaves like an elastic buffer which imparts the enzyme’s chameleon-like properties. This can be put to use in biotechnology, and the particular case of enzymes solubilized in hydrocarbon solvents with the help of reverse micelles is used as illustration. Here enzymes like lysozyme or chymotrypsin undergo gross conformational changes, without loss of activity (which actually in some cases becomes even greater than in bulk water).
It is therefore concluded, on the basis of the analysis of the active site, of the protein folding and of the protein surface, that a macromolecular chain is indeed necessary for the chemical properties of an enzyme. The question however, as to what extent does a long chain help in decreasing the activation energy in catalysis, could be answered with the present analysis only in an indirect form.
Finally, some considerations are made as to the philosophical implications of the question “Why are Enzymes Macromolecules” and to its analysis. This is viewed within the general framework of molecular Darwinistic evolution which is dominated by strict reductionism, at least at the level of the molecular structures. The points of view of Jacob and Monod in this respect are cited, and also some conceptual difficulties perceived in the Darwinistic reductionism are presented.