Molecular Biology: Protein Structure and Functions - Stepanov V.M. 2005

Enzymes
General Concepts of Enzymatic Catalysis

When analyzing the mode of action of Enzymes, A number of simplifications are used that, to a certain extent, capture the essential features of this process. First and foremost, it is taken into account that not the entire enzyme molecule directly contacts the substrate, but only a specific region—the Active Site. The BOUNDARIES OF THE active site cannot be strictly defined, since each of its components interacts in one way or another with other PARTS OF THE protein molecule. These interactions are usually crucial for the catalytic mechanism: they alter the reactivity of the functional groups within the active site, anchor them within the protein globule Structure, or create a specific microenvironment that favors catalysis. Thus, METABOLISM/2.html">THE CONCEPT OF the active site is, in a sense, an abstraction that highlights the essential features of an enzyme while somewhat oversimplifying the description of catalysis.

Simplifying the picture further, the active site is subdivided into a substrate-binding region and the catalytic center proper. It is generally assumed that the binding region is responsible for The formation of the enzyme-substrate complex (the so-called Michaelis complex), substrate Selection, its anchoring, and correct orientation relative to the catalytic center. The Functional groups of the catalytic center take a direct part in The conversion of the substrate. This simplification is also useful, provided one remembers its relative and conditional nature. In real enzyme-substrate complexes, the groups of the catalytic center are frequently involved in substrate binding, whereas the protein structures forming the binding region often participate in dynamic processes, directly influencing the catalytic mechanism.

The conventional Nature of the active site concept is further underscored by the fact that it cannot be physically separated from the rest of the enzyme molecule. Around the late 1950s and early 1960s, reports emerged regarding the successful “ excision” of active sites from enzymes, particularly proteinases. However, all of these proved to be the result of experimental errors. With the Determination of the three-dimensional structures of numerous enzymes, it became clear that their active sites are typically formed by amino acid residues that are distant from one another in the primary Amino Acid Sequence, but are brought into close proximity during the folding of the tertiary structure.

For instance, in the Active Site of Pepsin, a pivotal role is played by aspartic acid residues 35 and 215, which are brought together when the polypeptide chain—consisting of 321 amino acid residues—folds into its Spatial Structure. Obviously, any attempt to “cut out” the sequence regions containing the active site components from the protein globule would yield an extremely unstable structure composed of multiple peptide fragments. More importantly, it would destroy the specific microenvironment of the catalytic functional groups that dictates their chemical properties.

At the same time, the Enzyme Structure as a whole should not be regarded as untouchable. The molecules of many enzymes can withstand quite substantial damage, including individual cleavages of polypeptide chains, and tolerate numerous Amino Acid Substitutions; in some cases, it is even possible to significantly reduce their size without a loss of activity. In principle, it is also feasible to obtain relatively small catalytically active structures, provided, however, that they retain the stability of their three-dimensional architecture—meaning they must match at least the size and stability of a structural domain.