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Examples for domain shuffling are illustrated in Figure 2.14. Domain shuffling is important for the explanation of evolutionary development. It is not only individual point mutations that bring evolutionary advancement but also mainly new combinations of functional modules (prefabricated building blocks).
Figure 2.13 Structure of Src protein with four domains. The four domains are the (a) small kinase domain, (b) large kinase domain, (c) SH2 domain, and (d) SH3 domain.
Figure 2.14 Occurrence of domains in different proteins.
Many proteins contain binding sites for ligands; ligands can be not only lower‐molecular‐weight substances but also macromolecules such as nucleic acids or other proteins. The binding of a ligand to a binding site can be viewed as a molecular recognition process. Such molecular recognition processes are common in the cell, but these processes are only understood in detail in a few cases. However, these processes have an important relevance to cell function, metabolism, and “life” that should not be underestimated. Experiments in structural biology have already shown that the binding of a ligand in a binding site functions according to the lock‐and‐key principle. The binding site has a specific spatial structure in which a ligand fits selectively. Binding of the ligand involves the formation of several noncovalent bonds (Figure 2.15) between the functional groups of the ligand and those of the protein. Binding generally brings about a change of the protein conformation (induced fit). The binding site is not formed by amino acid residues that lie beside each other on the peptide chain, but often consists of amino acids located in different parts of a peptide chain and spatially form a binding site by appropriate specific folding (Figure 2.15).
Figure 2.15 Structure of binding sites within proteins. (a) Schematic illustration of the significance of noncovalent bonds in the lock‐and‐key principle. (b) cAMP is locked into a binding site via ionic and hydrogen bonds.
Interactions that occur between antigens and antibodies (see Chapter 28), between ligands and hormone receptors, and between enzymes and their substrates are particularly intimate and selective. The topic of protein–protein interactions is discussed further in Chapter 23.
Most of the cellular building blocks are inert molecules that are not prone to react chemically. Significant activation energy has to be overcome in order to start an energy‐consuming chemical reaction. In the laboratory, this can be achieved by heating and adding acids or bases. In biological systems, evolution has developed enzymes as biological catalysts that are able to catalyze all necessary reactions without higher temperatures being necessary. Enzymes do not change the reaction equilibrium, but usually alter the reaction rate. Enzymes contain an active center in which a substrate is bound. After the enzyme has catalyzed a reaction, the product is released, but the enzyme remains unchanged and is ready for a new reaction. Noncovalent interactions (hydrogen bonds, ionic bonds) and transient covalent bonds between protein and substrate play a key role during the binding and catalysis. Detailed elucidation of such interactions at the atomic scale is the task of biophysics and biochemistry. This research is also important for biotechnology in relation to the synthesis of new enzyme inhibitors or enzyme modulators.
Enzymes show high substrate specificity. It is believed that for almost every biosynthetic step that happens in the cell, a specific enzyme is also present. This does not rule out that enzymes that catalyze chemically similar reactions can be derived from a common original enzyme. Such enzymes belong to a common protein family. Most enzymes have particular pH and temperature optima. Enzymes are divided into different classes according to the processes catalyzed (Table 2.5). Coenzymes or inorganic ions often take part in the catalysis itself. Many coenzymes must be ingested in the forms of vitamins (Table 2.6) because the human body cannot synthesize them themselves. Biochemists and biotechnologists are interested in the elucidation of the enzymatic reaction mechanisms because hints for new catalysts for organic synthesis can be obtained. Apart from this, scientists are attempting to create new biological catalysts through the production of artificial enzymes through genetic engineering of existing enzymes.
Table 2.5 Important classes of enzymes.
| Enzyme | Reaction catalyzed |
|---|---|
| Hydrolases | Catalyze hydrolytic cleavage (amylase, lipase, glucosidase, esterase) |
| Nucleases | Hydrolyze nucleic acids (DNase, RNase) |
| Proteases | Cleave peptides (pepsin, trypsin, chymotrypsin) |
| Isomerases | Catalyze the rearrangement of bonds within a molecule |
| Synthases | General name for an enzyme that catalyzes condensation reactions in anabolic processes |
| Polymerases | Catalyze the formation of RNA and DNA |
| Kinases | Transfer phosphate residues; the protein kinases (PKA, PKC) are particularly important |
| Phosphatases | Remove phosphate residues from a molecule |
| ATPases | Hydrolyze ATP (e.g. H+‐ATPase, Na+, K+‐ATPase, Ca2+‐ATPase); motor proteins, such as myosin |
| GTPases | Hydrolyze GTP; many GTP‐binding proteins work as GTPases |
| Oxidoreductases | Enzymes that catalyze redox reactions, in which one molecule is reduced and another is oxidized; they are grouped into oxidases, reductases, and dehydrogenases |
Table 2.6 Many vitamins serve as essential coenzymes for enzyme reactions.
| Vitamin | Coenzyme | Enzyme reactions that require the coenzyme |
|---|---|---|
| Thiamine (vitamin B1) |
|