Читать книгу Enzyme-Based Organic Synthesis - Cheanyeh Cheng - Страница 13

The folding of long polypeptide chain to form tertiary or quaternary structure is caused by chemical or physical forces such as disulfide linkage, hydrogen bonding, acid–base interaction (salt bridge), and hydrophobic interaction. Folding of polypeptides into two or more stable globular units is called domains. Different domains often play distinct functions, such as binding molecules or interaction with other proteins. A molecule bound reversibly by a protein is called ligand. The site on the protein that binds the ligand is called the binding site. When a protein binds a ligand, the 3D structure of protein is often caused by a conformational change to permit a tighter binding to the ligand. This kind of binding with structural adaption between protein and ligand is called induced fit mechanism. Enzymes have catalytic function that binds and chemically rapidly transforms other molecules. For enzyme‐catalyzed reaction, the molecule bound and acted by the enzyme is called substrate; the binding site is called the active site or catalytic site.

Enzyme is an efficient catalyst and is responsible for thousands integrated chemical reactions of the biological process occurred in the living system. Just like the usual inorganic catalyst, enzymes catalyze a reaction by lowering the transition state energy (the activation energy) of the activated complex and by raising the ground state energy. On the other hand, the catalysis of enzymes, not like simple inorganic catalysts, proceeds by forming several transition states and each with low activation energy instead of one activated complex of greater activation energy. The rate of enzyme‐catalyzed reaction for a simple one enzyme, one substrate and one product system with the following mechanism was studied by Michaelis and Menten in 1913 (Scheme 1.2). In this mechanism, enzyme (E) binds the substrate (S) to form an enzyme–substrate (ES) complex and subsequently the ES breaks down to the product (P).

Scheme 1.2 The proposed enzyme reaction mechanism by Michaelis and Menten.

According to this mechanism, the enzyme‐catalyzed reaction rate equation called Michaelis–Menten equation (Eq. 1.1) was derived by Michaelis and Menten with the second step as the rate‐limiting step and derived by Briggs and Haldane using steady‐state assumption. The term V ₀ is the initial rate, V _max is the maximum reaction rate, [S] is the substrate concentration, and K_m is the Michaelis constant.

(1.1)

For a more common case, enzyme product complexes (EP) release, EP → E + P, is the rate‐limiting step, which is described as the reaction Scheme 1.3.

Therefore, a more general rate constant called the turnover number, k cat, is defined to describe the limiting rate of any enzyme‐catalyzed reaction at saturation, that is, V _max = k _cat[E _t]. In this situation, the Michaelis–Menten equation becomes Eq. 1.2

(1.2)

The turnover numbers of several enzymes are given in Table 1.1.

Scheme 1.3 A generalized enzyme‐catalyzed reaction.

Table 1.1 Turnover numbers for some enzymes.

Enzyme	Turnover number kcat (s−1)
Catalase	40 000 000
Carbonic anhydrase	400 000
Acetylcholinesterase	140 000
β‐Lactamase	2000
Fumarase	800
β‐Galactosidase	208
Phosphoglucomutase	21
Tryptophan synthetase	2
RecA protein (an ATPase)	0.4