Team:SCUT-China/Modeling/Simulation

Reactions and Mechanism

1.Mechanism

The model for enzyme action, first suggested by Brown and Henri but later established more thoroughly Michaelis and Menten, suggests the binding of free enzyme to the substrate forming a enzyme-substrate(ES) complex. This complex undergoes a transformation, releasing product and free enzyme. The free enzyme is then available for another round of binding to new substrate.

In the single substrate enzyme catalyzed reactions, the mechanism is often written as:

And the Michaelis-Menten equation is:

(2) Kinetics of multi substrates enzyme catalyzed reactions

We apply two mechanisms of kinetics of multi substrates enzyme catalyzed reactions to our modeling section, one is Theorell-Chance bi-bi (T-C bi-bi), the other is Ping-pong bi-bi.

Sequential bi-bi reaction means that all substrates must bind to the enzyme before any reaction takes place. Now we take two substrates as an example. In sequential bi-bi reaction, a ternary complex is formed when both substrates bind to the enzyme. But the complex is not steady and two products release after new covalent bonds are formed and old covalent bonds are broken in the complex.

Sequential bi-bi reaction can be random or ordered. The random sequential bi-bi means that any substrate can bind first to the enzyme and any product can release first. The ordered sequential bi-bi means that the substrates bind to the enzyme and the products release in a specific order.

T-C bi-bi reaction is a kind of the ordered sequential bi-bi reactions. Now we take two substrates as an example again. The characteristic of T-C bi-bi is that two products can release in a flash because of the extreme instability of the ternary complex. The allosteric process is not obvious.

Ping-pong bi-bi reaction is a double-displacement reaction. Substrate A bind first to the enzyme followed by product P release. Typically, product P is a fragment of the original substrate A. The rest of the substrate is covalently attached to the enzyme E, which we now designate as F. The second Substrate, B, binds and reacts with enzyme F. Substrate B form a covalent adduct with the covalent fragment of A in the enzyme F to form product Q. The enzyme is finally restored to its initial form, E.

In Ping-pong bi-bi reactions, the mechanism is often written as:

And the equation is: