Structural Biochemistry/Catalytic Mechanisms/Catalysis by Approximation

Catalysis by Approximation
Substrates that happen to come together through random collisions have an even smaller possibility of contact with the reactive portions of the substrate. Thus, enzymes can employ a strategy known as catalysis by approximation by which the enzyme brings together two substrates in order to increase the rate of reaction. This strategy takes advantage of binding energy and positions the substrates in the correct orientation for the reaction to proceed. Usually in a reaction, there will be a loss in translational entropy and rotational entropy. In the reaction, the transition state is much more ordered than it is at ground state, making delta S negative. This reaction takes place in the active site of an enzyme and the substrate and the catalytic group will than act as one molecule, preventing the loss of translational and rotational energy. The reaction first begins with two molecules that are able to find each other, which makes the rate of reaction dependent on the concentrations of the reactants. This is due to the higher probability of molecules to find each other.

Some Examples
An example of catalysis by approximation is when NMP kinases[] bring two nucleotides together to facilitate the transfer of a phosphoryl group from one nucleotide to the other. With the addition of adenosine triphosphate (ATP), a phosphate group is placed adjacently to the phosphate group of the NMP kinase. This facilitates in the transfer of the phosphate between the two molecules.