Enzyme catalysis

Enzyme catalysis is the increase in the rate of a process by an "enzyme", a biological molecule. Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, called the active site.
Most enzymes are made predominantly of proteins, either a single protein chain or many such chains in a multi-subunit complex. Enzymes often also incorporate non-protein components, such as metal ions or specialized organic molecules known as cofactor. Many cofactors are vitamins, and their role as vitamins is directly linked to their use in the catalysis of biological process within metabolism. Catalysis of biochemical reactions in the cell is vital since many but not all metabolically essential reactions have very low rates when uncatalysed. One driver of protein evolution is the optimization of such catalytic activities, although only the most crucial enzymes operate near catalytic efficiency limits, and many enzymes are far from optimal. Important factors in enzyme catalysis include general acid and base catalysis, orbital steering, entropic restriction, orientation effects, as well as motional effects involving protein dynamics
Mechanisms of enzyme catalysis vary, but are all similar in principle to other types of chemical catalysis in that the crucial factor is a reduction of energy barrier separating the reactants from the products. The reduction of activation energy increases the fraction of reactant molecules that can overcome this barrier and form the product. An important principle is that since they only reduce energy barriers between products and reactants, enzymes always catalyze reactions in both directions, and cannot drive a reaction forward or affect the equilibrium position – only the speed with which is it achieved. As with other catalysts, the enzyme is not consumed or changed by the reaction but is recycled such that a single enzyme performs many rounds of catalysis.
Enzymes are often highly specific, i.e. they only act on particular substrates, sometimes only one. Others show group specificity and can act on similar but not identical chemical groups such as peptide bonds. Many enzymes have stereochemical specificity and act on one stereoisomer but not another.

Induced fit

The classic model for the enzyme-substrate interaction is the induced fit model. This model proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding.
The advantages of the induced fit mechanism arise due to the stabilizing effect of strong enzyme binding. There are two mechanisms of substrate binding: uniform binding, which has strong substrate binding, and differential binding, which has strong transition state binding. The stabilizing effect of uniform binding increases both substrate and transition state binding affinity, while differential binding increases only transition state binding affinity. Both are used by enzymes and have been evolutionarily chosen to minimize the activation energy of the reaction. Enzymes that are saturated, that is, have a high affinity substrate binding, require differential binding to reduce the energy of activation, whereas small substrate unbound enzymes may use either differential or uniform binding.
These effects have led to most proteins using the differential binding mechanism to reduce the energy of activation, so most substrates have high affinity for the enzyme while in the transition state. Differential binding is carried out by the induced fit mechanism – the substrate first binds weakly, then the enzyme changes conformation increasing the affinity to the transition state and stabilizing it, so reducing the activation energy to reach it.
It is important to clarify, however, that the induced fit concept cannot be used to rationalize catalysis. That is, the chemical catalysis is defined as the reduction of E_a^‡ relative to E_a^‡ in the uncatalyzed reaction in water. The induced fit only suggests that the barrier is lower in the closed form of the enzyme but does not tell us what the reason for the barrier reduction is.
Induced fit may be beneficial to the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism.

Mechanisms of an alternative reaction route

These conformational changes also bring catalytic residues in the active site close to the chemical bonds in the substrate that will be altered in the reaction. After binding takes place, one or more mechanisms of catalysis lowers the energy of the reaction's transition state, by providing an alternative chemical pathway for the reaction. There are six possible mechanisms of "over the barrier" catalysis as well as a "through the barrier" mechanism:

Proximity and orientation

Enzyme-substrate interactions align the reactive chemical groups and hold them close together in an optimal geometry, which increases the rate of the reaction. This reduces the entropy of the reactants and thus makes addition or transfer reactions less unfavorable, since a reduction in the overall entropy when two reactants become a single product. However this is a general effect and is seen in non-addition or transfer reactions where it occurs due to an increase in the "effective concentration" of the reagents. This is understood when considering how increases in concentration leads to increases in reaction rate: essentially when the reactants are more concentrated, they collide more often and so react more often. In enzyme catalysis, the binding of the reagents to the enzyme restricts the conformational space of the reactants, holding them in the 'proper orientation' and close to each other, so that they collide more frequently, and with the correct geometry, to facilitate the desired reaction. The "effective concentration" is the concentration the reactant would have to be, free in solution, to experiences the same collisional frequency. Often such theoretical effective concentrations are unphysical and impossible to realize in reality – which is a testament to the great catalytic power of many enzymes, with massive rate increases over the uncatalyzed state.
However, the situation might be more complex, since modern computational studies have established that traditional examples of proximity effects cannot be related directly to enzyme entropic effects. Also, the original entropic proposal has been found to largely overestimate the contribution of orientation entropy to catalysis.

Proton donors or acceptors

Proton donors and acceptors, i.e. acids and base may donate and accept protons in order to stabilize developing charges in the transition state. This is related to the overall principle of catalysis, that of reducing energy barriers, since in general transition states are high energy states, and by stabilizing them this high energy is reduced, lowering the barrier. A key feature of enzyme catalysis over many non-biological catalysis, is that both acid and base catalysis can be combined in the same reaction. In many abiotic systems, acids or bases can increase the rate of the reaction; but of course the environment can only have one overall pH. However, since enzymes are large molecules, they can position both acid groups and basic groups in their active site to interact with their substrates, and employ both modes independent of the bulk pH.
Often general acid or base catalysis is employed to activate nucleophile and/or electrophile groups, or to stabilize leaving groups. Many amino acids with acidic or basic groups are this employed in the active site, such as the glutamic and aspartic acid, histidine, cystine, tyrosine, lysine and arginine, as well as serine and threonine. In addition, the peptide backbone, with carbonyl and amide N groups is often employed. Cystine and Histidine are very commonly involved, since they both have a pKa close to neutral pH and can therefore both accept and donate protons.
Many reaction mechanisms involving acid/base catalysis assume a substantially altered pKa. This alteration of pKa is possible through the local environment of the residue.

Conditions	Acids	Bases
Hydrophobic environment	Increase pKa	Decrease pKa
Adjacent residues of like charge	Increase pKa	Decrease pKa
Salt bridge formation	Decrease pKa	Increase pKa

pKa can also be influenced significantly by the surrounding environment, to the extent that residues which are basic in solution may act as proton donors, and vice versa.
The modification of the pKa's is a pure part of the electrostatic mechanism. The catalytic effect of the above example is mainly associated with the reduction of the pKa of the oxyanion and the increase in the pKa of the histidine, while the proton transfer from the serine to the histidine is not catalyzed significantly since it is not the rate determining barrier. Note that in the example shown, the histidine conjugate acid acts as a general acid catalyst for the subsequent loss of the amine from a tetrahedral intermediate. Evidence supporting this proposed mechanism has, however, been controverted.

Electrostatic catalysis

Stabilization of charged transition states can also be by residues in the active site forming ionic bonds with the intermediate. These bonds can either come from acidic or basic side chains found on amino acids such as lysine, arginine, aspartic acid or glutamic acid or come from metal cofactors such as zinc. Metal ions are particularly effective and can reduce the pKa of water enough to make it an effective nucleophile.
Systematic computer simulation studies have established that electrostatic effects give, by far, the largest contribution to catalysis, and can increase the rate of reaction by a factor of up to 10⁷. In particular, it has been found that enzymes provide an environment which is more polar than water, and that ionic transition states are stabilized by fixed dipoles. This is very different from transition state stabilization in water, where the water molecules must pay with "reorganization energy" in order to stabilize ionic and charged states. Thus, catalysis is associated with the fact that the enzyme polar groups are preorganized.
The magnitude of the electrostatic field exerted by an enzyme's active site has been shown to be highly correlated with the enzyme's catalytic rate enhancement.
Binding of substrate usually excludes water from the active site, thereby lowering the local dielectric constant to that of an organic solvent. This strengthens the electrostatic interactions between the charged/polar substrates and the active sites. In addition, studies have shown that the charge distributions about the active sites are arranged so as to stabilize the transition states of the catalyzed reactions. In several enzymes, these charge distributions apparently serve to guide polar substrates toward their binding sites so that the rates of these enzymatic reactions are greater than their apparent diffusion-controlled limits.