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Active region of an enzyme

In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that catalyse a reaction of that substrate, the catalytic site. Although the active site occupies only ~10–20% of the volume of an enzyme, it is the most important part as it directly catalyzes the chemical reaction. It usually consists of three to four amino acids, while other amino acids within the protein are required to maintain the tertiary structure of the enzymes. Each active site is evolved to be optimised to bind a particular substrate and catalyse a particular reaction, resulting in high specificity. This specificity is determined by the arrangement of amino acids within the active site and the structure of the substrates. Sometimes enzymes also need to bind with some cofactors to fulfil their function. The active site is usually a groove or pocket of the enzyme which can be located in a deep tunnel within the enzyme, or between the interfaces of multimeric enzymes. An active site can catalyse a reaction repeatedly as residues are not altered at the end of the reaction (they may change during the reaction, but are regenerated by the end). This process is achieved by lowering the activation energy of the reaction, so more substrates have enough energy to undergo reaction.

Usually, an enzyme molecule has only one active site, and the active site fits with one specific type of substrate. An active site contains a binding site that binds the substrate and orients it for catalysis. The orientation of the substrate and the close proximity between it and the active site is so important that in some cases the enzyme can still function properly even though all other parts are mutated and lose function. Initially, the interaction between the active site and the substrate is non covalent and transient. There are four important types of interaction that hold the substrate in a defined orientation and form an enzyme substrate complex (ES complex): hydrogen bonds, van der Waals interactions, hydrophobic interactions and electrostatic force interactions. The charge distribution on the substrate and active site must be complementary, which means all positive and negative charges must be cancelled out. Otherwise, there will be a repulsive force pushing them apart. The active site usually contains non polar amino acids, although sometimes polar amino acids may also occur. Most enzymes have deeply buried active sites, which can be accessed by a substrate via access channels.

This concept was suggested by the 19th century chemist Emil Fischer. He proposed that the active site and substrate are two stable structures that fit perfectly without any further modification, just like a key fits into a lock. If one substrate perfectly binds to its active site, the interactions between them will be strongest, resulting in high catalytic efficiency. As time went by, limitations of this model started to appear. For example, the competitive enzyme inhibitor methylglucoside can bind tightly to the active site of 4 alpha glucanotransferase and perfectly fits into it. However, 4 alpha glucanotransferase is not active on methylglucoside and no glycosyl transfer occurs. The Lock and Key hypothesis cannot explain this, as it would predict a high efficiency of methylglucoside glycosyl transfer due to its tight binding. Apart from competitive inhibition, this theory cannot explain the mechanism of action of non competitive inhibitors either, as they do not bind to the active site but nevertheless influence catalytic activity.

Daniel Koshland's theory of enzyme substrate binding is that the active site and the binding portion of the substrate are not exactly complementary. The induced fit model is a development of the lock and key model and assumes that an active site is flexible and changes shape until the substrate is completely bound. This model is similar to a person wearing a glove: the glove changes shape to fit the hand. The enzyme initially has a conformation that attracts its substrate. Enzyme surface is flexible and only the correct catalyst can induce interaction leading to catalysis. Conformational changes may then occur as the substrate is bound. After the reaction products will move away from the enzyme and the active site returns to its initial shape. This hypothesis is supported by the observation that the entire protein domain could move several nanometers during catalysis. This movement of protein surface can create microenvironments that favour the catalysis.

Electrostatic interaction: In an aqueous environment, the oppositely charged groups in amino acid side chains within the active site and substrates attract each other, which is termed electrostatic interaction. For example, when a carboxylic acid (R COOH) dissociates into RCOO− and H+ ions, COO− will attract positively charged groups such as protonated guanidine side chain of arginine. Hydrogen bond: A hydrogen bond is a specific type of dipole dipole interaction between a partially positive hydrogen atom and a partially negative electron donor that contain a pair of electrons such as oxygen, fluorine and nitrogen. The strength of hydrogen bond depends on the chemical nature and geometric arrangement of each group. Van der Waals force: Van der Waals force is formed between oppositely charged groups due to transient uneven electron distribution in each group. If all electrons are concentrated at one pole of the group this end will be negative, while the other end will be positive. Although the individual force is weak, as the total number of interactions between the active site and substrate is massive the sum of them will be significant. Hydrophobic interaction: Non polar hydrophobic groups tend to aggregate together in the aqueous environment and try to leave from polar solvent. These hydrophobic groups usually have long carbon chain and do not react with water molecules. When dissolving in water a protein molecule will curl up into a ball like shape, leaving hydrophilic groups in outside while hydrophobic groups are deeply buried within the centre.

Once the substrate is bound and oriented to the active site, catalysis can begin. The residues of the catalytic site are typically very close to the binding site, and some residues can have dual roles in both binding and catalysis. Catalytic residues of the site interact with the substrate to lower the activation energy of a reaction and thereby make it proceed faster. They do this by a number of different mechanisms including the approximation of the reactants, nucleophilic/electrophilic catalysis and acid/base catalysis. These mechanisms will be explained below.

During enzyme catalytic reaction, the substrate and active site are brought together in a close proximity. This approach has various purposes. Firstly, when substrates bind within the active site the effective concentration of it significantly increases than in solution. This means the number of substrate molecules involved in the reaction is also increased. This process also reduces the desolvation energy required for the reaction to occur. In solution substrate molecules are surrounded by solvent molecules and energy is required for enzyme molecules to replace them and contact with the substrate. Since bulk molecules can be excluded from the active site this energy output can be minimised. Next, the active site is designed to reorient the substrate to reduce the activation energy for the reaction to occur. The alignment of the substrate, after binding, is locked in a high energy state and can proceed to the next step. In addition, this binding is favoured by entropy as the energy cost associated with solution reaction is largely eliminated since solvent cannot enter active site. In the end, the active site may manipulate the Molecular orbital of the substrate into a suitable orientation to reduce activation energy. as do those with more rotatable bonds (although this may be a side effect of size). When the solvent is excluded from the active site, less flexible proteins result in longer residence times. More hydrogen bonds shielded from the solvent also decrease unbinding. If HIV protease is switched off the virion particle will lose function and cannot infect patients. Since it is essential in viral replication and is absent in healthy human, it is an ideal target for drug development. HIV protease belongs to aspartic protease family and has a similar mechanism. Firstly the aspartate residue activates a water molecule and turns it into a nucleophile. Then it attacks the carbonyl group within the peptide bond (NH CO) to form a tetrahedral intermediate. The nitrogen atom within the intermediate receives a proton, forming an amide group and subsequent rearrangement leads to the breakdown of the bond between it and the intermediate and forms two products. Inhibitors usually contain a nonhydrolyzable hydroxyethylene or hydroxyethylamine groups that mimic the tetrahedral intermediate. Since they share a similar structure and electrostatic arrangement to the transition state of substrates they can still fit into the active site but cannot be broken down, so hydrolysis cannot occur.

Strychnine is a neurotoxin that causes death by affecting nerves that control muscular contraction and cause respiration difficulty. The impulse is transmitted between the synapse through a neurotransmitter called acetylcholine. It is released into the synapse between nerve cells and binds to receptors in the postsynaptic cell. Then an action potential is generated and transmitted through the postsynaptic cell to start a new cycle. Glycine can inhibit the activity of neurotransmitter receptors, thus a larger amount of acetylcholinesterase is required to trigger an action potential. This makes sure that the generation of nerve impulses is tightly controlled. However, this control is broken down when strychnine is added. It inhibits glycine receptors(a chloride channel) and a much lower level of neurotransmitter concentration can trigger an action potential. Nerves now constantly transmit signals and cause excessive muscular contraction, leading to asphyxiation and death.

Diisopropyl fluorophosphate (DIFP) is an irreversible inhibitor that blocks the action of serine protease. When it binds to the enzyme a nucleophilic substitution reaction occurs and releases one hydrogen fluoride molecule. The OH group in the active site acts as a nucleophile to attack the phosphorus in DIFP and form a tetrahedral intermediate and release a proton. Then the P F bond is broken, one electron is transferred to the F atom and it leaves the intermediate as F− anion. It combines with a proton in solution to form one HF molecule. A covalent bond formed between the active site and DIFP, so the serine side chain is no longer available to the substrate.

Identification of active sites is crucial in the process of drug discovery. The 3 D structure of the enzyme is analysed to identify active site residues and design drugs which can fit into them. Proteolytic enzymes are targets for some drugs, such as protease inhibitors, which include drugs against AIDS and hypertension. These protease inhibitors bind to an enzyme's active site and block interaction with natural substrates. An important factor in drug design is the strength of binding between the active site and an enzyme inhibitor. If the enzyme found in bacteria is significantly different from the human enzyme then an inhibitor can be designed against that particular bacterium without harming the human enzyme. If one kind of enzyme is only present in one kind of organism, its inhibitor can be used to specifically wipe them out. Active sites can be mapped to aid the design of new drugs such as enzyme inhibitors. This involves the description of the size of an active site and the number and properties of sub sites, such as details of the binding interaction.

Example Mechanism of action Anti bacterial agent Penicillin The bacterial cell wall is composed of peptidoglycan. During bacterial growth the present crosslinking of peptidoglycan fibre is broken, so new cell wall monomer can be integrated into the cell wall. Penicillin works by inhibiting the transpeptidase which is essential for the formation of crosslinks, so the cell wall is weakened and will burst open due to turgor pressure. Anti fungi agent Azole Ergosterol is a sterol that forms the cell surface membrane of the fungi. Azole can inhibit its biosynthesis by inhibiting the Lanosterol 14 alpha demethylase, so no new ergosterol is produced and harmful 14α lanosterol is accumulated within the cell. Also, azole may generate reactive oxygen species. Anti viral agent Saquinavir HIV protease is needed to cleave Gag Pol polyprotein into 3 individual proteins so they can function properly and start viral packaging process. HIV protease inhibitors like Saquinavir inhibit it so no new mature viral particle can be made. Insecticides Physostigmine In the animal nervous system, Acetylcholinesterase is required to break down the neurotransmitter acetylcholine into acetate and choline. Physostigmine binds to its active site and inhibits it, so impulse signal cannot be transmitted through nerves. This results in the death of insects as they lose control of muscle and heart function. Herbicides Cyclohexanedione Cyclohexanedione targets the Acetyl CoA carboxylase which is involved in the first step of fat synthesis: ATP dependent carboxylation of acetyl CoA to malonyl CoA. Lipids are important in making up the cell membrane.

An allosteric site is a site on an enzyme, unrelated to its active site, which can bind an effector molecule. This interaction is another mechanism of enzyme regulation. Allosteric modification usually happens in proteins with more than one subunit. Allosteric interactions are often present in metabolic pathways and are beneficial in that they allow one step of a reaction to regulate another step. They allow an enzyme to have a range of molecular interactions, other than the highly specific active site.