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In chemistry, a reaction coordinate [1] is an abstract one-dimensional coordinate chosen to represent progress along a reaction pathway. Where possible it is usually a geometric parameter that changes during the conversion of one or more molecular entities, such as bond length or bond angle. For example, in the homolytic dissociation of ...
A catalytic triad is a set of three coordinated amino acid residues that can be found in the active site of some enzymes. [1] [2] Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, acylases, lipases and β-lactamases).
Enzymes are evolved to catalyze a particular reaction on a particular substrate with high catalytic efficiency (k cat /K M, cf.Michaelis–Menten kinetics).However, in addition to this main activity, they possess other activities that are generally several orders of magnitude lower, and that are not a result of evolutionary selection and therefore do not partake in the physiology of the organism.
Figure 6:Reaction Coordinate Diagrams showing reactions with 0, 1 and 2 intermediates: The double-headed arrow shows the first, second and third step in each reaction coordinate diagram. In all three of these reactions the first step is the slow step because the activation energy from the reactants to the transition state is the highest.
While a number of inhibitory strategies exist such as high temperature treatments(70-90 °C) to eliminate catechol oxidase catalytic activity, [6] a popular strategy is decreasing the pH with citric acid. Catechol oxidase is more catalytically active in the pH 4-8 range due to coordination of the histidine residues to the catalytic copper centers.
Chiral ligands work by asymmetric induction somewhere along the reaction coordinate. The image to the right illustrates how a chiral ligand may induce an enantioselective reaction. The ligand (in green) has C 2 symmetry with its nitrogen, oxygen or phosphorus atoms hugging a central metal atom (in red). In this particular ligand the right side ...
The concept of a transition state has been important in many theories of the rates at which chemical reactions occur. This started with the transition state theory (also referred to as the activated complex theory), which was first developed around 1935 by Eyring, Evans and Polanyi, and introduced basic concepts in chemical kinetics that are still used today.
To address such a paradox, Kuo-Chen Chou and his co-workers proposed a model by taking into account the spatial factor and force field factor between the enzyme and its substrate and found that the upper limit could reach 10 10 M −1 s −1, [6] [7] [8] and can be used to explain some surprisingly high reaction rates in molecular biology.