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In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continuously reshaped by interactions with the substrate as the substrate interacts with the enzyme. [42]
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.
One can think of molecular docking as a problem of “lock-and-key”, in which one wants to find the correct relative orientation of the “key” which will open up the “lock” (where on the surface of the lock is the key hole, which direction to turn the key after it is inserted, etc.). Here, the protein can be thought of as the “lock ...
Top: enzyme (E) accelerates conversion of substrates (S) to products (P). Bottom: by binding to the enzyme, inhibitor (I) blocks binding of substrate. Binding site shown in blue checkerboard, substrate as black rectangle, and inhibitor as green rounded rectangle. An enzyme inhibitor is a molecule that binds to an enzyme and blocks its activity.
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As shown on the right, enzymes with a substituted-enzyme mechanism can exist in two states, E and a chemically modified form of the enzyme E*; this modified enzyme is known as an intermediate. In such mechanisms, substrate A binds, changes the enzyme to E* by, for example, transferring a chemical group to the active site, and is then released.
Biosynthesis, i.e., chemical synthesis occurring in biological contexts, is a term most often referring to multi-step, enzyme-catalyzed processes where chemical substances absorbed as nutrients (or previously converted through biosynthesis) serve as enzyme substrates, with conversion by the living organism either into simpler or more complex ...
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 (large [H+]) or bases ( large concentration H+ sinks, or species with electron pairs) can increase the rate of the reaction; but of course the environment can only have ...
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