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Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg 2+ cofactor in yellow. (The different mechanisms of substrate binding. The classic model for the enzyme-substrate interaction is the induced fit model. [4]
Daniel Koshland's theory of enzyme-substrate binding is that the active site and the binding portion of the substrate are not exactly complementary. [10] 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.
The KNF model follows the structural theory of the induced fit model of substrate binding to an enzyme. [5] A slight change in the conformation of an enzyme improves its binding affinity to the transition state of the ligand, thus catalyzing a reaction.
For example, bacteria may become resistant to antibiotics such as penicillin because enzymes called beta-lactamases are induced that hydrolyse the crucial beta-lactam ring within the penicillin molecule. [93] Another example comes from enzymes in the liver called cytochrome P450 oxidases, which are important in drug metabolism.
During the course of the docking process, the ligand and the protein adjust their conformation to achieve an overall "best-fit" and this kind of conformational adjustment resulting in the overall binding is referred to as "induced-fit". [5] Molecular docking research focuses on computationally simulating the molecular recognition process.
The favoured model for the enzyme–substrate interaction is the induced fit model. [53] 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.
3-phosphoglycerate dehydrogenase works via an induced fit mechanism to catalyze the transfer of a hydride from the substrate to NAD+, a required cofactor.In its active conformation, the enzyme's active site has multiple cationic residues that likely stabilize the transition state of the reaction between the negatively charged substrate and NAD +.
Walker motif A-binding has been shown to cause structural changes in the bound nucleotide, along the line of the induced fit model of enzyme binding. [citation needed]