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A surprising discovery from the induced fit model: How do enzymes change shape to facilitate reactions?
In biology and biochemistry, the active site of an enzyme is the region where a substrate molecule binds and a chemical reaction occurs. These active sites are composed of amino acid residues that form temporary bonds with the substrate, called binding sites, while these amino acids also catalyze the reaction of the substrate, called catalytic sites. Although the active site accounts for only about 10% to 20% of the volume of the enzyme, it is the most important part because it directly catalyzes the chemical reaction. The active site usually consists of three to four amino acids, while the other amino acids within the protein are required to maintain the tertiary structure of the enzyme.
Each active site has been evolved and optimized to bind a specific substrate and catalyze a specific reaction, resulting in high specificity.
The structure of the active site enables it to lower the activation energy of a chemical reaction, thereby increasing the efficiency of the reaction. Although each enzyme usually has only one active site, its binding to the substrate requires precise coordination, which means that not only the chemical structure but also the orientation and charge distribution of amino acids can affect the function of the active site. In some cases, an enzyme can still function effectively even if other parts of the enzyme mutate and lose their function, because the interaction between the substrate and the active site is more critical.
Active site binding and catalytic process
The active site is usually a groove or pocket of one or more amino acids, with some remaining holes or channels that allow substrates to reach the active site and react. The active site can catalyze a reaction repeatedly because its residues are not changed at the end of the reaction.
In the binding of substrates to active sites, the main non-covalent interactions include hydrogen bonds, van der Waals forces, hydrophobic interactions, and electrostatic forces.
These interactions play an important role in stabilizing the enzyme-substrate complex (ES complex). Such specificity depends on the complementary charge distribution of the active site and the substrate, otherwise repulsion will occur. force, making it impossible to combine.
Structural model of the active site
There are three main models of enzyme action: the lock and key model, the induced fit model, and the conformational selection model. The lock and key model assumes that the binding between the active site and the substrate is absolute and there is always a fixed shape match. The induced fit model proposes that the active site deforms when the substrate binds, similar to how a glove fits your hand.
There is evidence that enzymes may change their overall structure during catalysis and that such structural changes can create a microenvironment that is favorable for catalysis.
The conformational selection model assumes that the enzyme already has multiple conformations before binding to the substrate, and only certain conformations can bind to the substrate. When a substrate enters the active site of an enzyme, it affects the balance of these conformations, favoring those shapes that can effectively bind to the substrate.
Enzyme catalytic mechanism
Enzyme-catalyzed reactions are typically accomplished through several mechanisms, including proximal amplification of substrates, covalent catalysis, and acid-base catalysis. In these mechanisms, catalytic residues often interact with the substrate, lowering the activation energy of the reaction and facilitating the catalytic process.
For example, amino acids at the active site in acid-base catalysis can act as Brønsted acids and bases, stabilizing nucleophiles or charged groups during the reaction by providing positive and negative charges.
In addition, for some enzymes, metal ions also play an important role in the catalytic process, increasing the electrical affinity of the substrate and promoting the reaction by bridging the active site with the substrate.
Examples of catalytic processes
For example, in glutathione reductase, glutathione (GSH) removes reactive oxygen species. The active site contains two cysteine residues that can form disulfide catalysis by bond. In the pancreas, trypsin (chymotrypsin) hydrolyzes proteins through the three-way catalytic action of its active site.
ConclusionThe diversity and coordinated nature of these catalytic mechanisms make the enzyme catalytic process more efficient and precise.
How enzymes improve catalytic efficiency by changing their shape is not only an interesting topic in biochemistry, but also a key to our understanding of life processes. The precise interaction between the active site of an enzyme and its substrate is not only a catalyst for chemical reactions in organisms, but also an example of the ingenuity and complexity of life. This amazing biological mechanism leads us to think: How many undiscovered mysteries are there in chemical reactions waiting for us to explore?
