active site

Examples of active site in the following topics:

• Enzyme Catalysis

  • They do this by binding the reactant(s), known as the substrate(s), to an active site within the enzyme.
  • At the active site, the substrate(s) can form an activated complex at lower energy.
  • Once the reaction completes, the product(s) leaves the active site, so the enzyme is free to catalyze more reactions.
  • This model proposes that the binding of the reactant, or substrate, to the enzyme active site results in a conformational change to the enzyme.
  • An enzyme catalyzes a biochemical reaction by binding a substrate at the active site.

• Enzyme Active Site and Substrate Specificity

  • The enzyme's active site binds to the substrate.
  • The positions, sequences, structures, and properties of these residues create a very specific chemical environment within the active site.
  • Environmental conditions can affect an enzyme's active site and, therefore, the rate at which a chemical reaction can proceed.
  • If the enzyme changes shape, the active site may no longer bind to the appropriate substrate and the rate of reaction will decrease.
  • The active site of an enzyme also creates an ideal environment, such as a slightly acidic or non-polar environment, for the reaction to occur.

• Biomolecules

  • Coordination complexes are found in many biomolecules, especially as essential ingredients for the active site of enzymes.
  • The transition metals, particularly zinc and iron, are often key components of enzyme active sites.
  • As with all enzymes, the shape of the active site is crucial.
  • The structure of the active site in carbonic anhydrases is well known from a number of crystal structures.
  • Active site of carbonic anhydrase.

• Control of Metabolism Through Enzyme Regulation

  • In noncompetitive inhibition, an inhibitor molecule binds to the enzyme at a location other than the active site (an allosteric site).
  • Their binding induces a conformational change that reduces the affinity of the enzyme's active site for its substrate. 
  • They bind to an allosteric site which induces a conformational change that increases the affinity of the enzyme's active site for its substrate.
  • Allosteric inhibitors modify the active site of the enzyme so that substrate binding is reduced or prevented.
  • In contrast, allosteric activators modify the active site of the enzyme so that the affinity for the substrate increases.

• Blocking of Hormone Receptors

  • Antagonists mediate their effects by binding to the active site or to allosteric sites on receptors, or they may interact at unique binding sites not normally involved in the biological regulation of the receptor's activity.
  • Binding to the active site on the receptor regulates receptor activation directly.
  • Competitive antagonists (also known as surmountable antagonists) reversibly bind to receptors at the same binding site (active site) as the endogenous ligand or agonist, but without activating the receptor.
  • The level of activity of the receptor will be determined by the relative affinity of each molecule for the site and their relative concentrations.
  • They do not compete with agonists for binding at the active site.

• ATP and Muscle Contraction

  • The energy released during ATP hydrolysis changes the angle of the myosin head into a "cocked" position, ready to bind to actin if the sites are available.
  • The muscle contraction cycle is triggered by calcium ions binding to the protein complex troponin, exposing the active-binding sites on the actin.
  • As soon as the actin-binding sites are uncovered, the high-energy myosin head bridges the gap, forming a cross-bridge.
  • ATP then binds to myosin, moving the myosin to its high-energy state, releasing the myosin head from the actin active site.
  • The cross-bridge muscle contraction cycle, which is triggered by Ca2+ binding to the actin active site, is shown.

• Regulatory Mechanisms for Cellular Respiration

  • A number of enzymes involved in each of the pathways (in particular, the enzyme catalyzing the first committed reaction of the pathway) are controlled by attachment of a molecule to an allosteric (non-active) site on the protein.
  • This site has an effect on the enzyme's activity, often by changing the conformation of the protein.
  • These regulators, known as allosteric effectors, may increase or decrease enzyme activity, depending on the prevailing conditions, altering the steric structure of the enzyme, usually affecting the configuration of the active site.
  • The attachment of a molecule to the allosteric site serves to send a signal to the enzyme, providing feedback.

• Regulatory Proteins

  • To keep actin from binding to the active site on myosin, regulatory proteins block the molecular binding sites.
  • Troponin, which regulates the tropomyosin, is activated by calcium, which is kept at extremely low concentrations in the sarcoplasm.
  • A change in the receptor conformation causes an action potential, activating voltage-gated L-type calcium channels, which are present in the plasma membrane.
  • The inward flow of calcium from the L-type calcium channels activates ryanodine receptors to release calcium ions from the sarcoplasmic reticulum.
  • Calcium then binds to troponin, causing the troponin to change shape and remove the tropomyosin from the binding sites.

• Hosting

  • A web site, obviously — but the full answer is a little more complicated than that.
  • The collaboration site would have the code repository, bug tracker, development wiki, links to development mailing lists, etc.
  • The two sites should link to each other, and in particular it's important that the user-facing site make it clear that the project is open source and where the open source development activity can be found.
  • (As of August 2013, a good example of a project with separate but cross-linked primary and developer sites is the Ozone Widget Framework: compare their main user-facing site at ozoneplatform.org with their development area at github.com/ozoneplatform/owf. ).
  • In the past, many projects set up the developer site and infrastructure themselves.

• Regulation of Sigma Factor Activity

  • Specifically, in bacteria, sigma factors are necessary for recognition of RNA polymerase to the gene promoter site.
  • The sigma factor allows the RNA polymerase to properly bind to the promoter site and initiate transcription which will result in the production of an mRNA molecule.
  • The activity of sigma factors within a cell is controlled in numerous ways.
  • However, if transcription of genes is not required, sigma factors will not be active.
  • The anti-sigma factors will bind to the RNA polymerase and prevent its binding to sigma factors present at the promoter site.