Binding site

Glucose binds to hexokinase in the active site at the beginning of glycolysis.

In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity.[1] The binding partner of the macromolecule is often referred to as a ligand.[2] Ligands may include other proteins (resulting in a protein–protein interaction),[3] enzyme substrates,[4] second messengers, hormones, or allosteric modulators.[5] The binding event is often, but not always, accompanied by a conformational change that alters the protein's function.[6] Binding to protein binding sites is most often reversible (transient and non-covalent), but can also be covalent reversible[7] or irreversible.[8][9]

  1. ^ "Binding site". Medical Subject Headings (MeSH). U.S. National Library of Medicine. The parts of a macromolecule that directly participate in its specific combination with another molecule.
  2. ^ "Ligands". Medical Subject Headings (MeSH). U.S. National Library of Medicine. A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule.
  3. ^ Amos-Binks A, Patulea C, Pitre S, Schoenrock A, Gui Y, Green JR, Golshani A, Dehne F (June 2011). "Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences". BMC Bioinformatics. 12: 225. doi:10.1186/1471-2105-12-225. PMC 3120708. PMID 21635751.
  4. ^ Hardin CC, Knopp JA (2013). "Chapter 8: Enzymes". Biochemistry - Essential Concepts. New York: Oxford University Press. pp. 51–69. ISBN 978-1-62870-176-0.
  5. ^ Kenakin TP (April 2016). "Characteristics of Allosterism in Drug Action". In Bowery NG (ed.). Allosteric Receptor Modulation in Drug Targeting. CRC Press. p. 26. ISBN 978-1-4200-1618-5.
  6. ^ Spitzer R, Cleves AE, Varela R, Jain AN (April 2014). "Protein function annotation by local binding site surface similarity". Proteins. 82 (4): 679–94. doi:10.1002/prot.24450. PMC 3949165. PMID 24166661.
  7. ^ Bandyopadhyay A, Gao J (October 2016). "Targeting biomolecules with reversible covalent chemistry". Current Opinion in Chemical Biology. 34: 110–116. doi:10.1016/j.cbpa.2016.08.011. PMC 5107367. PMID 27599186.
  8. ^ Bellelli A, Carey J (January 2018). "Reversible Ligand Binding". Reversible Ligand Binding: Theory and Experiment. John Wiley & Sons. p. 278. ISBN 978-1-119-23848-5.
  9. ^ Nazem, Fatemeh; Ghasemi, Fahimeh; Fassihi, Afshin; Mehri Dehnavi, Alireza (2021). "3D U-Net: A Voxel-based method in binding site prediction of protein structure". Journal of Bioinformatics and Computational Biology. 19 (2). doi:10.1142/S0219720021500062. PMID 33866960.