Editing Binding site (section)

{{Short description|Molecule-specific coordinate bonding area in biological systems}}
[[File:Glucose_binding_Hexokinase.png|thumb|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 [[Chemical specificity|specificity]].<ref name = "MeSH_Bind_Site">{{cite web | title = Binding site | quote = The parts of a macromolecule that directly participate in its specific combination with another molecule. | url = https://meshb.nlm.nih.gov/record/ui?name=Binding%20Sites | work = Medical Subject Headings (MeSH) | publisher = U.S. National Library of Medicine}}</ref>  The binding partner of the macromolecule is often referred to as a [[Ligand (biochemistry)|ligand]].<ref name = "MeSH_Ligand">{{cite web | title = Ligands | quote = A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule. | url = https://meshb.nlm.nih.gov/record/ui?name=Binding%20Sites | work = Medical Subject Headings (MeSH) | publisher = U.S. National Library of Medicine}}</ref> Ligands may include other proteins (resulting in a [[protein–protein interaction]]),<ref name="Amos-Binks_2011">{{cite journal | vauthors = Amos-Binks A, Patulea C, Pitre S, Schoenrock A, Gui Y, Green JR, Golshani A, Dehne F | title = Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences | journal = BMC Bioinformatics | volume = 12 | pages = 225 | date = June 2011 | pmid = 21635751 | pmc = 3120708 | doi = 10.1186/1471-2105-12-225 | doi-access = free }}</ref> [[enzyme substrate]]s,<ref name="Hardin_2013">{{cite book | chapter = Chapter 8: Enzymes |title=Biochemistry - Essential Concepts | vauthors = Hardin CC, Knopp JA  |publisher=Oxford University Press |year=2013 |isbn=978-1-62870-176-0 |location= New York |pages=51–69}}</ref> [[second messenger system|second messengers]], [[hormone]]s, or [[allosteric modulator]]s.<ref name = "Kenakin_2016">{{cite book | vauthors = Kenakin TP | veditors = Bowery NG | chapter = Characteristics of Allosterism in Drug Action | chapter-url = https://books.google.com/books?id=WRfgvOKfZMcC&pg=PA26 | title = Allosteric Receptor Modulation in Drug Targeting | publisher = CRC Press | date = April 2016 | isbn = 978-1-4200-1618-5 | page = 26 }}</ref>  The binding event is often, but not always, accompanied by a [[conformational change]] that alters the protein's [[Protein#Cellular functions|function]].<ref name=":12">{{cite journal | vauthors = Spitzer R, Cleves AE, Varela R, Jain AN | title = Protein function annotation by local binding site surface similarity | journal = Proteins | volume = 82 | issue = 4 | pages = 679–94 | date = April 2014 | pmid = 24166661 | pmc = 3949165 | doi = 10.1002/prot.24450 }}</ref>  Binding to protein binding sites is most often reversible (transient and [[non-covalent]]), but can also be covalent reversible<ref name="pmid27599186">{{cite journal | vauthors = Bandyopadhyay A, Gao J | title = Targeting biomolecules with reversible covalent chemistry | journal = Current Opinion in Chemical Biology | volume = 34 | pages = 110–116 | date = October 2016 | pmid = 27599186 | pmc = 5107367 | doi = 10.1016/j.cbpa.2016.08.011 }}</ref> or irreversible.<ref>{{cite book | vauthors = Bellelli A, Carey J | chapter = Reversible Ligand Binding | chapter-url = https://books.google.com/books?id=gPw6DwAAQBAJ | title = Reversible Ligand Binding: Theory and Experiment | publisher = John Wiley & Sons | date = January 2018 | isbn = 978-1-119-23848-5 | page = 278 }}</ref><ref>{{cite journal |last1=Nazem |first1=Fatemeh  |last2=Ghasemi |first2=Fahimeh |last3=Fassihi |first3=Afshin |last4=Mehri Dehnavi |first4=Alireza |title=3D U-Net: A Voxel-based method in binding site prediction of protein structure|journal=Journal of Bioinformatics and Computational Biology |date=2021 |volume=19 |issue=2 |doi= 10.1142/S0219720021500062 |pmid=33866960 }}</ref>