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Binding site
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== Function == Binding of a ligand to a binding site on protein often triggers a change in conformation in the protein and results in altered cellular function. Hence binding site on protein are critical parts of [[signal transduction]] pathways.<ref name=":0">{{cite journal | vauthors = Xu D, Jalal SI, Sledge GW, Meroueh SO | title = Small-molecule binding sites to explore protein-protein interactions in the cancer proteome | journal = Molecular BioSystems | volume = 12 | issue = 10 | pages = 3067β87 | date = October 2016 | pmid = 27452673 | pmc = 5030169 | doi = 10.1039/c6mb00231e }}</ref> Types of ligands include [[neurotransmitter]]s, [[toxin]]s, [[neuropeptide]]s, and [[steroid hormone]]s.<ref name="Wilson_2010">{{cite book | vauthors = Wilson K |date=March 2010 |title =Principles and Techniques of Biochemistry and Molecular Biology |pages=581β624 |publisher=Cambridge University Press |doi=10.1017/cbo9780511841477.016 |isbn=9780511841477 }}</ref> Binding sites incur functional changes in a number of contexts, including enzyme catalysis, molecular pathway signaling, homeostatic regulation, and physiological function. [[Electric charge]], steric shape and geometry of the site selectively allow for highly specific ligands to bind, activating a particular cascade of cellular interactions the protein is responsible for.<ref name=":03">{{Cite book|title=Biochemistry Free For All| vauthors = Ahern K |publisher=Oregon State University|year=2015|pages=110β141}}</ref><ref name=":4">{{cite journal | vauthors = Kumar AP, Lukman S | title = Allosteric binding sites in Rab11 for potential drug candidates | journal = PLOS ONE | volume = 13 | issue = 6 | pages = e0198632 | date = 2018-06-06 | pmid = 29874286 | pmc = 5991966 | doi = 10.1371/journal.pone.0198632 | bibcode = 2018PLoSO..1398632K | doi-access = free }}</ref><ref>{{cite journal |last1=Nazem |first1=Fatemeh |last2=Ghasemi |first2=Fahimeh |last3=Fassihi |first3=Afshin |last4=Mehri Dehnavi |first4=Alireza |title=Deep attention network for identifying ligand-protein binding sites |journal= Journal of Computational Science|date=2024 |volume=81 |doi= 10.1016/j.jocs.2024.102368 }}</ref> === Catalysis === [[File:ActivationEnergyInt.svg|thumb|[[Activation energy]] is decreased in the presence of an enzyme to catalyze the reaction.]] Enzymes incur catalysis by binding more strongly to [[transition state]]s than substrates and products. At the catalytic binding site, several different interactions may act upon the substrate. These range from electric catalysis, acid and base catalysis, covalent catalysis, and metal ion catalysis.<ref name="Wilson_2010" /> These interactions decrease the activation energy of a chemical reaction by providing favorable interactions to stabilize the high energy molecule. Enzyme binding allows for closer proximity and exclusion of substances irrelevant to the reaction. Side reactions are also discouraged by this specific binding.<ref name=":52">{{Cite book | vauthors = Dobson JA, Gerrard AJ, Pratt JA |title=Foundations of chemical biology |date=2008|publisher=Oxford University Press|isbn=9780199248995|oclc=487962823}}</ref><ref name="Wilson_2010" /> Types of enzymes that can perform these actions include oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases.<ref>{{cite book | vauthors = Azzaroni O, Szleifer I |date=2017-12-04|title=Polymer and Biopolymer Brushes |doi=10.1002/9781119455042 | isbn = 978-1-119-45501-1 }}</ref> For instance, the transferase hexokinase catalyzes the phosphorylation of glucose to make glucose-6-phosphate. Active site residues of hexokinase allow for stabilization of the glucose molecule in the active site and spur the onset of an alternative pathway of favorable interactions, decreasing the activation energy.<ref>{{Cite book|title=Dictionary of Food Science and Technology|publisher=International Food Information Service|year=2009|isbn=978-1-4051-8740-4|edition=2nd}}</ref> === Inhibition === Protein inhibition by inhibitor binding may induce obstruction in pathway regulation, homeostatic regulation and physiological function. [[Competitive inhibition|Competitive inhibitors]] compete with substrate to bind to free enzymes at active sites and thus impede the production of the enzyme-substrate complex upon binding. For example, carbon monoxide poisoning is caused by the competitive binding of carbon monoxide as opposed to oxygen in hemoglobin. [[Uncompetitive inhibitor]]s, alternatively, bind concurrently with substrate at active sites. Upon binding to an enzyme substrate (ES) complex, an enzyme substrate inhibitor (ESI) complex is formed. Similar to competitive inhibitors, the rate at product formation is decreased also.<ref name="Hardin_2013" /> Lastly, mixed inhibitors are able to bind to both the free enzyme and the enzyme-substrate complex. However, in contrast to competitive and uncompetitive inhibitors, mixed inhibitors bind to the allosteric site. Allosteric binding induces conformational changes that may increase the protein's affinity for substrate. This phenomenon is called positive modulation. Conversely, allosteric binding that decreases the protein's affinity for substrate is negative modulation.<ref>{{cite book | vauthors = Clarke KG |date=2013 |title=Bioprocess engineering |publisher=Woodhead Publishing |pages=79β84 |doi=10.1533/9781782421689 |isbn=978-1-78242-167-2 }}</ref>
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