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Binding site


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A binding site is a region on a protein to which signaling molecules called ligands may bind to induce a change in biological activity. Bonds formed at the binding site are noncovalent and transient so that the activated function may be easily regulated. These sites are also unique to its ligand to regulate the activation of the protein.[1] Characteristics of binding sites include chemical specificity, which measures the types of ligands that will bind, and affinity, which measures of the strength of the chemical bond. Hormones, neurotransmitters, substrates, toxins, inhibitors and activators some examples of biomolecules that interact with a unique binding site.


A biomolecule's binding site entails great information about its biological function.[2] For example, the steric shape, geometry and electrostatic charge of the site selectively allow for highly specific ligands to bind, activating a particular cascade of cellular interactions the protein is responsible for.[3][4]


The study of binding sites are relevant to many fields of research, including cancer mechanisms,[1] drug formulation,[5] and physiological regulation.[6]


Binding sites on cells are cell surface receptors and regulate different signaling pathways through signal transduction. Binding sites found on DNA and RNA are responsible for the onset transcription and eventually gene expression.[7]




Contents






  • 1 Binding curves


  • 2 Prediction


  • 3 See also


  • 4 References


  • 5 External links





Binding curves[edit]


Binding curves describe the binding behavior of ligand to a protein. Curves can be characterized by their shape, sigmoidal or hyperbolic, which reflect whether or not the protein exhibits cooperative or noncooperative binding behavior respectively.[3]



Prediction[edit]


A number of computational tools have been developed for the prediction of the location of binding sites on proteins.[8][9][10]



See also[edit]


  • NTP binding site


References[edit]





  1. ^ ab 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..mw-parser-output cite.citation{font-style:inherit}.mw-parser-output q{quotes:"""""""'""'"}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:inherit;padding:inherit}.mw-parser-output .cs1-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/6/65/Lock-green.svg/9px-Lock-green.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-limited a,.mw-parser-output .cs1-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/d/d6/Lock-gray-alt-2.svg/9px-Lock-gray-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/a/aa/Lock-red-alt-2.svg/9px-Lock-red-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{font-size:100%}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration,.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}


  2. ^ Xu D, Jalal SI, Sledge GW, Meroueh SO (October 2016). "Small-molecule binding sites to explore protein-protein interactions in the cancer proteome". Molecular bioSystems. 12 (10): 3067–87. doi:10.1039/c6mb00231e. PMC 5030169. PMID 27452673.


  3. ^ ab Ahern, Kevin (2015). Biochemistry Free For All. Oregon State University. pp. 110–141.


  4. ^ Kumar AP, Lukman S (2018-06-06). "Allosteric binding sites in Rab11 for potential drug candidates". PLOS One. 13 (6): e0198632. doi:10.1371/journal.pone.0198632. PMC 5991966. PMID 29874286.


  5. ^ Peng J, Li XP (October 2018). "Apolipoprotein A-IV: a potential therapeutic target for atherosclerosis". Prostaglandins & Other Lipid Mediators. doi:10.1016/j.prostaglandins.2018.10.004. PMID 30352313.


  6. ^ McNamara JW, Sadayappan S (October 2018). "Skeletal myosin binding protein-C: An increasingly important regulator of striated muscle physiology". Archives of Biochemistry and Biophysics. doi:10.1016/j.abb.2018.10.007. PMID 30339776.


  7. ^ Morris J, Hartl DL, Knoll AH, Lue R. Biology : how life works (Second ed.). New York, NY. ISBN 9781464126093. OCLC 937824456.


  8. ^ Konc J, Janežič D (April 2014). "Binding site comparison for function prediction and pharmaceutical discovery". Current Opinion in Structural Biology. 25: 34–9. doi:10.1016/j.sbi.2013.11.012. PMID 24878342.


  9. ^ Roche DB, Brackenridge DA, McGuffin LJ (December 2015). "Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods". International Journal of Molecular Sciences. 16 (12): 29829–42. doi:10.3390/ijms161226202. PMC 4691145. PMID 26694353.


  10. ^ Broomhead NK, Soliman ME (March 2017). "Can We Rely on Computational Predictions To Correctly Identify Ligand Binding Sites on Novel Protein Drug Targets? Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites". Cell Biochemistry and Biophysics. 75 (1): 15–23. doi:10.1007/s12013-016-0769-y. PMID 27796788.




External links[edit]


  • Drawing the active site of an enzyme












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