Binding site

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In biochemistry and pharmacology, a binding site describes the contact area when a biopolymer binds to another molecule .

properties

The biopolymer can be a nucleic acid , a protein or a carbohydrate , while the second molecule can also be a low molecular weight compound . In enzymes , the binding site for a substrate (substrate binding site) is in or near the active center . The binding site on a receptor or other ligate is its contact surface with ligands (ligand binding site) or inhibitors ( competitive , non- competitive , uncompetitive or allosteric binding site). Epitopes and paratopes are the binding sites between antigens and antibodies .

Various methods have been developed for the determination of protein-protein interactions , protein-DNA interactions , protein-lipid interactions, and protein-carbohydrate interactions . The binding site can partly be predicted by molecular modeling .

Individual evidence

  1. ↑ Martin Holtzhauer: Methods in protein analysis. Springer-Verlag, 2013, ISBN 978-3-642-61422-4 , pp. 32, 33.
  2. ^ H. Robert Horton et al .: Biochemistry. Pearson Deutschland GmbH, 2008, ISBN 978-3-827-37312-0 , p. 165.
  3. ↑ RJ Najmanovich: Evolutionary studies of ligand binding sites in proteins. In: Current opinion in structural biology. Volume 45, August 2017, pp. 85-90, doi : 10.1016 / j.sbi.2016.11.024 , PMID 27992825 .
  4. ↑ X. Jalencas, J. Mestres: Identification of Similar Binding Sites to Detect Distant Polypharmacology. In: Molecular informatics. Volume 32, number 11-12, December 2013, pp. 976-990, doi : 10.1002 / minf.201300082 , PMID 27481143 .
  5. ↑ A. Vulpetti, T. Kalliokoski, F. Milletti: Chemogenomics in drug discovery: computational methods based on the comparison of binding sites. In: Future medicinal chemistry. Volume 4, Number 15, October 2012, pp. 1971-1979, doi : 10.4155 / fmc.12.147 , PMID 23088277 .
  6. ^ D. Ghersi, R. Sanchez: Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures. In: Journal of structural and functional genomics. Volume 12, Number 2, July 2011, pp. 109-117, doi : 10.1007 / s10969-011-9110-6 , PMID 21537951 , PMC 3127736 (free full text).
  7. ↑ MM Gromiha, R. Nagarajan: Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. In: Advances in protein chemistry and structural biology. Volume 91, 2013, pp. 65-99, doi : 10.1016 / B978-0-12-411637-5.00003-2 , PMID 23790211 .