Nest (protein structural motif)

The Nest is a type of protein structural motif. It is a small recurring anion-binding feature of both proteins and peptides.[1][2][3][4][5][6][7][8][9] Each consists of the main chain atoms of three consecutive amino acid residues. The main chain NH groups bind the anions while the side chain atoms are often not involved. Proline residues lack NH groups so are rare in nests. About one in 12 of amino acid residues in proteins, on average, belongs to a nest.

RL nest bound to an egg oxygen. carbons grey, oxygens red and nitrogens blue. Hydrogen atoms omitted. Hydrogen bonds are grey dotted lines.
  1. ^ Watson, JD; Milner-White (2002). "A novel main-chain anion-binding site in proteins: The nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions". Journal of Molecular Biology. 315 (2): 171–182. doi:10.1006/jmbi.2001.5227. PMID 11779237.
  2. ^ Pal, D; Suhnel (2002). "New principles of protein structure: nests, eggs and what next?". Angew Chem Int Ed. 41 (24): 4663–4665. doi:10.1002/anie.200290009. PMID 12481319.
  3. ^ Milner-White, EJ; Nissink (2004). "Recurring main-chain anion-binding motifs in short polypeptides: nests". Acta Crystallographica Section D. D60 (11): 1935–1942. doi:10.1107/s0907444904021390. PMID 15502299.
  4. ^ Pajewski, R; Ferdani (2005). "Cation Dependence of Chloride Ion Complexation by Open-Chained Receptor Molecules in Chloroform Solution". Journal of the American Chemical Society. 127 (51): 18281–18295. doi:10.1021/ja0558894. PMID 16366583.
  5. ^ Berkessel, A; Koch (2006). "Asymmetric enone epoxidation by solid-phase bound peptides: further evidence for catalyst helicity and catalytic activity of individual strands". Biopolymers. 84 (1): 90–96. doi:10.1002/bip.20413. PMID 16283656.
  6. ^ Milner-White, EJ; Russell (2006). "Predicting the conformations of proteins and peptides in early evolution". Biology Direct. 3: 3. doi:10.1186/1745-6150-3-3. PMC 2241844. PMID 18226248.
  7. ^ Watson, JD; Laskowski (2005). "ProFunc: a server for predicting protein function from 3D structure". Nucleic Acids Research. 33 (Web Server): W89–W93. doi:10.1093/nar/gki414. PMC 1160175. PMID 15980588.
  8. ^ Langton, MJ; Serpell CJ; Beer PD (2016). "Anion recognition in water: Recent advances from a supramolecular and macromolecular perspective". Angewandte Chemie International Edition. 55 (6): 1974–1987. doi:10.1002/anie.201506589. PMC 4755225. PMID 26612067.
  9. ^ Cremer, P; Flood AS; Gibb BC; Mobley DL (2018). "Collaborative routes to clarifying the murky waters of aquaeous supramolcular chemistry". Nature Chemistry. 10 (1): 8–16. doi:10.1038/nchem.2894. PMID 29256514. S2CID 205298633.