Nest

The Nest is a type of protein structural motif. It is a small recurring anion-binding feature of both proteins and peptides. 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. Nest conformations The conformation of a nest is such that the NH groups of the first and third amino acid residues are liable to be hydrogen bonded to a negatively charged, or partially negatively charged, atom, often an oxygen atom. The NH of the second residue may also be hydrogen bonded to the same atom but usually points somewhat away. These main chain atoms form a concavity called a nest into which an anionic atom fits. Such anionic atoms are sometimes called eggs and more than one egg may occur bound to a nest. The oxyanion hole of the intestinal serine proteases is a functional example of a nest. Another occurs at the bottom of a deep cavity in the antibiotic peptide vancomycin which binds a key carboxylate group utilized during the final stages of bacterial cell wall synthesis, thereby preventing bacterial cells from multiplying. Nests are defined by the conformation of the main chain atoms, namely the phi, psi dihedral angles of the first two amino acids in the nest. For a typical (RL) nest phii=-90°; psii=0°; phii+1=80°; psii+1=20°.