Nest (protein structural motif)
The Nest is a type of protein structural motif. Peptide nests are small anion-binding molecular features of 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.
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 in the antibiotic peptide vancomycin which binds a key carboxylate group needed during bacterial cell wall synthesis, thereby preventing the 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°. Nests vary in their degree of concavity. A few have so little that the concavity is lost. Such peptides are less liable to act as anion binding sites. The specificity filter of the potassium channel and the channel of aquaporin exhibit this more linear conformation in which the carbonyl groups are employed by proteins to transport molecules across membranes. This near-linear conformation is also that found in a strand of alpha sheet
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