J Mol Biol (2002) 315: 183-91.
The conformations of polypeptide chains where the main-chain parts of successive
JD Watson, EJ Milner-White
We have investigated the shapes of polypeptides where successive residues have main-chain phi,psi conformations of opposite hand. A graph not unlike a Ramachandran plot is presented illustrating the various possible conformations. All are ring-shaped or extended. Some of these conformations occur in native proteins, the commonest approximating to a feature we propose calling a nest, described in the accompanying paper, where the main-chain NH groups point inwards relative to the ring and give rise to an anion-binding site. Another conformation is related but more extended and is found uniquely in the four stretches of polypeptide that line the tetrameric K(+) channel; their CO groups bind the K ions in the channel. In a different ring-shaped conformation that we propose calling a catgrip, the main-chain CO groups point into the ring; this is employed for specific Ca ion binding in the annexin, phospholipase A2 and subtilisin loops, and the regularly arranged beta-roll loops of the serralysin protease family.
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