The conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins.
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.
Watson
James D
JD
Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, Glasgow University, Glasgow, G12 8QQ, UK.
Milner-White
E James
EJ
D000838:Anions / Q000378:metabolism*; D017302:Annexins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D002248:Carbon Monoxide / Q000378:metabolism; D020134:Catalytic Domain; D002412:Cations / Q000378:metabolism*; D003198:Computer Simulation; D003500:Cyclization; D020782:Matrix Metalloproteinases / Q000737:chemistry / Q000378:metabolism; D008666:Metalloendopeptidases / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009584:Nitrogen / Q000378:metabolism; D010100:Oxygen / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D010741:Phospholipases A / Q000737:chemistry / Q000378:metabolism; D054467:Phospholipases A2; D011188:Potassium / Q000378:metabolism; D015221:Potassium Channels / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013381:Subtilisins / Q000737:chemistry / Q000378:metabolism
D000838:Anions; D017302:Annexins; D002412:Cations; D010455:Peptides; D015221:Potassium Channels; C011080:polyglycine; D002248:Carbon Monoxide; D010741:Phospholipases A; D054467:Phospholipases A2; D013381:Subtilisins; D020782:Matrix Metalloproteinases; D008666:Metalloendopeptidases; C095666:serralysin; D009584:Nitrogen; D011188:Potassium; D010100:Oxygen; D002118:Calcium