Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis

• Published in: Journal of molecular biology Vol. 236; no. 5; p. 1369
• Main Authors: Murzin, A G, Lesk, A M, Chothia, C
• Format: Journal Article
• Language: English
• Published: England 11-03-1994
• Subjects: Hydrogen Bonding; Models, Molecular; Protein Structure, Secondary
• DOI: 10.1016/0022-2836(94)90064-7
• ISSN: 0022-2836

The major feature of many proteins is a large beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last: the beta-sheet barrel. McLachlan classified barrels in terms of two integral parameters: the number of strands in the beta-sheet, n, and the "shear number", S, a measure of the stagger of the strands in the beta-sheet. He showed that the mean radius of a barrel and the extent to which strands are tilted relative to its axis are determined by the values of n and S. Here we show that the (n, S) values determine all the other general structural features of regular beta-sheet barrels, in particular, optimal values of the twist and coiling angles that produce the closed beta-sheet, the hyperboloidal shape and the arrangement of residues in the barrel interior. Consideration of the residue arrangements in the interiors of different potential barrel structures, and of side-chain volumes, suggest that barrels, in which the interiors are close packed by the residues in beta-sheets with good geometries, have structures that correspond to one of only ten different combinations of n and S. In the accompanying paper, we demonstrate, by an analysis of all observed protein structures that contain beta-sheet barrels and for which atomic co-ordinates are available, the validity of these theoretical results.