Shear Numbers of Protein &bgr;-Barrels: Definition Refinements and Statistics

Author: Thornton W-M.J.M.  

Publisher: Academic Press

ISSN: 0022-2836

Source: Journal of Molecular Biology, Vol.275, Iss.4, 1997-01, pp. : 541-545

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Abstract

The original definition of shear number for a &bgr;-barrel is not unique if it contains one or more uneven &bgr;-bulges. We define the shear number of a &bgr;-barrel as the minimal change of residue numbers in the backbone direction for all closed paths on the &bgr;-barrel. We also discuss how to overcome some computational difficulties. It is pointed out that some closed &bgr;-sheets should not be considered as &bgr;-barrels. The pertinent statistics obtained from a representative list of the Protein Data Bank entries are summarized. All &bgr;-barrels have positive shear numbers, i.e. they are right-twisted. The shear numbers of most &bgr;-barrels are even, but exceptions do exist. The sizes of &bgr;-ladders in a &bgr;-barrel vary significantly. Most &bgr;-barrels contain uneven &bgr;-bulges, which may have important biological functions.