Packing constraints of hydrophobic side chains in (alpha/beta)8 barrels.
An analysis of possible tight packing of hydrophobic groups simultaneously at the both surfaces of beta-hyperboloid-8 was conducted. This analysis shows that the disposition of amino acid side chains at the real beta-structure's surface is unique. If we sign the mean distance between adjacent beta-strands as "a," and the mean distance along beta-strand between C alpha atoms, whose side chains are directed to one side of the beta-sheet, as "b," the ratio b/a = square root of 2 very precisely. This ratio ensures the most efficient packing of side hydrophobic groups at the outer surface of beta-hyperboloid-8, forming, at the same time, the second by efficiency packing at its inner surface.
Vtyurin
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Department of Biopolymers Structure and Function Research, Russian Academy of Sciences, Moscow.
Panov
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V
D008433:Mathematics; D008958:Models, Molecular; D011487:Protein Conformation