On the Significance of Alternating Patterns of Polar and Non-polar Residues in Beta-strands

J. Mol. Biol. (2002) 323, 453-461

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Abstract:

Alternating patterns of polar and non-polar residues were thought to reflect the interior/exterior geometry of amino acid residue side-chains on a β-sheet. The authors studied the occurrence of alternating polar/non-polar binary patterns in parallel and antiparallel β-sheets in proteins of known structure and in the sequences of amyloidogenic proteins. β-Strand windows of five residues in binary patterns were computed in 1911 non-homologous proteins. The purely alternating hydrophobic/polar patterns (PNPNP and NPNPN) are most frequent in β-sheets, typically occurring in antiparallel strands. The overall distribution of the pentapeptide binary patterns is significantly different in strands within parallel and antiparallel sheets. Complementary patterns (where the hydrophobic and polar residues pair with one another) associate preferentially in both parallel and antiparallel sheets. Alternating patterns were not found to be prevalent in amyloidogenic proteins or in short fragments involved directly in amyloid formation.

Reference:

Richardson, J. S. & Richardson, D. C. (2002). Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl Acad. Sci. USA, 99, 2754–2759.

Sipe, J. D. & Cohen, A. S. (2000). Review: history of the amyloid fibril. J. Struct. Biol. 130, 88–98.