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Bioinformatics Advance Access originally published online on November 15, 2005
Bioinformatics 2006 22(3):297-302; doi:10.1093/bioinformatics/bti775
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Mean curvature as a major determinant of ß-sheet propensity

Eunhee Koh 1,*, Taehyo Kim 3 and Hyun-soo Cho 1,2

1Department of Biology, Yonsei University 134, Sinchon-dong, Seodaemun-gu, Seoul, 120-749, Korea
2Protein Network Research Center, Yonsei University 134, Sinchon-dong, Seodaemun-gu, Seoul, 120-749, Korea
3POSCO, Technical Research Laboratories 699, Gumho-dong, Gwangyang-si, Jeonnam, 545-090, Korea

*To whom correspondence should be addressed.

Motivation: Despite the importance of ß-sheets as building blocks in proteins and also toxic elements in the pathological disorders, ranging from Alzheimer's disease to mad cow diease, the principles underlying their stability are not well understood. Non-random ß-sheet propensities of amino acids have been revealed both by their distinct statistical preferences within known protein structures and by the relative thermodynamic scales through the experimental host-guest systems. However, recent fitting analysis has proved that a native ß-sheet conforms to a minimal surface with zero mean curvature, like the physical model of soap films.

Results: We here suggest that the stability of a residue in the all ß-sheet proteins can be measured with its mean curvature parameter, using discrete differential geometry. The sharply decreasing mean curvature with increasing number of ß-strands identifies a significant cooperative effect whereby the interstrand interaction increases in strength with the number of ß-strands. Furthermore, strong correlations of mean curvatures with previous ß-sheet propensities of amino acids show that their intrinsic differences in adopting the ideal ß-sheet structure are affected by the water-accessible area of side-chains, and result in the distinct statistical and thermodynamic ß-sheet propensities. Therefore, we conclude that mean curvature should be considered as the significant stability index of a ß-sheet structure.

Contact: ehkoh{at}yonsei.ac.kr

Received on September 26, 2005; revised on November 9, 2005; accepted on November 9, 2005

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