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The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands



The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands



Biochemical and Biophysical Research Communications 386(3): 537-543



It is widely considered that it is not appropriate to treat beta-pairs in isolation, since other secondary structural models (such as helices, coils), protein topology and protein tertiary structures would limit beta-strand pairing. However, to understand the underlying mechanisms of beta-sheet formation, studies ought to be performed separately on more concrete aspects. In this study, we focus on the parallel or antiparallel orientation of beta-strands. First, statistical analysis was performed on the relative frequencies of the interstrand amino acid pairs within parallel and antiparallel beta-strands. Consequently, features were extracted by singular value decomposition from the statistical results. By using the support vector machine to distinguish the features extracted from the two types of beta-strands, high accuracy was achieved (up to 99.4%). This suggests that the interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands. These results may provide useful information for developing other useful algorithms to examine to the beta-strand folding pathways, and could eventually lead to protein structure predictions.

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Accession: 056389979

Download citation: RISBibTeXText

PMID: 19540200

DOI: 10.1016/j.bbrc.2009.06.072



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