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, 68 (4), 915-21

New Classification of Supersecondary Structures of Sandwich-Like Proteins Uncovers Strict Patterns of Strand Assemblage

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New Classification of Supersecondary Structures of Sandwich-Like Proteins Uncovers Strict Patterns of Strand Assemblage

Yih-Shien Chiang et al. Proteins.

Abstract

To describe the supersecondary structure (SSS) of beta sandwich-like proteins (SPs), we introduce a structural unit called the "strandon." A strandon is defined as a set of sequentially consecutive strands connected by hydrogen bonds in 3D structures. Representing beta-proteins as the assembly of strandons exposes the underlying similarities in their SSS and enables us to construct a novel classification scheme of SPs. Classification of all known SPs is based on shared supersecondary structural features and is presented in the SSS database (http://binfs.umdnj.edu/sssdb/). Analysis of the SSS reveals two common specific patterns. The first pattern defines the arrangement of strandons and was found in 95% of all examined SPs. The second pattern establishes the ordering of strands in the protein domain and was observed in 82% of the analyzed SPs. Knowledge of these two patterns that uncover the spatial arrangement of strands will likely prove useful in protein structure prediction.

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