New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage.
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.
Chiang
Yih-Shien
YS
Department of Health Informatics, SHRP, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07107, USA.
Gelfand
Tatiana I
TI
Kister
Alexander E
AE
Gelfand
Israel M
IM
D030562:Databases, Protein; D006860:Hydrogen Bonding; D007091:Image Processing, Computer-Assisted; D007700:Kinetics; D046911:Macromolecular Substances; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D046911:Macromolecular Substances; D011506:Proteins