Prediction of the Structural Motifs of Sandwich Proteins

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 101; no. 48; pp. 16780 - 16783
• Main Authors: Fokas, A. S., Gelfand, I. M., Kister, A. E.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 30.11.2004; National Acad Sciences
• Subjects: Amino Acid Sequence; Biological Sciences; Biophysics; Family structure; Hydrogen bonds; Models, Molecular; Molecular Sequence Data; Molecular structure; Protein Structure, Secondary; Proteins; Proteins - chemistry; Sandwich structures; Sandwiches
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0407570101

We investigate the supersecondary structure of a large group of proteins, the so-called sandwich proteins. The analysis of a large number of such proteins has led us to propose a set of rules that can be used to predict the possible arrangements of strands in the two β-sheets forming a given sandwich structure. These rules imply the existence of certain invariant supersecondary substructures common to all sandwich proteins. Furthermore, they dramatically restrict the number of permissible arrangements. For example, whereas for proteins consisting of three strands in each β-sheet 180 possible strand arrangements exist a priori, our rules imply that only 15 of them are permissible. Five of these predicted arrangements describe all currently known sandwich proteins with six strands.