PMID: 8968959Oct 1, 1996Paper

Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank

Journal of Protein Chemistry
Z Sun, B Jiang

Abstract

Short peptides connecting alpha-helices and beta-strands have been analyzed in 240 proteins refined at resolutions of 0.25 nm or better. Connecting peptides of lengths between one and five residues have been classified as part of supersecondary motifs of four types: alpha alpha, alpha beta, beta alpha, and beta beta. Careful consideration has been given to the definition of secondary structures on the basis of hydrogen bonds and main-chain conformational angles. Using five classes of residue conformation-a, b, e, l, t-in the nonregular structure regions of phi, psi space, 34 classes of supersecondary motifs occurring at least five times have been identified. Among these 34 classes, 11 classes that occur more than 25 times are commonly occurring supersecondary structure motifs. The patterns and conformations of the 11 commonly occurring supersecondary structure motifs have been characterized, demonstrating that patterns and conformations adopted by supersecondary structure motifs are limited. The results have relevance to structure prediction, comparative modeling, and protein folding.

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Citations

Jan 28, 2009·Computer Methods in Biomechanics and Biomedical Engineering·M V JudyK Murugesan
Jul 20, 2006·Journal of the Royal Society, Interface·Vincenzo CutelloGiuseppe Nicosia
Aug 19, 1999·Protein Science : a Publication of the Protein Society·C J TsaiR Nussinov
Jun 23, 2015·The Journal of Physical Chemistry. B·Debarati DasGuptaB Jayaram
Sep 1, 2013·Supramolecular Chemistry·Laura NevolaAndrew D Hamilton
Aug 6, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Bruno BorguesanMárcio Dorn
May 2, 2002·Protein Engineering·Silvio C E TosattoReinhard Männer
Oct 2, 2002·Journal of Biomolecular Structure & Dynamics·Mark HsiehBrooke Lustig

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