Linkers of secondary structures in proteins

Protein Science : a Publication of the Protein Society
V Geetha, P J Munson

Abstract

Linkers that connect repeating secondary structures fall into conformational classes based on distance and main-chain torsion clustering. A data set of 300 unique protein chains with low pairwise sequence identity was clustered into only a few groups representing the preferred motifs. The linkers of two to eight residues for the nonredundant data set are designated H-Ln-H, H-Ln-E, E-Ln-H, E-Ln-E, where n is the length, H stands for alpha-helices, and E for beta-strands. Most of the clusters identified here corroborate earlier findings. However, 19 new clusters are identified in this paper, with many of them having seven and eight residue linkers. In our first analysis, the secondary structures flanking the linkers are both interacting and noninteracting and there is no precise angle of orientation between them. A second analysis was performed on a set of proteins with restricted orientations for the flanking elements, namely, mainly alpha class of proteins with orthogonal architecture. Two definite clusters are identified, one corresponding to linkers of orthogonal helices and the other to linkers of antiparallel helices. Loops forming binding sites or involved in catalytic activity are important determinants of the function of...Continue Reading

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Citations

Apr 27, 2000·Progress in Biophysics and Molecular Biology·L D BarronA F Bell
Jul 1, 1999·Protein Science : a Publication of the Protein Society·E W BlanchL D Barron
Jul 6, 2015·Women's Health Issues : Official Publication of the Jacobs Institute of Women's Health·Gretchen Sisson
Oct 19, 2010·Journal of Child Language·Carol Stoel-Gammon
May 2, 2002·Protein Engineering·Silvio C E TosattoReinhard Männer
Jul 31, 2002·The Journal of Biological Chemistry·Josefine EderthRobert Landick

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