Internally symmetric proteins with multiple axes

Wednesday, October 10, 2012 — Poster Session II
Noon – 2:00 p.m	Natcher Conference Center, Building 45	NCI	STRUCTBIO-9

Authors

• C.H. Tai
• D. Kc
• B.K. Lee

Abstract

The functional form of a protein is often symmetric and the type of symmetry affects the function and stability of the protein. Most proteins form a symmetric complex through oligomerization while others are symmetric in their monomeric form. Our program, SymD, found 10% to 15% of protein domains are internally symmetric; most have single symmetry element, cyclic, helical or superhelical. Here we describe protein domains with multiple symmetry elements and the procedure to find them. We took advantage of the multiple symmetric transformation output from SymD and grouped them into distinct clusters with common or nearly common symmetry axes. In contrast to the oligomeric complexes many of which have the dihedral symmetry, very few internally symmetric proteins have more than one symmetry element. Among the 10,569 ASTRAL 1.75 domains with less than 40% sequence identity, only 29 domains with more than one symmetry axis. They can be divided into two groups, 16 with a dihedral symmetry and 13 with a bent helical structure. In the dihedral group, there are α-helix bundles, β-sandwiches, double-stranded β-helices and domains of the IF-3 fold. In the bent helix group, there are domains of single α-helix, single β-helix, β-hairpin stack and α- superhelical structures.

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