Towards Symmetry-Based Explanation of (Approximate) Shapes of Alpha-Helices and Beta-Sheets (and Beta-Barrels) in Protein Structure

Authors

Jaime Nava, The University of Texas at El PasoFollow
Vladik Kreinovich, The University of Texas at El PasoFollow

Publication Date

1-2012

Comments

Technical Report: UTEP-CS-11-38a

To appear in Chemistry.

Abstract

Protein structure is invariably connected to protein function. There are two important secondary structure elements: alpha helices and beta-sheets (which sometimes come in a shape of beta-barrels). The actual shapes of these structures can be complicated, but in the first approximation, they are usually approximated by, correspondingly, cylindrical spirals and planes (and cylinders, for beta-barrels). In this paper, following the ideas pioneered by a renowned mathematician M. Gromov, we use natural symmetries to show that, under reasonable assumptions, these geometric shapes are indeed the best approximating families for secondary structures.