A simple topological representation of protein structure: implications for new, fast, and robust structural classification

Proteins
David BostickIosif I Vaisman

Abstract

A topological representation of proteins is developed that makes use of two metrics: the Euclidean metric for identifying natural nearest neighboring residues via the Delaunay tessellation in Cartesian space and the distance between residues in sequence space. Using this representation, we introduce a quantitative and computationally inexpensive method for the comparison of protein structural topology. The method ultimately results in a numerical score quantifying the distance between proteins in a heuristically defined topological space. The properties of this scoring scheme are investigated and correlated with the standard Calpha distance root-mean-square deviation measure of protein similarity calculated by rigid body structural alignment. The topological comparison method is shown to have a characteristic dependence on protein conformational differences and secondary structure. This distinctive behavior is also observed in the comparison of proteins within families of structural relatives. The ability of the comparison method to successfully classify proteins into classes, superfamilies, folds, and families that are consistent with standard classification methods, both automated and human-driven, is demonstrated. Furthermor...Continue Reading

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Citations

Apr 14, 2006·Journal of Molecular Evolution·Lorraine Marsh
Jan 27, 2006·BMC Bioinformatics·Xiaobo ZhouStephen T C Wong
May 28, 2010·BMC Structural Biology·Todd J Taylor, Iosif I Vaisman
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