A modular perspective of protein structures: application to fragment-based loop modeling using ArchPred

Technology

Modeling

Summary

"Smotifs" are composed of two secondary structures connected by a loop. These generically defined supersecondary structure elements were used to explore the evolution and current variety of structure building blocks. The Smotifs classifications were used in a loop conformation modeling algorithm, ArchPred.

Description

Proteins can be decomposed into supersecondary structure modules. We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular secondary structures connected by a loop, to explore the evolution and current variety of structure building blocks. Here, we discuss recent observations about the saturation of Smotif geometries in protein structures and how it opens new avenues in protein structure modeling and design. As a first application of these observations, we describe our loop conformation modeling algorithm, ArchPred, which takes advantage of Smotifs classification. In this application, instead of focusing on specific loop properties, the method narrows down possible template conformations in other, often not homologous structures, by identifying the most likely supersecondary structure environment that cradles the loop. Beyond identifying the correct starting supersecondary structure geometry, it takes into account information of fit of anchor residues, steric clashes, matching of predicted and observed dihedral angle preferences, and local sequence signal.

Publication

Fernandez-Fuentes N, Fiser A. "A modular perspective of protein structures: application to fragment based loop modeling." Methods Mol. Biol. 932:141-58 (2013). PubMed ID: 22987351 | Search SBKB Publications portal | PMC Link

Contact

Andras Fiser, Email: andras.fiser@einstein.yu.edu

New York Structural Genomics Research Consortium

Link




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Last edited:Tue 01 Oct 2013 - 3 years, 6 months ago