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Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

Xuefeng Cui1, Shuai Cheng Li2, Dongbo Bu3, Babak Alipanahi1 and Ming Li1*

Author Affiliations

1 University of Waterloo, Ontario, Canada

2 City University of Hong Kong, Hong Kong, China

3 Chinese Academy of Sciences, Beijing, China

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Algorithms for Molecular Biology 2013, 8:5  doi:10.1186/1748-7188-8-5

Published: 25 February 2013

Abstract

Previous studies show that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these Gaussian distributions have been widely used as ideal bond lengths and angles in bioinformatics. However, we are not aware of any research done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles.

Here, we introduce the protein structure idealization problem. We focus on the protein backbone structure idealization. We describe a fast O(nm/ε) dynamic programming algorithm to find an idealized protein backbone structure that is approximately optimal according to our scoring function. The scoring function evaluates not only the free energy, but also the similarity with the target structure. Thus, the idealized protein structures found by our algorithm are guaranteed to be protein-like and close to the target protein structure.

We have implemented our protein structure idealization algorithm and idealized the high resolution protein structures with low sequence identities of the CULLPDB_PC30_RES1.6_R0.25 data set. We demonstrate that idealized backbone structures always exist with small changes and significantly better free energy. We also applied our algorithm to refine protein pseudo-structures determined in NMR experiments.

Keywords:
Protein structure idealization; Ideal bond length and angle; Dihedral angle space