Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Mathematics, Bioinformatics and Computational Biology

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

2011

Journal or Book Title

Journal of Structural and Functional Genomics

Volume

12

Issue

2

First Page

119

Last Page

136

DOI

10.1007/s10969-011-9104-4

Abstract

Background

The atomic-level structural properties of proteins, such as bond lengths, bond angles, and torsion angles, have been well studied and understood based on either chemistry knowledge or statistical analysis. Similar properties on the residue-level, such as the distances between two residues and the angles formed by short sequences of residues, can be equally important for structural analysis and modeling, but these have not been examined and documented on a similar scale. While these properties are difficult to measure experimentally, they can be statistically estimated in meaningful ways based on their distributions in known proteins structures.

Results

Residue-level structural properties including various types of residue distances and angles are estimated statistically. A software package is built to provide direct access to the statistical data for the properties including some important correlations not previously investigated. The distributions of residue distances and angles may vary with varying sequences, but in most cases, are concentrated in some high probability ranges, corresponding to their frequent occurrences in either α-helices or β-sheets. Strong correlations among neighboring residue angles, similar to those between neighboring torsion angles at the atomic-level, are revealed based on their statistical measures. Residue-level statistical potentials can be defined using the statistical distributions and correlations of the residue distances and angles. Ramachandran-like plots for strongly correlated residue angles are plotted and analyzed. Their applications to structural evaluation and refinement are demonstrated.

Conclusions

With the increase in both number and quality of known protein structures, many structural properties can be derived from sets of protein structures by statistical analyses and data mining, and these can even be used as a supplement to the experimental data for structure determinations. Indeed, the statistical measures on various types of residue distances and angles provide more systematic and quantitative assessments on these properties, which can otherwise be estimated only individually and qualitatively. Their distributions and correlations in known protein structures show their importance for providing insights into how proteins may fold naturally to various residue-level structures.

Comments

This is a manuscript of an article published as Huang, Yuanyuan, Stephen Bonett, Andrzej Kloczkowski, Robert Jernigan, and Zhijun Wu. "Statistical measures on residue-level protein structural properties." Journal of structural and functional genomics 12, no. 2 (2011): 119-136. The final publication is available at Springer via http://dx.doi.org/10.1007/s10969-011-9104-4. Posted with permission.

Copyright Owner

Springer Science+Business Media B.V.

Language

en

File Format

application/pdf

Published Version

Share

COinS