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MBE Advance Access published online on October 13, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl143
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted October 5, 2006

Research Article

Molecular Architecture of the DNA Binding Region and its Relationship to Classification of Basic Helix-Loop-Helix Proteins

William R. Atchley 1 * and Jieping Zhao 1

1 Department of Genetics and Center for Computational Biology, North Carolina State University, Raleigh, NC 27695-7614

* To whom correspondence should be addressed.
William R. Atchley, E-mail: bill{at}atchleylab.org


  Abstract

Multivariate statistical analyses are used to explore the molecular architecture of the DNA binding and dimerization regions of basic helix-loop-helix (bHLH) proteins. Alphabetic amino acid data are transformed to biologically meaningful quantitative values using a set of five multivariate "indices." These multivariate indices summarize variation in a large suite of amino acid physiochemical attributes and reflect variability in polarity-accessibility-hydrophobicity, propensity for secondary structure, molecular size, codon composition and electrostatic charge. Using these index score data, discriminant analyses describe the multidimensional aspects of physiochemical variation and clarify the structural basis of the prevailing evolutionary classification of bHLH proteins. A small number of amino acids from both the binding dimerization domains, when considered simultaneously, accurately distinguish the five known DNA binding groups. The relevant sites often have well-documented structural and functional characteristics.

Keywords: computational biology; bHLH proteins; molecular architecture; multivariate statistics; DNA binding specificity; molecular evolution.
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