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Molecular Architecture of the DNA-Binding Region and Its Relationship to Classification of Basic HelixLoopHelix Proteins

Summary: Molecular Architecture of the DNA-Binding Region and Its Relationship to
Classification of Basic Helix­Loop­Helix Proteins
William R. Atchley and Jieping Zhao
Department of Genetics and Center for Computational Biology, North Carolina State University
Multivariate statistical analyses are used to explore the molecular architecture of the DNA-binding and dimerization
regions of basic helix­loop­helix (bHLH) proteins. Alphabetic amino acid data are transformed to biologically meaningful
quantitative values using a set of 5 multivariate ``indices.'' These multivariate indices summarize variation in a large suite of
amino acid physiochemical attributes and reflect variability in polarity­accessibility­hydrophobicity, propensity for sec-
ondary 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 5 known DNA-binding groups. The relevant sites often have
well-documented structural and functional characteristics.
Eukaryotic genes contain specific short DNA se-
quences that regulate gene expression by binding to a special
class of proteins called transcription factors. Variation in
transcriptional machinery underlies the myriad of gene ex-
pression patterns responsible, in large measure, for the ob-
served patterns of evolutionary diversity. Understanding


Source: Atchley, William R.- Department of Genetics, North Carolina State University


Collections: Biology and Medicine