Molecular architecture of the DNA-binding region and its relationship to classification of basic helix-loop-helix proteins.
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 5 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 5 known DNA-binding groups. The relevant sites often have well-documented structural and functional characteristics.
Atchley
William R
WR
Department of Genetics and Center for Computational Biology, North Carolina State University, USA. bill@atchleylab.org
Zhao
Jieping
J
D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D003062:Codon / Q000235:genetics; D004247:DNA / Q000378:metabolism*; D019281:Dimerization; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D055672:Static Electricity
D051792:Basic Helix-Loop-Helix Proteins; D003062:Codon; D004247:DNA