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ORIGINAL RESEARCH Evolutionary Bioinformatics Online 2006: 2 201210 201

Evolutionary Bioinformatics Online 2006: 2 201210 201
Spectral Analysis of Sequence Variability in
Basic-Helix-loop-helix (bHLH) Protein Domains
Zhi Wang1
and William R. Atchley1,2
Graduate Program In Biomathematics And Bioinformatics, 2
Department Of Genetics and Center For
Computational Biology, North Carolina State University, Raleigh, NC 27695-7614, USA.
Abstract: The basic helix-loop-helix (bHLH) family of transcription factors is used as a paradigm to explore structural
implications of periodicity patterns in amino acid sequence variability. A Boltzmann-Shannon entropy profile represents
site-by-site amino acid variation in the bHLH domain. Spectral analysis of almost 200 bHLH sequences documents the
periodic nature of the bHLH sequence variation. Spectral analyses provide strong evidence that the patterns of amino acid
variation in large numbers of sequences conform to the classical a-helix three-dimensional structure periodicity of 3.6
amino acids per turn. Multivariate indices of amino acid physiochemical attributes derived from almost 500 amino acid
attributes are used to provide information regarding the underlying causal components of the bHLH sequence variability.
Five multivariate attribute indices are used that reflect patterns in i) polarity - hydrophobicity - accessibility, ii) propensity
for secondary structures, iii) molecular volume, iv) codon composition and v) electrostatic charge. Multiple regression
analyses of the entropy values as dependent variables and the factor score means and variances as independent variables


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


Collections: Biology and Medicine