Criteria for confirming sequence periodicity identified by Fourier transform analysis: Application to GCR2, a candidate plant GPCR?

Christopher J.R. Illingworth, Kevin E. Parkes, Christopher R. Snell, Philip M. Mullineaux, Christopher A. Reynolds

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

Methods to determine peridiodicity in protein sequences are useful for inferring function. Fourier transformation is one approach but care is required to ensure the periodicity is genuine. Here we have shown that empirically-derived statistical tables can be used as a measure of significance. Genuine protein sequences data rather than randomly generated sequences were used as the statistical backdrop. The method has been applied to G-protein coupled receptor (GPCR) sequences, by Fourier transformation of hydrophobicity values, codon frequencies and the extent of over-representation of codon pairs; the latter being related to translational step times. Genuine periodicity was observed in the hydrophobicity whereas the apparent periodicity (as inferred from previously reported measures) in the translation step times was not validated statistically. GCR2 has recently been proposed as the plant GPCR receptor for the hormone abscisic acid. It has homology to the Lanthionine synthetase C-like family of proteins, an observation confirmed by fold recognition. Application of the Fourier transform algorithm to the GCR2 family revealed strongly predicted seven fold periodicity in hydrophobicity, suggesting why GCR2 has been reported to be a GPCR, despite negative indications in most transmembrane prediction algorithms. The underlying multiple sequence alignment, also required for the Fourier transform analysis of periodicity, indicated that the hydrophobic regions around the 7 GXXG motifs commence near the C-terminal end of each of the 7 inner helices of the α-toroid and continue to the N-terminal region of the helix. The results clearly explain why GCR2 has been understandably but erroneously predicted to be a GPCR.

Original languageEnglish
Pages (from-to)28-35
Number of pages8
JournalBiophysical Chemistry
Volume133
Issue number1-3
Early online date15 Nov 2007
DOIs
Publication statusPublished - 1 Mar 2008
Externally publishedYes

Keywords

  • Codon pairs
  • Codons
  • Fourier transform
  • G-protein coupled receptors
  • Hydrophobicity
  • Periodicity

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Organic Chemistry

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