F1000Research (Apr 2016)

Sequence and intramolecular distance scoring analyses of microbial rhodopsins [version 2; referees: 2 approved]

  • Miki Asano,
  • Shunta Ide,
  • Atsushi Kamata,
  • Kiyohiro Takahasi,
  • Tetsuji Okada

DOI
https://doi.org/10.12688/f1000research.7920.2
Journal volume & issue
Vol. 5

Abstract

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Recent accumulation of sequence and structural data, in conjunction with systematical classification into a set of families, has significantly advanced our understanding of diverse and specific protein functions. Analysis and interpretation of protein family data requires comprehensive sequence and structural alignments. Here, we present a simple scheme for analyzing a set of experimental structures of a given protein or family of proteins, using microbial rhodopsins as an example. For a data set comprised of around a dozen highly similar structures to each other (overall pairwise root-mean-squared deviation < 2.3 Å), intramolecular distance scoring analysis yielded valuable information with respect to structural properties, such as differences in the relative variability of transmembrane helices. Furthermore, a comparison with recent results for G protein-coupled receptors demonstrates how the results of the present analysis can be interpreted and effectively utilized for structural characterization of diverse protein families in general.

Keywords