Sequence and intramolecular distance scoring analyses of microbial rhodopsins.
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.
Department of Life Science, Gakushuin University, Tokyo, Japan.
Miki
M
Asano
Department of Life Science, Gakushuin University, Tokyo, Japan.
Shunta
S
Ide
Department of Life Science, Gakushuin University, Tokyo, Japan.
Atsushi
A
Kamata
Department of Life Science, Gakushuin University, Tokyo, Japan.
Kiyohiro
K
Takahasi
Department of Life Science, Gakushuin University, Tokyo, Japan.
Tetsuji
T
Okada
Membrane; coordinates; crystallography; opsin; receptor