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

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. Tetsuji Okada ( ) Corresponding author: [email protected] Asano M, Ide S, Kamata A How to cite this article: et al. Sequence and intramolecular distance scoring analyses of microbial rhodopsins 2016, :165 (doi: ) [version 2; referees: 2 approved] F1000Research 5 10.12688/f1000research.7920.2 © 2016 Asano M . This is an open access article distributed under the terms of the , which Copyright: et al Creative Commons Attribution Licence permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions. Data associated with the article are available under the terms of the Creative (CC0 1.0 Public domain dedication). Commons Zero "No rights reserved" data waiver Supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan (S1312002 to Department of Life Grant information: Science, Gakushuin University). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: No competing interests were disclosed. 12 Feb 2016, :165 (doi: ) First published: 5 10.12688/f1000research.7920.1 Referee Status: