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A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs

  • Published:
Journal of Structural and Functional Genomics

Abstract

The study of the protein–protein interactions (PPIs) of unique ORFs is a strategy for deciphering the biological roles of unique ORFs of interest. For uniform reference, we define unique ORFs as those for which no matching protein is found after PDB-BLAST search with default parameters. The uniqueness of the ORFs generally precludes the straightforward use of structure-based approaches in the design of experiments to explore PPIs. Many open-source bioinformatics tools, from the commonly-used to the relatively esoteric, have been built and validated to perform analyses and/or predictions of sorts on proteins. How can these available tools be combined into a protocol that helps the non-expert bioinformaticist researcher to design experiments to explore the PPIs of their unique ORF? Here we define a pragmatic protocol based on accessibility of software to achieve this and we make it concrete by applying it on two proteins—the ImuB and ImuA’ proteins from Mycobacterium tuberculosis. The protocol is pragmatic in that decisions are made largely based on the availability of easy-to-use freeware. We define the following basic and user-friendly software pathway to build testable PPI hypotheses for a query protein sequence: PSI-PRED → MUSTER → metaPPISP → ASAView and ConSurf. Where possible, other analytical and/or predictive tools may be included. Our protocol combines the software predictions and analyses with general bioinformatics principles to arrive at consensus, prioritised and testable PPI hypotheses.

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Abbreviations

ORF:

Open reading frame

TB:

Tuberculosis

PPIs:

Protein–protein interactions

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Acknowledgments

A. Z. holds a Sydney Brenner Fellowship. Y. S. holds a Claude Leon Fellowship. We would like to thank Professor Sir Tom Blundell of the University of Cambridge UK for reading the manuscript and making helpful suggestions. We thank Professor Yang Zhang of the University of Michigan USA for reading the manuscript. We thank Mr. Renxiang Yan of the University of Michigan USA for technical assistance with local runs of the MUSTER program. We thank Dr Tichaona Mangwende for helpful discussions and suggestions.

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  1. Gene Expression and Biophysics Group, Synthetic Biology, ERA, Building 20, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, 0001, South Africa

    Alexander Zawaira & Youtaro Shibayama

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  1. Alexander Zawaira
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  2. Youtaro Shibayama
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Correspondence to Alexander Zawaira.

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Zawaira, A., Shibayama, Y. A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. J Struct Funct Genomics 13, 185–200 (2012). https://doi.org/10.1007/s10969-012-9141-7

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  • DOI: https://doi.org/10.1007/s10969-012-9141-7

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