Protein lipograms

Laurie, Jason, Chattopadhyay, Amit K and Flower, Darren R (2017). Protein lipograms. Journal of Theoretical Biology, 430 , pp. 109-116.

Abstract

Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this article, we establish a usable terminology for the decomposition of a sequence collection in terms of the lipogram. Next, we characterize Uniref50 using a lipogram decomposition. At the global level, protein lipograms exhibit power-law properties. A clear correlation with metabolic cost is seen. Finally, we use the lipogram construction to assign proteomes to the four branches of the tree-of-life: archaea, bacteria, eukaryotes and viruses. We conclude from this pilot study that the lipogram demonstrates considerable potential as an additional tool for sequence analysis and proteome classification.

Publication DOI: https://doi.org/10.1016/j.jtbi.2017.07.009
Divisions: Engineering & Applied Sciences
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Engineering & Applied Sciences > Mathematics
Life & Health Sciences > Pharmacy
Life & Health Sciences
Life & Health Sciences > Applied Health Research Group
Additional Information: © 2017, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/
Uncontrolled Keywords: Amino Acid Sequence,Archaea,Bacteria,Eukaryota,Evolution, Molecular,Pilot Projects,Proteins/chemistry,Proteome/classification,Viruses,Statistics and Probability,Medicine(all),Modelling and Simulation,Immunology and Microbiology(all),Biochemistry, Genetics and Molecular Biology(all),Agricultural and Biological Sciences(all),Applied Mathematics
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Related URLs: http://www.scopus.com/inward/record.url?scp=85024840569&partnerID=8YFLogxK (Scopus URL)
Published Date: 2017-10-07
Authors: Laurie, Jason ( 0000-0002-3621-6052)
Chattopadhyay, Amit K
Flower, Darren R ( 0000-0002-8542-7067)

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