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A New Bioinformatics Approach to Natural Protein Collections: Permutation Structure Contrasts of Viral and Cellular Systems

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Abstract

Biological cells and viruses operate by different replication and symmetry paradigms. Cells are able to replicate independently and express little spatial symmetry; viruses require cells for replication while manifesting high symmetry. The author inquired whether different paradigms were reflected in the permutations of amino acid sequences. The hypothesis was that the permutation structure level and symmetry within viral protein collections exceed that of living cells. The rationale was that one symmetry aspect generally accompanies and promotes others in a system. The inquiry was readily answered given abundant sequence archives for proteins. The analysis of collections from diverse viral and cellular sources lends strong support. Additional insights into protein primary structure, the design of collections, and the role of information are provided as well.

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Abbreviations

NCBI:

National Center for Biotechnology Information

BLAST:

Basic Local Alignment Search Tool

UniProt:

Universal Protein Resources

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Acknowledgments

The authors thank Professors Miguel Ballicora and Ken Olsen for discussions about individual proteins and proteomes. The assistance and suggestions of Donald May, John Zumpf, Shelby Grztec, and Julius Aguas are equally appreciated. Thanks are also extended to an anonymous reviewer for criticism and suggestions.

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Authors and Affiliations

  1. Department of Chemistry, Loyola University Chicago, 6525 North Sheridan Road, Chicago, IL, 60626, USA

    Daniel J. Graham

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  1. Daniel J. Graham
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Correspondence to Daniel J. Graham.

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Graham, D.J. A New Bioinformatics Approach to Natural Protein Collections: Permutation Structure Contrasts of Viral and Cellular Systems. Protein J 32, 275–287 (2013). https://doi.org/10.1007/s10930-013-9485-2

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  • DOI: https://doi.org/10.1007/s10930-013-9485-2

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