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A Geometrical Perspective on the Insulin Evolution

Authors: Yuhei Kunihiro; Sorin V. Sabau; Kazuhiro Shibuya;

A Geometrical Perspective on the Insulin Evolution

Abstract

{"references": ["E. N. Baker, T. L. Blundell, J. F. Cutfield, S. M. Cutfield, E. J. Dodson, G. G. Dodson, D. M. C. Hodgkin, R. E. Hubbard, N. W. Isacs, C. D. Reynolds, K. Sakabe, N. Sakabe and N. M. Vijayan, The structure 2 Zn pig insulin crystal at 1.5 A resolution, Philos. Trans. R. Soc. London Ser. B 319: 369-456, 1988.", "J. Baussand and A. Carbone, Inconsistent distances in substitution matrices can be avoided by properly handling hydrophobic residues, Evol. Bioinform online, 4, 255-261, 2008.", "D. Burago, Y. Burago and S. Ivanov, A course in Metric Geometry,GSM, 33, American Mathematical Soceiety. 2001.", "J. M. Conlon, Molecular Evolution of Insulin in Non-Mammalian Vertebrates, Amer. Zool., 40: 200-212, 2000.", "R. H. M. Ebberink, A. B. Smit and J. Van Minnen, The insulin family: evolution of structure and function in vertebrates and invertebrates, Biol, Bull, 177: 176-182, 1989.", "F. M. Gregoire, N. Chomiki, D. Kachinskas and C. H. Warden, Cloning and developmental regulation of a novel member of the insulin-like gene family in Caenorhabditis elegans,\nBiochemical and Biophysical Research Communications; 249, 385 - 390, 1998.", "M. Kimura, The neutral theory of molecular evolution, Cambridge University Press, 1983.", "H. Koshiyama, Explanation of the Insulin Paradox From the Evolutionary Point of View, Jpn Clin Med. 2012; 3: 2124, 2012.", "C. Kristensen, T. Kjeldsen, F. C. Wiberg, L. Schaffer, M. Hach, S. Havelund, J. Bass, D. F. Steiner and A. S. Andersen, Alanine scanning mutagenesis of insulin, J. Biol. Chem, 272: 12978-12983, 1997.\n[10] Y. Kunihiro and S. V. Sabau, Quasi-metrics. Geometry of Sequence Comparison,\nProceedings of Asia Symposium on Engineering and Information, 2013, p. 186-196.\n[11] H. P. A. Kunzi and V. Vajner, Weighted quasi-metrics, in: Papers on General topology and Applic., Annals New York Acad. Sci. 728, 64-77, 1994.\n[12] S. G. Mattews, Partial metric topology, in: Papers on General topology and Applic.,\nNinth Summer Conf. Slippery Rock, PA, Annals of the New York Acad. Sci. 728, 183-197, 1993.\n[13] J. Pevnser, Bioinformatics and Functional Genomics, Second Edition, 2003.\n[14] S. V. Sabau, K. Shibuya and H. Shimada, Metric structures associated to Finsler metrics, arXiv: 1305. 5880 [math.DG], 2013.\n[15] A. Stojmirovi\u00b4c and Y. Yu, Geometric aspects of biological sequence comparison, J. Comput. Biol., 16(4), 579-601, 2009."]}

We study the molecular evolution of insulin from metric geometry point of view. In mathematics, and in particular in geometry, distances and metrics between objects are of fundamental importance. Using a weaker notion than the classical distance, namely the weighted quasi-metrics, one can study the geometry of biological sequences (DNA, mRNA, or proteins) space. We analyze from geometrical point of view a family of 60 insulin homologous sequences ranging on a large variety of living organisms from human to the nematode C. elegans. We show that the distances between sequences provide important information about the evolution and function of insulin.

Keywords

evolution, insulin., Metric geometry

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