The polar profile of ancient proteins: a computational extrapolation from prebiotics to paleobiochemistry

Carlos Polanco; Thomas Buhse; Vladimir Uversky; Gloria Vizcaino; Jacobo Levy Picciotto

doi:10.18388/abp.2016_1311

Carlos Polanco Faculty of Sciences Universidad Nacional Autonoma de Mexico http://orcid.org/0000-0003-1673-2006
Thomas Buhse Universidad Autónoma del Estado de Morelos
Vladimir Uversky University of South Florida
Gloria Vizcaino Instituto Nacional de Ciencias Médicas y Nutrición
Jacobo Levy Picciotto Universidad Anahuac

DOI: https://doi.org/10.18388/abp.2016_1311

Keywords: origin of life, prebiotic protein formation, abiogenesis

Abstract

This paper addresses the polar profile of ancient proteins using a comparative study of amino acids found in 25,000,000-year-old shells as described in Abelson's work. We simulated the polar profile with a computer platform that represented an evolutionary computational toy model that mimics the generation of small proteins starting from a pool of amino acid monomers and that included several dynamic properties such as self-replication and fragmentation-recombination of the proteins. The simulations were taken up to 15 generations and produced a considerable number of proteins of 25 amino acids in length. The computational model included the amino acids found in the ancient shells, the thermal degradation factor and the relative abundance of the amino acids observed in the Miller-Urey experimental simulation on prebiotic amino acid formation. We found that the amino acid polar profiles of the ancient shells and those simulated and extrapolated from the Miller-Urey abundances are coincident.

References

Abelson, P.H. (1966) Chemical events on the primitive earth. Proc Natl Acad Sci USA.55, 1365-1372.

Abelson, P.H. (1959) Geochemistry and organic substances. Researchers in geochemistry. pp. 79-103 Wiley.

Abelson, P.H. (1957) Some aspects of Paleobiochemistry. Ann N Y Acad Sci 69, 276-285.

Bag, B.G & von Kiedrowski, G. (1996) Templates, autocatalysis and molecular replication. Pure Appl Chem 68:2145-2152.

Bissette, A.J. & Fletcher, S.P. (2013) Mechanisms of autocatalysis. Angew Chem Int 52:2-30.

Chen, Y.P. & Chen, F. (2008) Identifying targets for drug discovery using bioinformatics. Expert Opin Ther Targets 12:383-389 DOI: 10.1517/14728222. 12.4.383.

Delaye L, Becerra A, Lazcano A. (2005) The last common ancestor: what’s in a name? Orig Life Evol Biosph 35:537–554.

Fernald, G.H. et al. (2011) Bioinformatics challenges for personalized medicine. Bioinformatics 27: 1741–1748 DOI: 10.1093/bioinformatics/btr295.

Forslund, K. & Sonnhammer, E.L. (2012) Evolution of protein domain architectures. Methods Mol Biol 856:187-216 DOI: 10.1007/978-1-61779-585-5_8.

González-Díaz, H. et al. (2008) Predicting antimicrobial drugs and targets with the MARCH-INSIDE approach. Curr Top Med Chem 8:1676-90.

Issac, R. et al. (2001) The design of self-replicating helical peptides. Curr Opin Struct Biol 11:458-463.

Lee, D.H. (1997) Emergence of symbiosis in peptide self-replication through a hypercyclic network, Nature 390:591-594.

Lee, D.H. et al. (1996) A self-replicating peptide. Nature 382:525-528.

Maccari, G. et al. (2013) Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization. PLoS Comput Biol 9:e1003212. DOI: 10.1371/journal. pcbi.1003212.

Meyn, S.P. & Tweedie, R.L. (2005) Markov Chains and Stochastic Stability. 622pp University Press, Cambridge.

Orgel, L.E. (1992) Molecular replication. Nature 358:203-209.

Pauling, L. General Chemistry [Química General] 3rd edition W. H. Freeman & Company Publishers, pp. 227,621 (1955).

Polanco, C. et al. (2013) A toy model of prebiotic peptide evolution: the possible role of relative amino acid abundances. Acta Biochim Pol 60:175-182.

Polanco, C. et al. (2014) Computational model of abiogenic amino acid condensation to obtain a polar amino acid profile. Acta Biochim Pol 61:253-8.

Polanco, C. et al. (2013a) Detection of selective antibacterial peptides by the Polarity Profile method. Acta Biochim Pol 60:183-189.

Polanco, C. et al. (2014a) Discrete dynamic system oriented on the formation of prebiotic dipeptides from Rode's experiment. Acta Biochim Pol 61:717-726.

Polanco, C. et al. (2015) Identification of proteins associated with amyloidosis by polarity index method. Acta Biochim Pol 62:41-55.

Reinhoudt, D.N. et al. (1996) Kinetic analysis of the Rebek self-replicating system: is there a controversy? J Am Chem Soc 118:6880-6889.

Robertson, A. et al. (2000) Minimal self-replicating systems, Chem Soc Rev 29:141-152.

Severin, K. et al. (1998) Dynamic error correction in autocatalytic peptide networks, Angew. Chem Int Ed Engl 37:126-128.

Severin, K. et al. (1997) Peptide self-replication via template-directed ligation. Chem Eur J 3:1017-1024.

Zhou XX. et al. (2008) Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids 34:25-33.