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2014 | 61 | 4 | 717-726
Article title

Discrete dynamic system oriented on the formation of prebiotic dipeptides from Rode's experiment

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EN
Abstracts
EN
This work attempts to rationalize the possible prebiotic profile of the first dipeptides of about 4 billion years ago based on a computational discrete dynamic system that uses the final yields of the dipeptides obtained in Rode's experiments of salt-induced peptide formation (Rode et al., 1999, Peptides 20: 773-786). The system built a prebiotic scenario that allowed us to observe that (i) the primordial peptide generation was strongly affected by the abundances of the amino acid monomers, (ii) small variations in the concentration of the monomers have almost no effect on the final distribution pattern of the dipeptides and (iii) the most plausible chemical reaction of prebiotic peptide bond formation can be linked to Rode's hypothesis of a salt-induced scenario. The results of our computational simulations were related to former simulations of the Miller, and Fox & Harada experiments on amino acid monomer and oligomer generation, respectively, offering additional information to our approach.
Year
Volume
61
Issue
4
Pages
717-726
Physical description
Dates
published
2014
received
2013-11-08
revised
2014-07-12
accepted
2014-10-17
(unknown)
2014-12-16
References
  • Abelson PH (1956) Amino acids formed in primitive atmospheres. Science 124: 935.
  • Bahadur K, Ranganayaki S, Santamaria L (1958) Photosynthesis of amino-acids from paraformaldehyde involving the fixation of nitrogen in the presence of colloidal molybdenum oxide as catalyst. Nature 182: 1668.
  • Boschke FL (1972) Die Herkunft des Lebens, pp 187. Verlag GmbH, Dusseldorf un Wien.
  • Bujdák J, Faybíková K, Eder A, Yongyai Y, Rode BM (1995) Peptide chain elongation: a possible role of montmorillonite in prebiotic synthesis of protein precursors. Orig Life Evol Biosph 25: 431−441.
  • Cloud P (1973) Paleo ecological significance of Precambrian banded iron-formations. Econ Geol 68: 1135−1143.
  • Derossi D, Chassaing G, Prochiantz A (1998) Trojan peptides: the penetratin system for intracellular delivery. Trends Cell Biol 8: 84−87.
  • Delaye L, Becerra A, Lazcano A (2005) The last common ancestor: what's in a name? Orig Life Evol Biosph 35: 537-554.
  • Fine S, Singer Y, Tishby N (1998) The Hierarchical Hidden Markov Model: Analysis and Applications. Machine Learning 32: 41-62.
  • Fox SW, Harada K (1958) Thermal copolymerization of amino acids to a product resembling protein. Science 128: 1214.
  • Fox SW, Harada K (1960) The thermal copolymerization of amino acids common to protein. J Am Chem Soc 82: 3745-3751.
  • Fraser DG, Fitz D, Jakschitz T, Rode BM (2011) Selective adsorption and chiral amplification of amino acids in vermiculite clay-implications for the origin of biochirality. Phys Chem Chem Phys 13: 831-838.
  • Garrison WM, Morrison DC, Hamilton JG, Benson AA, Calvin M (1951) Reduction of carbon dioxide in aqueous solutions by ionizing radiation. Science 114: 416-418.
  • Gautam A, Singh H, Tyagi A, Chaudhary K, Kumar R, Kapoor P, Raghava GP (2012) CPPsite: a curated database of cell penetrating peptides. Database (Oxford) 2012: bas015.
  • Groth W, Weyssenhoff H (1957) Photochemische Bildung von Aminosäuren aus Mischungen einfacher Gase. Naturwissenschaften 44: 510-511.
  • Hanic F, Morvova M, (1998) Eleventh symposium on elementary processes and chemical reactions in low temperature plasma. Low Tatras, Slovakia.
  • Hulett HR, Bar-Nun A, Bar-Nun N, Bauer SH, Sagan C (1970) Amino acid synthesis in stimulated primitive environments. Science 170: 1000-1002.
  • Isaacson DL, Madsen WR (1976) Markov chains, theory and applications. pp 14-16, Wiley Series in Probability and Mathematical Statistics. Inc. USA.
  • Jakschitz TA, Rode BM. (2012) Chemical evolution from simple inorganic compounds to chiral peptides. Chem Soc Rev 41: 5484-5489.
  • Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30.
  • Kobayashi K, Tsuchiya M, Oshima T, Yanagawa H (1990) Abiotic synthesis of amino acids and imidazole by proton irradiation of simulated primitive earth atmospheres. Orig Life Evol Biosph 20: 99-109.
  • Lawless JG, Boynton CD (1973) Thermal synthesis of amino acids from a simulated primitive atmosphere. Nature 243: 405-407.
  • Miller SL (1953) A Production of amino acids under possible primitive earth conditions. Science 117: 528-529.
  • Ochiai EI (1978) The evolution of the environment and its influence on the evolution of life. Orig Life 9: 81-91.
  • Oro J (1980) Prebiological synthesis of the organic molecules and the origin of life. The Origins of Life and Evolution, pp 47-63. Alan R. Liss Inc., USA.
  • Palm C, Calvin M (1962) Primordial organic chemistry. I. Compounds resulting from electron irradiation of C14H4. J Am Chem Soc 84: 2115-2121.
  • Pavolvskaya TE, Pasynskii AL (1959) The origin of life on the earth (Proceedings of the first international symposium held at Moscow 19-24 August 1957). New York: Pergamon Press Inc. USA.
  • Plankensteiner K, Reiner H, Rode BM (2006) Amino acids on the rampant primordial Earth: electric discharges and the hot salty ocean. Mol Divers 10: 3-7.
  • Plankensteiner K, Reiner H, Rode BM (2005) Stereoselective differentiation in the Salt-induced Peptide Formation reaction and its relevance for the origin of life. Peptides 26: 535-541.
  • Plankensteiner K, Reiner H, Rode BM. (2004) From earth's primitive atmosphere to chiral peptides--the origin of precursors for life. Chem Biodivers 1: 1308-1315.
  • Polanco C, Samaniego JL (2009) Detection of selective cationic amphipatic antibacterial peptides by Hidden Markov models. Acta Biochim Pol 56: 167-176.
  • Polanco C, Samaniego JL, Buhse T, Mosqueira FG, Negron-Mendoza A, Ramos-Bernal S, Castanon-Gonzalez JA (2012) Characterization of selective antibacterial peptides by polarity index. Int J Pept 585027.
  • Polanco C, Buhse T, Samaniego JL, Castañón González JA (2013a) A toy model of prebiotic peptide evolution: the possible role of relative amino acid abundances. Acta Biochim Pol 60: 175-182.
  • Polanco C, Buhse T, Samaniego JL, Castañón-González JA (2013b) Detection of selective antibacterial peptides by the Polarity. Acta Biochim Pol 60: 183-189.
  • Polanco C, Buhse T, Samaniego JL, Castañón González JA, Estrada MA (2014) Computational model of abiogenic amino acid condensation to obtain a polar amino acid profile. Acta Biochim Pol 61: 253-258.
  • Polanco C, Castañón-González JA, Samaniego JL, Buhse T (2014) Letter to Editor. A Global Challenge. Sci. Transl. Med 6: DOI: 10.1126/scitranslmed.3009315.
  • Poole D (2011) Linear Algebra, A Modern Introduction. pp 461-490. Brooks & Cole, Cengage Learning Inc, UK.
  • Reiner H, Plankensteiner K, Fitz D, Rode BM (2006) The possible influence of L-histidine on the origin of the first peptides on the primordial Earth. Chem Biodivers 3: 611-621.
  • Rode BM (1999) Peptides and the origin of life. Peptides 20: 773-786.
  • Rode BM, Fitz D, Jakschitz T. (2007) The first steps of chemical evolution towards the origin of life. Chem Biodivers >12: 2674-2702.
  • Sagan C, Khare BN (1971) Long-wavelength ultraviolet photoproduction of amino acids on the primitive earth. Science 173: 417-420.
  • Saetia S, Liedl KR, Eder AH, Rode BM (1993) Evaporation cycle experiments - a simulation of salt-induced peptide synthesis under possible prebiotic conditions. Origins of Life Evol Biosph 23: 167-176.
  • Schwendinger MG, Rode BM (1989) Possible role of copper and sodium chloride in prebiotic evolution of peptides. Analyt Sci 5: 411-414.
  • Schwendinger MG, Rode BM (1992) Investigations on the mechanism of the salt-induced peptide formation. Orig Life Evol Biosph 22: 349-359.
  • Thakur N, Qureshi A, Kumar M (2012) AVPpred: collection and prediction of highly effective antiviral peptides. Nucleic Acids Res W199-W204.
  • Thom R (1975) Stabilité structurelle et morphogénèse: essai d'une théorie générale des modèles. pp 348-362. Addison-Wesley, Inc, USA.
  • Vogel G (1998) A sulfurous start for protein synthesis? Science 281: 627-629.
  • Wang G, Li X, Wang Z (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37: D933-D937.
  • Watson JD, Crick FHC (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171: 737-738.
  • Wolman Y, Haverland WJ, Miller SL. (1972) Nonprotein amino acids from spark discharges and their comparison with the murchison meteorite amino acids. Proc Natl Acad Sci USA 69: 809-811.
  • UniProt Consortium (2013) Update on activities at the Universal Protein Resource. Nucleic Acids Res 41: D43-D47.
  • Urey HC (1952) The Planets: Their Origin and Development. New Haven, CT: Yale Universtity Press.
  • Yanagawa H, Kobayashi Y, Egami F (1980) Genesis of amino acids in the primeval sea. Formation of amino acids from sugars and ammonia in a modified sea medium. J Biochem 87: 359-362.
  • Yoshino D, Hayatsu K, Anders E (1971) Origin of organic matter in early solar system - III. Amino acids: Catalytic synthesis. Geochimica et Cosmochimica. Acta Geochim Cosmochim Acta 35: 927-938.
Document Type
Publication order reference
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv61p717kz
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