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Lopez A, Vauchez A, Ajram G, Shvetsova A, Leveau G, Fiore M, Strazewski P. From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More. Life (Basel) 2024; 14:108. [PMID: 38255723 PMCID: PMC10817532 DOI: 10.3390/life14010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/25/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were likely all present on the early Earth and all necessary for the emergence of cellular life. In this study, we intended to explore conditions that were at the same time conducive to chemical reactions critical for the origins of life (peptide-oligonucleotide couplings and templated ligation of oligonucleotides) and compatible with the presence of prebiotic lipid vesicles. For that, random peptides were generated from activated amino acids and analysed using NMR and MS, whereas short oligonucleotides were produced through solid-support synthesis, manually deprotected and purified using HPLC. After chemical activation in prebiotic conditions, the resulting mixtures were analysed using LC-MS. Vesicles could be produced through gentle hydration in similar conditions and observed using epifluorescence microscopy. Despite the absence of coupling or ligation, our results help to pave the way for future investigations on the origins of life that may gather all three types of biomolecules rather than studying them separately, as it is still too often the case.
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Affiliation(s)
- Augustin Lopez
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Antoine Vauchez
- Centre Commun de la Spectrométrie de Masse (CCSM), ICBMS, Bâtiment Edgar Lederer, 1 rue Victor Grignard, 69100 Villeurbanne, France;
| | - Ghinwa Ajram
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Anastasiia Shvetsova
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Gabrielle Leveau
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Michele Fiore
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Peter Strazewski
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
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Dubrovskii VG, Sibirev NV, Eliseev IE, Vyazmin SY, Boitsov VM, Natochin YV, Dubina MV. Rate equation approach to understanding the ion-catalyzed formation of peptides. J Chem Phys 2013; 138:244906. [PMID: 23822273 DOI: 10.1063/1.4811280] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The salt-induced peptide formation is important for assessing and approaching schemes of molecular evolution. Here, we present experimental data and an exactly solvable kinetic model describing the linear polymerization of L-glutamic amino acid in water solutions with different concentrations of KCl and NaCl. The length distributions of peptides are well fitted by the model. Strikingly, we find that KCl considerably enhances the peptide yield, while NaCl does not show any catalytic effect in most cases under our experimental conditions. The greater catalytic effect of potassium ions is entirely interpreted by one and single parameter, the polymerization rate constant that depends on the concentration of a given salt in the reaction mixture. We deduce numeric estimates for the rate constant at different concentrations of the ions and show that it is always larger for KCl. This leads to an exponential increase of the potassium- to sodium-catalyzed peptide concentration ratio with length. Our results show that the ion-catalyzed peptides have a higher probability to emerge in excess potassium rather than in sodium-rich water solutions.
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Affiliation(s)
- V G Dubrovskii
- St. Petersburg Academic University, Nanotechnology Research and Education Centre RAS, 8∕3 Khlopina str., St. Petersburg 194021, Russia.
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Dubina MV, Vyazmin SY, Boitsov VM, Nikolaev EN, Popov IA, Kononikhin AS, Eliseev IE, Natochin YV. Potassium ions are more effective than sodium ions in salt induced peptide formation. ORIGINS LIFE EVOL B 2013; 43:109-17. [PMID: 23536046 PMCID: PMC3676736 DOI: 10.1007/s11084-013-9326-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 01/17/2013] [Indexed: 11/25/2022]
Abstract
Prebiotic peptide formation under aqueous conditions in the presence of metal ions is one of the plausible triggers of the emergence of life. The salt-induced peptide formation reaction has been suggested as being prebiotically relevant and was examined for the formation of peptides in NaCl solutions. In previous work we have argued that the first protocell could have emerged in KCl solution. Using HPLC-MS/MS analysis, we found that K+ is more than an order of magnitude more effective in the L-glutamic acid oligomerization with 1,1'-carbonyldiimidazole in aqueous solutions than the same concentration of Na+, which is consistent with the diffusion theory calculations. We anticipate that prebiotic peptides could have formed with K+ as the driving force, not Na+, as commonly believed.
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Affiliation(s)
- Michael V Dubina
- St Petersburg Academic University - Nanotechnology Research and Education Centre RAS, 8/3 Khlopin str, 194021, St Petersburg, Russia.
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4
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Primitive Membrane Formation, Characteristics and Roles in the Emergent Properties of a Protocell. ENTROPY 2011. [DOI: 10.3390/e13020466] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Illos RA, Bisogno FR, Clodic G, Bolbach G, Weissbuch I, Lahav M. Oligopeptides and Copeptides of Homochiral Sequence, via β-Sheets, from Mixtures of Racemic α-Amino Acids, in a One-Pot Reaction in Water; Relevance to Biochirogenesis. J Am Chem Soc 2008; 130:8651-9. [DOI: 10.1021/ja709969v] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roni A. Illos
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-Rehovot, Israel and Plate-Forme Spectrométrie de Masse et Protéomique, Université Pierre et Marie Curie, 75252 Paris Cedex 05, Paris France
| | - Fabricio R. Bisogno
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-Rehovot, Israel and Plate-Forme Spectrométrie de Masse et Protéomique, Université Pierre et Marie Curie, 75252 Paris Cedex 05, Paris France
| | - Gilles Clodic
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-Rehovot, Israel and Plate-Forme Spectrométrie de Masse et Protéomique, Université Pierre et Marie Curie, 75252 Paris Cedex 05, Paris France
| | - Gerard Bolbach
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-Rehovot, Israel and Plate-Forme Spectrométrie de Masse et Protéomique, Université Pierre et Marie Curie, 75252 Paris Cedex 05, Paris France
| | - Isabelle Weissbuch
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-Rehovot, Israel and Plate-Forme Spectrométrie de Masse et Protéomique, Université Pierre et Marie Curie, 75252 Paris Cedex 05, Paris France
| | - Meir Lahav
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-Rehovot, Israel and Plate-Forme Spectrométrie de Masse et Protéomique, Université Pierre et Marie Curie, 75252 Paris Cedex 05, Paris France
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6
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Lamy C, Lemoine J, Bouchu D, Goekjian P, Strazewski P. Glutamate–Glycine and Histidine–Glycine Co-oligopeptides: Batch Co-oligomerization versus Pulsed Addition ofN-Carboxyanhydrides. Chembiochem 2008; 9:710-3. [DOI: 10.1002/cbic.200700720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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7
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Kricheldorf HR. Polypeptides and 100 years of chemistry of alpha-amino acid N-carboxyanhydrides. Angew Chem Int Ed Engl 2006; 45:5752-84. [PMID: 16948174 DOI: 10.1002/anie.200600693] [Citation(s) in RCA: 458] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Syntheses and polymerizations of alpha-amino acid N-carboxyanhydrides (NCAs) were reported for the first time by Hermann Leuchs in 1906. Since that time, these cyclic and highly reactive amino acid derivatives were used for stepwise peptide syntheses but mainly for the formation of polypeptides by ring-opening polymerizations. This review summarizes the literature after 1985 and reports on new aspects of the polymerization processes, such as the formation of cyclic polypeptides or novel organometal catalysts. Polypeptides with various architectures, such as diblock, triblock, and multiblock sequences, and star-shaped or dendritic structures are also mentioned. Furthermore, lyotropic and thermotropic liquid-crystalline polypeptides will be discussed and the role of polypeptides as drugs or drug carriers are reviewed. Finally, the hypothetical role of NCAs in molecular evolution on the prebiotic Earth is discussed.
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Affiliation(s)
- Hans R Kricheldorf
- Institut für Technische und Makromolekulare Chemie, Universität Hamburg, Bundesstrasse 45, 20146 Hamburg, Germany.
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8
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Kricheldorf HR. Polypeptide und 100 Jahre Chemie der α-Aminosäure-N-carboxyanhydride. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600693] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Weber AL. Aqueous synthesis of peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole. ORIGINS LIFE EVOL B 2005; 35:421-7. [PMID: 16231206 DOI: 10.1007/s11084-005-4070-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Accepted: 09/05/2005] [Indexed: 11/28/2022]
Abstract
A new method was developed for the synthesis of peptide thioesters from free amino acids and thiols in water. This one-pot simple method involves two steps: (1) activation in water of an amino acid presumably as its N-carboxyanhydride (NCA) using 1,1'-carbonyldiimidazole (CDI), and (2) subsequent condensation of the activated amino acid-NCA in the presence of a thiol. With this method citrulline peptide thioesters containing up to 10 amino acid residues were prepared in a single reaction. This aqueous synthetic method provides a simple way to prepare peptide thioesters for studies of peptide replication involving ligation of peptide thioesters on peptide templates. The relevance of peptide replication to the origin-of-life process is supported by previous studies showing that amino acid thioesters (peptide thioester precursors) can be synthesized under prebiotic conditions by reaction of small sugars with ammonia and a thiol.
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Affiliation(s)
- Arthur L Weber
- SETI Institute, Mail Stop 239-4, NASA Ames Research Center, Moffett Field, CA, 94035-1000, U.S.A.
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10
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Wang KJ, Yao N, Li C. Sodium chloride enhanced oligomerization of L-glutamic acid in aqueous solution. ORIGINS LIFE EVOL B 2005; 35:313-22. [PMID: 16228645 DOI: 10.1007/s11084-005-2041-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Accepted: 05/25/2004] [Indexed: 10/25/2022]
Abstract
The presence of NaCl was found to significantly enhance the formation of longer peptides in N,N'-carbonyldiimidazole induced oligomerization of L-glutamic acid in homogeneous aqueous solution. The enhancement was detected in the presence of as low as 0.01-M NaCl and the highest yield of longer oligomers was achieved in the presence of 1-M NaCl. The possible prebiotic relevance is discussed.
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Affiliation(s)
- Kong-Jiang Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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11
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Abstract
NaCl significantly enhanced the longer oligoarginine formation in the oligomerization of L-arginine activated by N,N'-carbonyldiimidazole (CDI) in homogeneous aqueous solution. The optimal concentration of NaCl for the highest yield of longer oligoarginine formation is around 1M. It is suggested that the weak interactions of Cl(-) with the positive-charged guanidinium group of the oligoarginines formed in the oligomerization of L-arginine are responsible for the enhancement by NaCl.
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Affiliation(s)
- Liang Xin
- Institute of Biophysics, Chinese Academy of Sciences, Beijing
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12
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Plasson R, Biron JP, Cottet H, Commeyras A, Taillades J. Kinetic study of the polymerization of alpha-amino acid N-carboxyanhydrides in aqueous solution using capillary electrophoresis. J Chromatogr A 2002; 952:239-48. [PMID: 12064535 DOI: 10.1016/s0021-9673(02)00018-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
N-Carboxyanhydrides of amino acids (NCAs) are very reactive monomers able to polymerize into oligopeptides. They are assumed to be prebiotic precursors of the first polypeptides. Few reports have been published on the study of NCA polymerization in aqueous solution. In this work, a kinetic study focused on the hydrolysis of NCA and its coupling with amino acids and homopeptides (up to tripeptide) was carried out, taking L-valine derivatives as model compounds. For that purpose, capillary electrophoresis appeared to be an effective and reliable technique for the measurement of the kinetic constants. The electrophoretic separation conditions, the procedure for stopping NCA reactivity, as well as the conditions of reaction are discussed in detail. We report the variation of the kinetic constant of the coupling reaction of the NCA of valine with an oligovaline as a function of its degree of polymerization. Finally, a temperature study also allowed us to estimate the activation energies associated with the NCA of valine hydrolysis and its coupling reaction with valine.
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Affiliation(s)
- R Plasson
- Laboratoire Organisation Moléculaire, Evolution et Matériaux Fluorés, UMR 5073, Université Montpellier II, France
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Ueki M, Watanabe S, Ishii Y, Okunaka O, Uchino K, Saitoh T, Higashi K, Nakashima H, Yamamoto N, Ogawara H. Synthesis and anti-HIV activity of nonatyrosine N- and O1-9-decasulfate. Bioorg Med Chem 2001; 9:477-86. [PMID: 11249139 DOI: 10.1016/s0968-0896(00)00269-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To develop a potent and effective anti-HIV compound with a definite polyanionic structure, synthesis of oligotyrosine sulfates by oligomerization with simultaneous sulfation of tyrosine was tried. One component was successfully isolated from the mixture containing many products as its sodium salt (Y-ART-4) and was identified as the salt of nonatyrosine N- and O1-9-decasulfate, NaO3S-[Tyr(SO3Na)]9-ONa. Anti-HIV activity of Y-ART-4, determined from the protection it provided against HIV-induced cytopathic effects, was almost the same with that of dextran sulfate and curdlan sulfate.
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Affiliation(s)
- M Ueki
- Department of Applied Chemistry, Science University of Tokyo, Japan.
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14
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Abstract
Monomeric cysteine residues attached to cysteine-containing peptides by disulfide bonds can be activated by carbonyldiimidazole. If two monomeric cysteine residues, attached to a 'scaffold' peptide Gly-Cys-Glyn-Cys-Glu10, (n = 0, 1, 2, 3) are activated, they react to form the dipeptide Cys-Cys. in 25-65% yield. Similarly, the activation of a cysteine residue attached to the 'scaffold' peptide Gly-Cys-Gly-Glu10 in the presence of Arg5 leads to the formation of Cys-Arg5 in 50% yield. The significance of these results for prebiotic chemistry is discussed.
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Affiliation(s)
- B C Chu
- Salk Institute for Biological Studies, San Diego, CA 92186-5800, USA
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15
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Abstract
Unlike glutamic acid, L-gamma-carboxyglutamic acid does not oligomerize efficiently when treated with carbonyldiimidazole in aqueous solution. However, divalent ions such as Mg2+ catalyze the reaction, and lead to the formation of oligomers in good yield. In the presence of hydroxylapatite, L-gamma-carboxyglutamic acid oligomerizes efficiently in a reaction that proceeds in the absence of divalent ions but is further catalyzed when they are present. After 'feeding' 50 times with activated amino acid in the presence of the Mg2+ ion, oligomers longer than the 20-mer could be detected. The effect of hydroxylapatite on peptide elongation is very sensitive to the nature of the activated amino acid and the acceptor peptide. Glutamic acid oligomerizes more efficiently than L-gamma-carboxyglutamic acid on hydroxylapatite and adds more efficiently to decaglutamic acid in solution. One might, therefore, expect that glutamic acid would add more efficiently than L-gamma-carboxyglutamic acid to decaglutamic acid on hydroxylapatite. The contrary is true--the addition of L-gamma-carboxyglutamic acid is substantially more efficient. This suggests that oligomerization on the surface of hydroxylapatite depends on the detailed match between the structure of the surface of the mineral and the structure of the oligomer.
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Affiliation(s)
- A R Hill
- Salk Institute for Biological Studies, San Diego, CA 92186-5800, USA
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Hill AR, Böhler C, Orgel LE. Polymerization on the rocks: negatively-charged alpha-amino acids. ORIGINS LIFE EVOL B 1998; 28:235-43. [PMID: 9611764 DOI: 10.1023/a:1006572112311] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oligomers of the negatively-charged amino acids, glutamic acid, aspartic acid, and O-phospho-L-serine are adsorbed by hydroxylapatite and illite with affinities that increase with oligomer length. In the case of oligo-glutamic acids adsorbed on hydroxylapatite, addition of an extra residue results in an approximately four-fold increase in the strength of adsorption. Oligomers much longer than the 7-mer are retained tenaciously by the mineral. Repeated incubation of short oligo-glutamic acids adsorbed on hydroxylapatite or illite with activated monomer leads to the accumulation of oligomers at least 45 units long. The corresponding reactions of aspartic acid and O-phospho-L-serine on hydroxylapatite are less effective in generating long oligomers, while illite fails to accumulate substantial amounts of long oligomers of aspartic acid or of O-phospho-L-serine.
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Affiliation(s)
- A R Hill
- Salk Institute for Biological Studies, San Diego, CA 92186-5800, USA
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Abstract
We have compared carbonyl diimidazole (CDI) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as activating agents for the oligomerization of negatively-charged alpha- and beta-amino acids in homogeneous aqueous solution. alpha-Amino acids can be oligomerized efficiently using CDI, but not by EDAC. beta-Amino acids can be oligomerized efficiently using EDAC, but not by CDI. Aspartic acid, an alpha- and beta-dicarboxylic acid is oligomerized efficiently by both reagents. These results are explained in terms of the mechanisms of the reactions, and their relevance to prebiotic chemistry is discussed.
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Affiliation(s)
- R Liu
- The Salk Institute for Biological Studies, San Diego, CA 92186-5800, USA
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