451
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Singh N, Kumar M, Miravet JF, Ulijn RV, Escuder B. Peptide-Based Molecular Hydrogels as Supramolecular Protein Mimics. Chemistry 2016; 23:981-993. [PMID: 27530095 DOI: 10.1002/chem.201602624] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Indexed: 12/14/2022]
Abstract
This Minireview concerns recent advances in the design, synthesis, and application of low molecular-weight peptidic hydrogelators. The sequence-specific combinations of amino acid side chain functionalities combined with hydrogen bonding of amide backbones and hydrophobic (aromatic) capping groups give these peptidic molecules the intrinsic tendency to self-assemble. The most prevalent designs include N-capped amino acid residues, bolamphiphilic peptides, and amphipathic peptides. Factors such as hydrophobic effects, the Hofmeister effect, and tunable ionization influence their aggregation properties. The self-assembly of simple bio-inspired building blocks into higher organized structures allows comparisons to be drawn with proteins and their complex functionalities, providing preliminary insights into complex biological functions and also enabling their application in a wide range of fields including catalysis, biomedical applications, and mimicry of natural dissipative systems. The Minireview is concluded by a short summary and outlook, highlighting the advances and steps required to bridge the gaps in the understanding of such systems.
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Affiliation(s)
- Nishant Singh
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Av. Sos Baynat, s/n, 12071, Castelló, Spain
| | - Mohit Kumar
- Advanced Science Research Centre (ASRC), City University of New York, 85 St Nicholas Terrace, New York, NY, 10031, USA
| | - Juan F Miravet
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Av. Sos Baynat, s/n, 12071, Castelló, Spain
| | - Rein V Ulijn
- Advanced Science Research Centre (ASRC), City University of New York, 85 St Nicholas Terrace, New York, NY, 10031, USA.,WestCHEM/Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.,Department of Chemistry and Biochemistry, City University of New York-Hunter College, 695 Park Ave., New York, NY, 10065, USA.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Beatriu Escuder
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Av. Sos Baynat, s/n, 12071, Castelló, Spain
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452
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Black RA, Blosser MC. A Self-Assembled Aggregate Composed of a Fatty Acid Membrane and the Building Blocks of Biological Polymers Provides a First Step in the Emergence of Protocells. Life (Basel) 2016; 6:E33. [PMID: 27529283 PMCID: PMC5041009 DOI: 10.3390/life6030033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/02/2016] [Accepted: 08/09/2016] [Indexed: 02/01/2023] Open
Abstract
We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then explain how the conformational constraints and altered chemical environment due to binding of the components to the membrane could facilitate the formation of nucleosides, oligonucleotides and peptides. We conclude by discussing how the resulting oligomers, even if short and random, could have increased vesicle stability and growth more than their building blocks did, and how competition among these vesicles could have led to longer polymers with complex functions.
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Affiliation(s)
- Roy A Black
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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453
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Aiba S, Takamatsu N, Sasai T, Tokunaga Y, Kawasaki T. Replication of α-amino acids via Strecker synthesis with amplification and multiplication of chiral intermediate aminonitriles. Chem Commun (Camb) 2016; 52:10834-7. [PMID: 27492553 DOI: 10.1039/c6cc05544c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Replication of chiral l- and d-α-(p-tolyl)glycine has been achieved in combination with the asymmetric induction, amplification and multiplication of their own chiral intermediates, l- and d-aminonitriles, in the solid-phase via the Strecker reaction between three achiral components, which is a plausible prebiotic mechanism for amino acid synthesis.
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Affiliation(s)
- Shohei Aiba
- Department of Materials Science and Engineering, University of Fukui, Bunkyo, Fukui 910-8507, Japan.
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454
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Mirzaei M, Gülseren O, Hadipour N. DFT explorations of quadrupole coupling constants for planar 5-fluorouracil pairs. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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455
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Lavado N, Escamilla JC, Ávalos M, Babiano R, Cintas P, Jiménez JL, Palacios JC. Prebiotic-Like Condensations of Cyanamide and Glyoxal: Revisiting Intractable Biotars. Chemistry 2016; 22:13632-42. [PMID: 27455123 DOI: 10.1002/chem.201601999] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 11/10/2022]
Abstract
We report a detailed investigation into the nature of products that are generated by the reactions of cyanamide and glyoxal, two small molecules of astrochemical and prebiotic significance, under different experimental conditions. The experimental data suggest that the formation of oligomeric structures is related in part to the formation of insoluble tholins in the presence of oxygen-containing molecules. Although oligomerization proceeds well in water, product isolation turned out to be impractical. Instead, solid precipitates were obtained easily in acetone. Crude mixtures have been thoroughly scrutinized by spectroscopic methods, in particular NMR and mass spectroscopy (ESI mode), which are all consistent with the generation of a few functional groups that are embedded into regular chains of five- and six-membered rings, thereby pointing to a supramolecular organization. Three different models of cross-condensation and chain growth are suggested. These synthetic explorations provide further insights into the formation of complex organic matter in interstellar scenarios and extraterrestrial bodies that might have played a pivotal role in chemical evolution.
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Affiliation(s)
- Nieves Lavado
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, IACYS-Unidad de Química Verde y Desarrollo Sostenible, 06006, Badajoz, Spain.
| | - Juan Carlos Escamilla
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, IACYS-Unidad de Química Verde y Desarrollo Sostenible, 06006, Badajoz, Spain
| | - Martín Ávalos
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, IACYS-Unidad de Química Verde y Desarrollo Sostenible, 06006, Badajoz, Spain
| | - Reyes Babiano
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, IACYS-Unidad de Química Verde y Desarrollo Sostenible, 06006, Badajoz, Spain.
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, IACYS-Unidad de Química Verde y Desarrollo Sostenible, 06006, Badajoz, Spain
| | - José Luis Jiménez
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, IACYS-Unidad de Química Verde y Desarrollo Sostenible, 06006, Badajoz, Spain
| | - Juan Carlos Palacios
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, IACYS-Unidad de Química Verde y Desarrollo Sostenible, 06006, Badajoz, Spain
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456
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Ichihashi N, Yomo T. Constructive Approaches for Understanding the Origin of Self-Replication and Evolution. Life (Basel) 2016; 6:life6030026. [PMID: 27420098 PMCID: PMC5041002 DOI: 10.3390/life6030026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022] Open
Abstract
The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules. Using this approach, we are able to employ design principles to reproduce life-specific functions, and the knowledge gained through the reproduction process provides clues as to their origins. In this mini-review, we introduce recent insights gained using this approach, and propose important future directions for advancing our understanding of the origins of life.
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Affiliation(s)
- Norikazu Ichihashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Tetsuya Yomo
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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457
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Kamimura A, Kaneko K. Negative scaling relationship between molecular diversity and resource abundances. Phys Rev E 2016; 93:062419. [PMID: 27415310 DOI: 10.1103/physreve.93.062419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 11/07/2022]
Abstract
Cell reproduction involves replication of diverse molecule species, in contrast to a simple replication system with fewer components. To address this question of diversity, we study theoretically a cell system with catalytic reaction dynamics that grows by uptake of environmental resources. It is shown that limited resources lead to increased diversity of components within the system, and the number of coexisting species increases with a negative power of the resource uptake. The relationship is explained from the optimum growth speed of the cell, determined by a tradeoff between the utility of diverse resources and the concentration onto fewer components to increase the reaction rate.
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Affiliation(s)
- Atsushi Kamimura
- Department of Basic Science, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiko Kaneko
- Department of Basic Science, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
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458
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459
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Schaufelberger F, Ramström O. Kinetic Self-Sorting of Dynamic Covalent Catalysts with Systemic Feedback Regulation. J Am Chem Soc 2016; 138:7836-9. [DOI: 10.1021/jacs.6b04250] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH−Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm, Sweden
| | - Olof Ramström
- Department of Chemistry, KTH−Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm, Sweden
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460
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Wollrab E, Scherer S, Aubriet F, Carré V, Carlomagno T, Codutti L, Ott A. Chemical Analysis of a "Miller-Type" Complex Prebiotic Broth: Part I: Chemical Diversity, Oxygen and Nitrogen Based Polymers. ORIGINS LIFE EVOL B 2016; 46:149-69. [PMID: 26508401 DOI: 10.1007/s11084-015-9468-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/27/2015] [Indexed: 10/22/2022]
Abstract
In a famous experiment Stanley Miller showed that a large number of organic substances can emerge from sparking a mixture of methane, ammonia and hydrogen in the presence of water (Miller, Science 117:528-529, 1953). Among these substances Miller identified different amino acids, and he concluded that prebiotic events may well have produced many of Life's molecular building blocks. There have been many variants of the original experiment since, including different gas mixtures (Miller, J Am Chem Soc 77:2351-2361, 1955; Oró Nature 197:862-867, 1963; Schlesinger and Miller, J Mol Evol 19:376-382, 1983; Miyakawa et al., Proc Natl Acad Sci 99:14,628-14,631, 2002). Recently some of Miller's remaining original samples were analyzed with modern equipment (Johnson et al. Science 322:404-404, 2008; Parker et al. Proc Natl Acad Sci 108:5526-5531, 2011) and a total of 23 racemic amino acids were identified. To give an overview of the chemical variety of a possible prebiotic broth, here we analyze a "Miller type" experiment using state of the art mass spectrometry and NMR spectroscopy. We identify substances of a wide range of saturation, which can be hydrophilic, hydrophobic or amphiphilic in nature. Often the molecules contain heteroatoms, with amines and amides being prominent classes of molecule. In some samples we detect ethylene glycol based polymers. Their formation in water requires the presence of a catalyst. Contrary to expectations, we cannot identify any preferred reaction product. The capacity to spontaneously produce this extremely high degree of molecular variety in a very simple experiment is a remarkable feature of organic chemistry and possibly prerequisite for Life to emerge. It remains a future task to uncover how dedicated, organized chemical reaction pathways may have arisen from this degree of complexity.
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Affiliation(s)
- Eva Wollrab
- Biologische Experimentalphysik, Universität des Saarlandes, Campus, Geb. B2 1, 66123, Saarbrücken, Germany.
- Laboratory of Microbial Morphogenesis and Growth, Institut Pasteur, 75724, Paris Cedex 15, France.
| | - Sabrina Scherer
- Biologische Experimentalphysik, Universität des Saarlandes, Campus, Geb. B2 1, 66123, Saarbrücken, Germany
| | - Frédéric Aubriet
- Laboratoire de Chimie et Physique Multi-échelle des Milieux Complexes (LCP-A2MC), Université de Lorraine, 1 Boulevard Arago, 57078, Metz, France
| | - Vincent Carré
- Laboratoire de Chimie et Physique Multi-échelle des Milieux Complexes (LCP-A2MC), Université de Lorraine, 1 Boulevard Arago, 57078, Metz, France
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
- Helmoltz Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124, Braunschweig, Germany
- Centre of Biomolecular Drug Research, Leibniz University, Schneiderberg 38, 30167, Hannover, Germany
| | - Luca Codutti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
- Centre of Biomolecular Drug Research, Leibniz University, Schneiderberg 38, 30167, Hannover, Germany
| | - Albrecht Ott
- Biologische Experimentalphysik, Universität des Saarlandes, Campus, Geb. B2 1, 66123, Saarbrücken, Germany.
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461
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Adam ZR. Temperature oscillations near natural nuclear reactor cores and the potential for prebiotic oligomer synthesis. ORIGINS LIFE EVOL B 2016; 46:171-87. [PMID: 26680444 DOI: 10.1007/s11084-015-9478-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/04/2015] [Indexed: 12/01/2022]
Abstract
Geologic settings capable of driving prebiotic oligomer synthesis reactions remain a relatively unexplored aspect of origins of life research. Natural nuclear reactors are an example of Precambrian energy sources that produced unique temperature fluctuations. Heat transfer models indicate that water-moderated, convectively-cooled natural fission reactors in porous host rocks create temperature oscillations that resemble those employed in polymerase chain reaction (PCR) devices to artificially amplify oligonucleotides. This temperature profile is characterized by short-duration pulses up to 70-100 °C, followed by a sustained period of temperatures in the range of 30-70 °C, and finally a period of relaxation to ambient temperatures until the cycle is restarted by a fresh influx of pore water. For a given reactor configuration, temperature maxima and the time required to relax to ambient temperatures depend most strongly on the aggregate effect of host rock permeability in decreasing the thermal expansion and increasing the viscosity and evaporation temperature of the pore fluids. Once formed, fission-fueled reactors can sustain multi-kilowatt-level power production for 10(5)-10(6) years, ensuring microenvironmental longevity and chemical output. The model outputs indicate that organic synthesis on young planetary bodies with a sizeable reservoir of fissile material can involve more sophisticated energy dissipation pathways than modern terrestrial analog settings alone would suggest.
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Affiliation(s)
- Zachary R Adam
- Department of Earth and Planetary Sciences, Harvard University, 26 Oxford Street, Room 51, Cambridge, MA, 02138, USA.
- Blue Marble Space Institute of Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA.
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462
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Ikegami T, Kageyama Y, Obara K, Takeda S. Dissipative and Autonomous Square-Wave Self-Oscillation of a Macroscopic Hybrid Self-Assembly under Continuous Light Irradiation. Angew Chem Int Ed Engl 2016; 55:8239-43. [DOI: 10.1002/anie.201600218] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/09/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Tomonori Ikegami
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; Sapporo 060-0810 Japan
| | - Yoshiyuki Kageyama
- Department of Chemistry; Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
- JST PRESTO; Kawaguchi 332-0012 Japan
| | - Kazuma Obara
- Department of Chemistry; Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Sadamu Takeda
- Department of Chemistry; Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
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463
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Ikegami T, Kageyama Y, Obara K, Takeda S. Dissipative and Autonomous Square-Wave Self-Oscillation of a Macroscopic Hybrid Self-Assembly under Continuous Light Irradiation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tomonori Ikegami
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; Sapporo 060-0810 Japan
| | - Yoshiyuki Kageyama
- Department of Chemistry; Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
- JST PRESTO; Kawaguchi 332-0012 Japan
| | - Kazuma Obara
- Department of Chemistry; Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Sadamu Takeda
- Department of Chemistry; Faculty of Science; Hokkaido University; Sapporo 060-0810 Japan
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464
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Saladino R, Botta G, Bizzarri B, Di Mauro E, Garcia
Ruiz JM. A Global Scale Scenario for Prebiotic Chemistry: Silica-Based Self-Assembled Mineral Structures and Formamide. Biochemistry 2016; 55:2806-11. [PMID: 27115539 PMCID: PMC4872262 DOI: 10.1021/acs.biochem.6b00255] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/26/2016] [Indexed: 11/30/2022]
Abstract
The pathway from simple abiotically made organic compounds to the molecular bricks of life, as we know it, is unknown. The most efficient geological abiotic route to organic compounds results from the aqueous dissolution of olivine, a reaction known as serpentinization (Sleep, N.H., et al. (2004) Proc. Natl. Acad. Sci. USA 101, 12818-12822). In addition to molecular hydrogen and a reducing environment, serpentinization reactions lead to high-pH alkaline brines that can become easily enriched in silica. Under these chemical conditions, the formation of self-assembled nanocrystalline mineral composites, namely silica/carbonate biomorphs and metal silicate hydrate (MSH) tubular membranes (silica gardens), is unavoidable (Kellermeier, M., et al. In Methods in Enzymology, Research Methods in Biomineralization Science (De Yoreo, J., Ed.) Vol. 532, pp 225-256, Academic Press, Burlington, MA). The osmotically driven membranous structures have remarkable catalytic properties that could be operating in the reducing organic-rich chemical pot in which they form. Among one-carbon compounds, formamide (NH2CHO) has been shown to trigger the formation of complex prebiotic molecules under mineral-driven catalytic conditions (Saladino, R., et al. (2001) Biorganic & Medicinal Chemistry, 9, 1249-1253), proton irradiation (Saladino, R., et al. (2015) Proc. Natl. Acad. Sci. USA, 112, 2746-2755), and laser-induced dielectric breakdown (Ferus, M., et al. (2015) Proc Natl Acad Sci USA, 112, 657-662). Here, we show that MSH membranes are catalysts for the condensation of NH2CHO, yielding prebiotically relevant compounds, including carboxylic acids, amino acids, and nucleobases. Membranes formed by the reaction of alkaline (pH 12) sodium silicate solutions with MgSO4 and Fe2(SO4)3·9H2O show the highest efficiency, while reactions with CuCl2·2H2O, ZnCl2, FeCl2·4H2O, and MnCl2·4H2O showed lower reactivities. The collections of compounds forming inside and outside the tubular membrane are clearly specific, demonstrating that the mineral self-assembled membranes at the same time create space compartmentalization and selective catalysis of the synthesis of relevant compounds. Rather than requiring odd local conditions, the prebiotic organic chemistry scenario for the origin of life appears to be common at a universal scale and, most probably, earlier than ever thought for our planet.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento
di Scienze Ecologiche e Biologiche, Università
della Tuscia, Via San
Camillo De Lellis, 01100 Viterbo, Italy
| | - Giorgia Botta
- Dipartimento
di Scienze Ecologiche e Biologiche, Università
della Tuscia, Via San
Camillo De Lellis, 01100 Viterbo, Italy
| | - Bruno
Mattia Bizzarri
- Dipartimento
di Scienze Ecologiche e Biologiche, Università
della Tuscia, Via San
Camillo De Lellis, 01100 Viterbo, Italy
| | - Ernesto Di Mauro
- Istituto
Pasteur-Fondazione Cenci Bolognetti c/o Dipartimento di Biologia e
Biotecnologie “Charles Darwin”, University “Sapienza”, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Juan Manuel Garcia
Ruiz
- Laboratorio
de Estudios Crystalográficos, Instituto Andauz de Ciencias
de la Tierra, CSIC-Universidad de Granada, Avenida de las Palmeras 4, E-18100 Armilla, Granada, Spain
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465
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Noble-Terán ME, Buhse T, Cruz JM, Coudret C, Micheau JC. Nonlinear Effects in Asymmetric Synthesis: A Practical Tool for the Discrimination between Monomer and Dimer Catalysis. ChemCatChem 2016. [DOI: 10.1002/cctc.201600216] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- María E. Noble-Terán
- Centro de Investigaciones Químicas; Universidad Autónoma del Estado de Morelos; Avenida Universidad 1001 62209 Cuernavaca, Morelos Mexico
| | - Thomas Buhse
- Centro de Investigaciones Químicas; Universidad Autónoma del Estado de Morelos; Avenida Universidad 1001 62209 Cuernavaca, Morelos Mexico
| | - José-Manuel Cruz
- Centro de Investigaciones Químicas; Universidad Autónoma del Estado de Morelos; Avenida Universidad 1001 62209 Cuernavaca, Morelos Mexico
- Institute of Chemistry of Sao Carlos; University of Sao Paulo, CP 780, CEP; 13560-970 Sao Carlos, Sao Paulo Brazil
| | - Christophe Coudret
- Laboratoire des IMRCP, UMR au CNRS No. 5623; Université Paul Sabatier; 118, Route de Narbonne 31062 Toulouse Cedex France
| | - Jean-Claude Micheau
- Laboratoire des IMRCP, UMR au CNRS No. 5623; Université Paul Sabatier; 118, Route de Narbonne 31062 Toulouse Cedex France
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466
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Calvo F, Bacchus-Montabonel MC, Clavaguéra C. Stepwise Hydration of 2-Aminooxazole: Theoretical Insight into the Structure, Finite Temperature Behavior and Proton-Induced Charge Transfer. J Phys Chem A 2016; 120:2380-9. [PMID: 27035034 DOI: 10.1021/acs.jpca.5b12392] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It was recently suggested that 2-aminooxazole (AO) could contribute to the formation of RNA nucleotides on primitive earth. In this article we have considered by means of computational modeling the influence of microhydration on the structural and spectral properties of this potential prebiotic molecule. The stable structures of AO(H2O)n were obtained first by sampling the potential energy landscapes of clusters containing up to n = 20 water molecules, using a simple but reasonably accurate force field and replica-exchange molecular dynamics simulations. Through reoptimization using an explicit description of electronic structure at the level of density functional theory with the M06-2X functional, the formation energies, ionization energies and electron affinities were determined in the vertical and adiabatic treatments, as well as vibrational and optical spectra covering the far-IR, mid-IR, and lower part of the UV ranges. The results generally show a clear segregation between the aminooxazole solute and the water molecules, a water cluster being formed near the nitrogen and amino group side leaving the hydrocarbon side dry even at temperatures corresponding to the liquid state. The spectral signatures generally concur and show distinct contributions of the solute and solvent, spectral shifts to lower energies being in agreement with earlier calculations in bulk solvent. We have also investigated the importance of microhydration on the charge transfer cross section upon collision with a proton, thereby extending an earlier investigation on the bare AO molecule. The presence of water molecules generally reduces the propensity for charge transfer at small sizes, but the influence of the solvent steadily decreases in larger droplets.
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Affiliation(s)
- F Calvo
- LiPhy, Université Grenoble Alpes and CNRS UMR 5588 , 140 Avenue de la Physique, 38402 St Martin d'Hères, France
| | - M-C Bacchus-Montabonel
- ILM, Université Lyon I and CNRS UMR 5306, Université de Lyon , 43 Bd du 11 Novembre 1918, F69622 Villeurbanne Cedex, France
| | - C Clavaguéra
- LCM, CNRS, Ecole Polytechnique, Université Paris Saclay , 91128 Palaiseau, France
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467
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Tena-Solsona M, Nanda J, Díaz-Oltra S, Chotera A, Ashkenasy G, Escuder B. Emergent Catalytic Behavior of Self-Assembled Low Molecular Weight Peptide-Based Aggregates and Hydrogels. Chemistry 2016; 22:6687-94. [PMID: 27004623 DOI: 10.1002/chem.201600344] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 01/19/2023]
Abstract
We report a series of short peptides possessing the sequence (FE)n or (EF)n and bearing l-proline at their N-terminus that self-assemble into high aspect ratio aggregates and hydrogels. We show that these aggregates are able to catalyze the aldol reaction, whereas non-aggregated analogues are catalytically inactive. We have undertaken an analysis of the results, considering the accessibility of catalytic sites, pKa value shifts, and the presence of hydrophobic pockets. We conclude that the presence of hydrophobic regions is indeed relevant for substrate solubilization, but that the active site accessibility is the key factor for the observed differences in reaction rates. The results presented here provide an example of the emergence of a new chemical property caused by self-assembly, and support the relevant role played by self-assembled peptides in prebiotic scenarios. In this sense, the reported systems can be seen as primitive aldolase I mimics, and have been successfully tested for the synthesis of simple carbohydrate precursors.
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Affiliation(s)
- Marta Tena-Solsona
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Jayanta Nanda
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Santiago Díaz-Oltra
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Agata Chotera
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Beatriu Escuder
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain.
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468
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Adamala KP, Engelhart AE, Szostak JW. Collaboration between primitive cell membranes and soluble catalysts. Nat Commun 2016; 7:11041. [PMID: 26996603 PMCID: PMC4802160 DOI: 10.1038/ncomms11041] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/15/2016] [Indexed: 12/23/2022] Open
Abstract
One widely held model of early life suggests primitive cells consisted of simple RNA-based catalysts within lipid compartments. One possible selective advantage conferred by an encapsulated catalyst is stabilization of the compartment, resulting from catalyst-promoted synthesis of key membrane components. Here we show model protocell vesicles containing an encapsulated enzyme that promotes the synthesis of simple fatty acid derivatives become stabilized to Mg2+, which is required for ribozyme activity and RNA synthesis. Thus, protocells capable of such catalytic transformations would have enjoyed a selective advantage over other protocells in high Mg2+ environments. The synthetic transformation requires both the catalyst and vesicles that solubilize the water-insoluble precursor lipid. We suggest that similar modified lipids could have played a key role in early life, and that primitive lipid membranes and encapsulated catalysts, such as ribozymes, may have acted in conjunction with each other, enabling otherwise-impossible chemical transformations within primordial cells. Early cells likely consisted of fatty acid vesicles enclosing magnesium-dependent ribozymes. Here, the authors show that fatty acid derivatives can form vesicles that, unlike those formed from only unmodified fatty acids, are stable in the presence of magnesium and could support ribozyme catalysis.
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Affiliation(s)
- Katarzyna P Adamala
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | - Aaron E Engelhart
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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469
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Lavado N, Ávalos M, Babiano R, Cintas P, Light ME, Jiménez JL, Palacios JC. On the Plausibility of Pseudosugar Formation in Cometary Ices and Oxygen-rich Tholins. ORIGINS LIFE EVOL B 2016; 46:31-49. [PMID: 26428515 DOI: 10.1007/s11084-015-9456-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
Abstract
We revisit herein the formation and structure of dihydroxy dioxanes, which can be obtained from prebiotically available precursors and can be regarded as primeval sugar surrogates. Previous studies dealing with the heterogeneous composition of interstellar bodies point to the existence of significant amounts of small polyalcohols along with oxygen-containing oligomers. Even though such derivatives did not give rise to nucleosides and oligonucleotides, nor they were incorporated into subsequent metabolic routes, molecular chimeras based on sugar-like species could be opportunistic scaffolds in pre-evolutionary scenarios. We could figure out that pseudosugars, assembled by hemiacetalic bonds from available precursors in both interstellar and terrestrial scenarios, were presumably more abundant than thought. Moreover, these species share some key features with naturally-occurring sugar rings, such as anomeric preferences, coordinating ability, and the prevalent occurrence of racemic compounds.
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Affiliation(s)
- Nieves Lavado
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain.
| | - Martín Ávalos
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain
| | - Reyes Babiano
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain.
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain
| | - Mark E Light
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - José Luis Jiménez
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain
| | - Juan C Palacios
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain
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470
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Xie L, Huang F, Sun C, Liu J, Chen D. Mechanistic insight into the prebiotic syntheses of pyrimidine ribonucleotide and pyrimidine deoxynucleotide precursors. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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471
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Ball R, Brindley J. The Life Story of Hydrogen Peroxide III: Chirality and Physical Effects at the Dawn of Life. ORIGINS LIFE EVOL B 2016; 46:81-93. [PMID: 26399407 DOI: 10.1007/s11084-015-9465-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022]
Abstract
It is a remarkable observed fact that all life on Earth is homochiral, its biology using exclusively the D-enantiomer of ribose, the sugar moiety of the ribonucleic acids, and the L-enantiomers of the chiral amino acids. Motivated by concurrent work that elaborates further the role of hydrogen peroxide in providing an oscillatory drive for the RNA world (Ball & Brindley 2015a, J. R. Soc. Interface 12, 20150366, and Ball & Brindley 2015b, this journal, in press), we reappraise the structure and physical properties of this small molecule within this context. Hydrogen peroxide is the smallest, simplest molecule to exist as a pair of non-superimposable mirror images, or enantiomers, a fact which leads us to develop the hypothesis that its enantiospecific interactions with ribonucleic acids led to enantioselective outcomes. We propose a mechanism by which these chiral interactions may have led to amplification of D-ribonucleic acids and extinction of L-ribonucleic acids.
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Affiliation(s)
- Rowena Ball
- Mathematical Sciences Institute and Research School of Chemistry, The Australian National University, Canberra, 2602, Australia.
| | - John Brindley
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
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472
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Yin Y, Niu L, Zhu X, Zhao M, Zhang Z, Mann S, Liang D. Non-equilibrium behaviour in coacervate-based protocells under electric-field-induced excitation. Nat Commun 2016; 7:10658. [PMID: 26876162 PMCID: PMC4756681 DOI: 10.1038/ncomms10658] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/11/2016] [Indexed: 12/17/2022] Open
Abstract
Although numerous strategies are now available to generate rudimentary forms of synthetic cell-like entities, minimal progress has been made in the sustained excitation of artificial protocells under non-equilibrium conditions. Here we demonstrate that the electric field energization of coacervate microdroplets comprising polylysine and short single strands of DNA generates membrane-free protocells with complex, dynamical behaviours. By confining the droplets within a microfluidic channel and applying a range of electric field strengths, we produce protocells that exhibit repetitive cycles of vacuolarization, dynamical fluctuations in size and shape, chaotic growth and fusion, spontaneous ejection and sequestration of matter, directional capture of solute molecules, and pulsed enhancement of enzyme cascade reactions. Our results highlight new opportunities for the study of non-equilibrium phenomena in synthetic protocells, provide a strategy for inducing complex behaviour in electrostatically assembled soft matter microsystems and illustrate how dynamical properties can be activated and sustained in microcompartmentalized media.
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Affiliation(s)
- Yudan Yin
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lin Niu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaocui Zhu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zexin Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Stephen Mann
- Centre for Protolife Research, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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473
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Murillo-Sánchez S, Beaufils D, González Mañas JM, Pascal R, Ruiz-Mirazo K. Fatty acids' double role in the prebiotic formation of a hydrophobic dipeptide. Chem Sci 2016; 7:3406-3413. [PMID: 29997836 PMCID: PMC6007129 DOI: 10.1039/c5sc04796j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/09/2016] [Indexed: 02/06/2023] Open
Abstract
In search of a connection between prebiotic peptide chemistry and lipid compartments, the reaction of a 5(4H)-oxazolone with leucinamide was extensively explored under buffered aqueous conditions, where diverse amphiphiles and surfactants could form supramolecular assemblies. Significant increases in yield and changes in stereoselectivity were observed when fatty acids exceeded their critical aggregation concentration, self-assembling into vesicles in particular. This effect does not take place below the fatty acid solubility limit, or when other anionic amphiphiles/surfactants are used. Data from fluorimetric and Langmuir trough assays, complementary to the main HPLC results reported here, demonstrate that the dipeptide product co-localizes with fatty acid bilayers and monolayers. Additional experiments in organic solvents suggest that acid-base catalysis operates at the water-aggregate interface, linked to the continuous proton exchange dynamics that fatty acids undergo at pH values around their effective pKa. These simple amphiphiles could therefore play a dual role as enhancers of peptide chemistry under prebiotic conditions, providing soft and hydrophobic organic domains through self-assembly and actively inducing catalysis at their interface with the aqueous environment. Our results support a systems chemistry approach to life's origin.
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Affiliation(s)
| | - Damien Beaufils
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS/Université de Montpellier/ENSCM) , Montpellier , France .
| | | | - Robert Pascal
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS/Université de Montpellier/ENSCM) , Montpellier , France .
| | - Kepa Ruiz-Mirazo
- Biophysics Unit (CSIC, UPV/EHU) , University of the Basque Country , Spain . .,Department of Logic and Philosophy of Science , University of the Basque Country , Spain
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474
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Stirling A, Rozgonyi T, Krack M, Bernasconi M. Prebiotic NH3 Formation: Insights from Simulations. Inorg Chem 2016; 55:1934-9. [PMID: 26831570 DOI: 10.1021/acs.inorgchem.5b02911] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulations of prebiotic NH₃ synthesis from NO₃⁻ and NO₂⁻ on pyrite surfaces under hydrothermal conditions are reported. Ab initio metadynamics calculations have successfully explored the full reaction path which explains earlier experimental observations. We have found that the reaction mechanism can be constructed from stepwise single atom transfers which are compatible with the expected reaction time scales. The roles of the hot-pressurized water and of the pyrite surfaces have been addressed. The mechanistic picture that emerged from the simulations strengthens the theory of chemoautotrophic origin of life by providing plausible reaction pathways for the formation of ammonia within the iron-sulfur-world scenario.
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Affiliation(s)
- András Stirling
- Institute of Organic Chemistry, Research Centre for Natural Sciences of the Hungarian Academy of Sciences , POB 286, Budapest, 1519, Hungary
| | - Tamás Rozgonyi
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences of the Hungarian Academy of Sciences , POB 286, Budapest, 1519, Hungary
| | - Matthias Krack
- Laboratory for Reactor Physics and Systems Behaviour, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Marco Bernasconi
- Department of Materials Science, University of Milano-Bicocca , Via R. Cozzi 55, Milano, Italy
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475
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Vallée Y, Milet A, Raghavendra Rao KV. Was methionine the molecular trigger of life on early earth? PHOSPHORUS SULFUR 2016. [DOI: 10.1080/10426507.2015.1034314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Yannick Vallée
- Département de Chimie Moléculaire, Univ. Grenoble Alpes, CNRS, Grenoble, France
| | - Anne Milet
- Département de Chimie Moléculaire, Univ. Grenoble Alpes, CNRS, Grenoble, France
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476
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Kaddi CD, Bennett RV, Paine MRL, Banks MD, Weber AL, Fernández FM, Wang MD. DetectTLC: Automated Reaction Mixture Screening Utilizing Quantitative Mass Spectrometry Image Features. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:359-65. [PMID: 26508443 PMCID: PMC5003040 DOI: 10.1007/s13361-015-1293-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 05/25/2023]
Abstract
Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimize yields, and elucidate secondary reaction pathways. Molecular-level information for species in such mixtures can be readily obtained by coupling mass spectrometry imaging (MSI) with thin layer chromatography (TLC) separations. User-guided investigation of imaging data for mixture components with known m/z values is generally straightforward; however, spot detection for unknowns is highly tedious, and limits the applicability of MSI in conjunction with TLC. To accelerate imaging data mining, we developed DetectTLC, an approach that automatically identifies m/z values exhibiting TLC spot-like regions in MS molecular images. Furthermore, DetectTLC can also spatially match m/z values for spots acquired during alternating high and low collision-energy scans, pairing product ions with precursors to enhance structural identification. As an example, DetectTLC is applied to the identification and structural confirmation of unknown, yet significant, products of abiotic pyrazinone and aminopyrazine nucleoside analog synthesis. Graphical Abstract ᅟ.
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Affiliation(s)
- Chanchala D Kaddi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Rachel V Bennett
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- The Coca-Cola Company, 1 Coca-Cola Plaza, Atlanta, GA, 30313, USA
| | - Martin R L Paine
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Mitchel D Banks
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Arthur L Weber
- SETI Institute, Ames Research Center, Moffett Field, CA, 94035, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - May D Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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477
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Feng X, Jia Y, Cai P, Fei J, Li J. Coassembly of Photosystem II and ATPase as Artificial Chloroplast for Light-Driven ATP Synthesis. ACS NANO 2016; 10:556-61. [PMID: 26615669 DOI: 10.1021/acsnano.5b05579] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Adenosine triphosphate (ATP) is one of the most important energy sources in living cells, which can drive serial key biochemical processes. However, generation of a proton gradient for ATP production in an artificial way poses a great challenge. In nature, photophosphorylation occurring in chloroplasts is an ideal prototype of ATP production. In this paper we imitate the light-to-ATP conversion process occurring in the thylakoid membrane by construction of FoF1-ATPase proteoliposome-coated PSII-based microspheres with well-defined core@shell structures using molecular assembly. Under light illumination, PSII can split water into protons, oxygen, and electrons and can generate a proton gradient for ATPase to produce ATP. Thus, an artificially designed chloroplast for PSII-driven ATP synthesis is realized. This biomimetic system will help to understand the photophosphorylation process and may facilitate the development of ATP-driven devices by remote light control.
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Affiliation(s)
- Xiyun Feng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Peng Cai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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478
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Dharmarathne L, Grieser F. Formation of Amino Acids on the Sonolysis of Aqueous Solutions Containing Acetic Acid, Methane, or Carbon Dioxide, in the Presence of Nitrogen Gas. J Phys Chem A 2016; 120:191-9. [PMID: 26695890 DOI: 10.1021/acs.jpca.5b11858] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sonolysis of aqueous solutions containing acetic acid, methane, or carbon dioxide in the presence of nitrogen gas was found to produce a number of different amino acids at a rate of ∼1 to 100 nM/min, using ultrasound at an operating power of 70 W and 355 kHz. Gas-phase elementary reactions are suggested, and discussed, to account for the formation of the complex biomolecules from the low molar mass solutes used. On the basis of the results, a new hypothesis is presented to explain the formation of amino acids under primitive atmospheric conditions and how their formation may be linked to the eventual abiotic genesis of life on Earth.
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Affiliation(s)
- Leena Dharmarathne
- Particulate Fluids Processing Centre, School of Chemistry, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Franz Grieser
- Particulate Fluids Processing Centre, School of Chemistry, The University of Melbourne , Parkville, Victoria 3010, Australia
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479
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Sadownik JW, Mattia E, Nowak P, Otto S. Diversification of self-replicating molecules. Nat Chem 2016; 8:264-9. [PMID: 26892559 DOI: 10.1038/nchem.2419] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 11/13/2015] [Indexed: 12/26/2022]
Abstract
How new species emerge in nature is still incompletely understood and difficult to study directly. Self-replicating molecules provide a simple model that allows us to capture the fundamental processes that occur in species formation. We have been able to monitor in real time and at a molecular level the diversification of self-replicating molecules into two distinct sets that compete for two different building blocks ('food') and so capture an important aspect of the process by which species may arise. The results show that the second replicator set is a descendant of the first and that both sets are kinetic products that oppose the thermodynamic preference of the system. The sets occupy related but complementary food niches. As diversification into sets takes place on the timescale of weeks and can be investigated at the molecular level, this work opens up new opportunities for experimentally investigating the process through which species arise both in real time and with enhanced detail.
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Affiliation(s)
- Jan W Sadownik
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute for Chemistry, Nijenborgh 4, AG Groningen 9747, The Netherlands
| | - Elio Mattia
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute for Chemistry, Nijenborgh 4, AG Groningen 9747, The Netherlands
| | - Piotr Nowak
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute for Chemistry, Nijenborgh 4, AG Groningen 9747, The Netherlands
| | - Sijbren Otto
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute for Chemistry, Nijenborgh 4, AG Groningen 9747, The Netherlands
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480
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Abplanalp MJ, Förstel M, Kaiser RI. Exploiting single photon vacuum ultraviolet photoionization to unravel the synthesis of complex organic molecules in interstellar ices. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.029] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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481
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Girka Q, Estrine B, Hoffmann N, Le Bras J, Marinković S, Muzart J. Simple efficient one-pot synthesis of 5-hydroxymethylfurfural and 2,5-diformylfuran from carbohydrates. REACT CHEM ENG 2016. [DOI: 10.1039/c5re00004a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A one-pot procedure for the synthesis of DFF starting from mono-, di- or polysaccharides or from primary biomass has been developed. HMF is formed as intermediate and can also be isolated.
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Affiliation(s)
- Quentin Girka
- CNRS
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims
- UMR 7312
- UFR des Sciences Exactes et Naturelles
| | - Boris Estrine
- Agro-Industrie Recherches et Développements
- Green Chemistry Departement
- 51110 Pomacle
- France
| | - Norbert Hoffmann
- CNRS
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims
- UMR 7312
- UFR des Sciences Exactes et Naturelles
| | - Jean Le Bras
- CNRS
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims
- UMR 7312
- UFR des Sciences Exactes et Naturelles
| | - Siniša Marinković
- Agro-Industrie Recherches et Développements
- Green Chemistry Departement
- 51110 Pomacle
- France
| | - Jacques Muzart
- CNRS
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims
- UMR 7312
- UFR des Sciences Exactes et Naturelles
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482
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Alfonso I. From simplicity to complex systems with bioinspired pseudopeptides. Chem Commun (Camb) 2016; 52:239-50. [DOI: 10.1039/c5cc07596c] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).
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Affiliation(s)
- Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- Jordi Girona
- 18-26
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483
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Nhlabatsi ZP, Bhasi P, Sitha S. Possible interstellar formation of glycine through a concerted mechanism: a computational study on the reaction of CH2NH, CO2 and H2. Phys Chem Chem Phys 2016; 18:20109-17. [DOI: 10.1039/c5cp07124k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Computational studies on the reaction of CH2NH, CO2 and H2 show the possible interstellar formation of glycine in both hot-cores and cold interstellar clouds.
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Affiliation(s)
- Zanele P. Nhlabatsi
- Department of Chemistry
- University of Johannesburg
- Auckland Park
- South Africa 2006
| | - Priya Bhasi
- Department of Chemistry
- University of Johannesburg
- Auckland Park
- South Africa 2006
| | - Sanyasi Sitha
- Department of Chemistry
- University of Johannesburg
- Auckland Park
- South Africa 2006
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484
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Nhlabatsi ZP, Bhasi P, Sitha S. Possible interstellar formation of glycine from the reaction of CH2NH, CO and H2O: catalysis by extra water molecules through the hydrogen relay transport. Phys Chem Chem Phys 2016; 18:375-81. [DOI: 10.1039/c5cp04987c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Computational study shows the interstellar formation of glycine from CH2NH, CO2 and H2, both in the hot-cores and cold interstellar clouds.
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Affiliation(s)
| | - Priya Bhasi
- Department of Chemistry
- University of Johannesburg
- Johannesburg
- South Africa
| | - Sanyasi Sitha
- Department of Chemistry
- University of Johannesburg
- Johannesburg
- South Africa
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485
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Introduction to Virus Origins and Their Role in Biological Evolution. VIRUS AS POPULATIONS 2016. [PMCID: PMC7204881 DOI: 10.1016/b978-0-12-800837-9.00001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Viruses are extremely abundant and diverse parasites of cells. They might have arisen during an early phase of the evolution of life on Earth dominated by RNA or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate: viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via lateral transfers of genes. These two models bear on considering viruses predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.
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486
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Vuradi RK, Putta VR, Nancherla D, Sirasani S. Luminescent Behavior of Ru(II) Polypyridyl Morpholine Complexes, Synthesis, Characterization, DNA, Protein Binding, Sensor Effect of Ions/Solvents and Docking Studies. J Fluoresc 2015; 26:689-701. [DOI: 10.1007/s10895-015-1755-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/14/2015] [Indexed: 12/28/2022]
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487
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Zhou Y, Li L, Ye H, Zhang L, You L. Quantitative Reactivity Scales for Dynamic Covalent and Systems Chemistry. J Am Chem Soc 2015; 138:381-9. [DOI: 10.1021/jacs.5b11361] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Yuntao Zhou
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China
| | - Lijie Li
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hebo Ye
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China
| | - Ling Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China
| | - Lei You
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China
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488
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Kosikova T, Mackenzie H, Philp D. Probing the Limits of Selectivity in a Recognition-Mediated Reaction Network Embedded within a Dynamic Covalent Library. Chemistry 2015; 22:1831-9. [DOI: 10.1002/chem.201503740] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/30/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM; University of St. Andrews, North Haugh; St. Andrews KY16 9ST UK
| | - Harry Mackenzie
- School of Chemistry and EaStCHEM; University of St. Andrews, North Haugh; St. Andrews KY16 9ST UK
- UCB; 216 Bath Road Slough Berks SL1 3WE UK
| | - Douglas Philp
- School of Chemistry and EaStCHEM; University of St. Andrews, North Haugh; St. Andrews KY16 9ST UK
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489
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Du N, Song R, Li H, Song S, Zhang R, Hou W. A Nonconventional Model of Protocell-like Vesicles: Anionic Clay Surface-Mediated Formation from a Single-Tailed Amphiphile. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12579-12586. [PMID: 26524569 DOI: 10.1021/acs.langmuir.5b03477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report a novel model system of precursor cellular membranes, self-assembled from micellar solution of a common anionic single-tailed amphiphile (STA), including sodium dodecyl sulfate (SDS) and sodium dodecylbenzenesulfonate (SDBS). The self-assembly process was mediated with solid surfaces of Mg2Al-CO3 hydrotalcite-like compound (HTlc), an anionic clay, in the absence of cosurfactants or any additives. The resultant STA vesicles were characterized using negative-staining and cryogenic transmission electron microscopies, as well as dynamic light scattering and steady state fluorescence techniques. Interestingly, the obtained STA vesicles displayed good stability even after the removal of the anionic clay surface (ACS), and a self-reproduction phenomenon was observed for the "preformed" STA vesicles when mixing with corresponding STA micellar solutions. More importantly, the micelle-to-vesicle transition for SDS could be still arisen in high-salinity artificial seawater under the ACS mediation. Instead of conventional fatty acid scenario, our finding provides another novel possible model for protocell-like vesicles, which are easily formed under the plausible prebiotic conditions.
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Affiliation(s)
- Na Du
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), Shandong University , Jinan 250100, P.R. China
| | - Ruiying Song
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), Shandong University , Jinan 250100, P.R. China
| | - Haiping Li
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), Shandong University , Jinan 250100, P.R. China
| | - Shue Song
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), Shandong University , Jinan 250100, P.R. China
| | - Renjie Zhang
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), Shandong University , Jinan 250100, P.R. China
| | - Wanguo Hou
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), Shandong University , Jinan 250100, P.R. China
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490
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Tu Y, Peng F, Adawy A, Men Y, Abdelmohsen LKEA, Wilson DA. Mimicking the Cell: Bio-Inspired Functions of Supramolecular Assemblies. Chem Rev 2015; 116:2023-78. [DOI: 10.1021/acs.chemrev.5b00344] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yingfeng Tu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Fei Peng
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alaa Adawy
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yongjun Men
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Loai K. E. A. Abdelmohsen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Daniela A. Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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491
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Singh A, Singh P. Formation of amino acids from NH3 /NO2, CO2 and H2O: implications for the prebiotic origin of biomolecules. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2090-2094. [PMID: 26443411 DOI: 10.1002/rcm.7303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The search for the conditions which must have prevailed in the long-distant past during the conversion of inanimate matter into animate matter is a fascinating area of research and it continues to draw the attention of the scientific community. The initiation of life on this planet must have been preceded by the development of biomolecules, amongst which amino acids have unique importance. Formation of amino acids under a certain set of conditions is shown in the present experiments. METHODS Solutions of ammonium carboxylates or the mixture of two such salts were prepared in 3:6.9:0.1 (v/v/v) acetonitrile/water/formic acid at a concentration of 50 μM. The studies were performed using a quadrupole time-of-flight (QqTOF) mass spectrometer. The formation of different amino acids was detected with high-resolution mass spectrometry. RESULTS Here, we show the formation of amino acids when a solution of ammonium salts was injected into an electrospray ionization (ESI)-QqTOF-MS instrument. The ammonium salts were the source of NH3 and CO2 and H2 O was available in the medium. It seems that the combination of NH3 , CO2 , and H2 O leads to the formation of amino acids. CONCLUSIONS Further to the literature reports of formation of amino acids under the reduced atmosphere represented by gases such as NH3 , CH4 , H2 and H2 O, here we demonstrate the formation of amino acids by the combination of NH3 /NO2 , CO2 and water vapours in the ESI source of the mass spectrometer.
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Affiliation(s)
- Amrinder Singh
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar, -143005, India
| | - Palwinder Singh
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar, -143005, India
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492
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Villani M, Roli A, Filisetti A, Fiorucci M, Poli I, Serra R. The Search for Candidate Relevant Subsets of Variables in Complex Systems. ARTIFICIAL LIFE 2015; 21:412-431. [PMID: 26545160 DOI: 10.1162/artl_a_00184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We describe a method to identify relevant subsets of variables, useful to understand the organization of a dynamical system. The variables belonging to a relevant subset should have a strong integration with the other variables of the same relevant subset, and a much weaker interaction with the other system variables. On this basis, extending previous work on neural networks, an information-theoretic measure, the dynamical cluster index, is introduced in order to identify good candidate relevant subsets. The method does not require any previous knowledge of the relationships among the system variables, but relies on observations of their values over time. We show its usefulness in several application domains, including: (i) random Boolean networks, where the whole network is made of different subnetworks with different topological relationships (independent or interacting subnetworks); (ii) leader-follower dynamics, subject to noise and fluctuations; (iii) catalytic reaction networks in a flow reactor; (iv) the MAPK signaling pathway in eukaryotes. The validity of the method has been tested in cases where the data are generated by a known dynamical model and the dynamical cluster index is applied in order to uncover significant aspects of its organization; however, it is important that it can also be applied to time series coming from field data without any reference to a model. Given that it is based on relative frequencies of sets of values, the method could be applied also to cases where the data are not ordered in time. Several indications to improve the scope and effectiveness of the dynamical cluster index to analyze the organization of complex systems are finally given.
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Affiliation(s)
- M Villani
- European Centre for Living Technology and University of Modena e Reggio Emilia
| | | | | | - M Fiorucci
- European Centre for Living Technology and Ca' Foscari University of Venice
| | - I Poli
- European Centre for Living Technology and Ca' Foscari University of Venice
| | - R Serra
- European Centre for Living Technology and University of Modena e Reggio Emilia
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493
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Pross A. Physical Organic Chemistry and the Origin of Life Problem: A Personal Perspective. Isr J Chem 2015. [DOI: 10.1002/ijch.201500073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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494
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Kosikova T, Hassan NI, Cordes DB, Slawin AMZ, Philp D. Orthogonal Recognition Processes Drive the Assembly and Replication of a [2]Rotaxane. J Am Chem Soc 2015; 137:16074-83. [DOI: 10.1021/jacs.5b09738] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Tamara Kosikova
- School
of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom
| | - Nurul Izzaty Hassan
- School
of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom
- School
of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - David B. Cordes
- School
of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom
| | - Alexandra M. Z. Slawin
- School
of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom
| | - Douglas Philp
- School
of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom
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495
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Sutherland JD. The Origin of Life--Out of the Blue. Angew Chem Int Ed Engl 2015; 55:104-21. [PMID: 26510485 DOI: 10.1002/anie.201506585] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 01/28/2023]
Abstract
Either to sustain autotrophy, or as a prelude to heterotrophy, organic synthesis from an environmentally available C1 feedstock molecule is crucial to the origin of life. Recent findings augment key literature results and suggest that hydrogen cyanide--"Blausäure"--was that feedstock.
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Affiliation(s)
- John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (UK).
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496
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497
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Tschierske C, Ungar G. Mirror Symmetry Breaking by Chirality Synchronisation in Liquids and Liquid Crystals of Achiral Molecules. Chemphyschem 2015; 17:9-26. [DOI: 10.1002/cphc.201500601] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Carsten Tschierske
- Institute of Chemistry, Organic Chemistry; Martin Luther University Halle-Wittenberg; Kurt-Mothes Str. 2 06120 Halle/Saale Germany
| | - Goran Ungar
- Department of Physics; Zhejiang Sci-Tech University; Xiasha College Park 310018 Hangzhou China
- Department of Materials Science and Engineering; University of Sheffield; Sheffield S1 3JD Sheffield UK
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498
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Lafuente M, Atcher J, Solà J, Alfonso I. Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding. Chemistry 2015; 21:17002-9. [DOI: 10.1002/chem.201501415] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Indexed: 11/08/2022]
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499
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Sahoo PK, Bose A, Mal P. Solvent-Free Ball-Milling Biginelli Reaction by Subcomponent Synthesis. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501039] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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500
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Formation of oligopeptides in high yield under simple programmable conditions. Nat Commun 2015; 6:8385. [PMID: 26442968 PMCID: PMC4633627 DOI: 10.1038/ncomms9385] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Many high-yielding reactions for forming peptide bonds have been developed but these are complex, requiring activated amino-acid precursors and heterogeneous supports. Herein we demonstrate the programmable one-pot dehydration–hydration condensation of amino acids forming oligopeptide chains in around 50% yield. A digital recursive reactor system was developed to investigate this process, performing these reactions with control over parameters such as temperature, number of cycles, cycle duration, initial monomer concentration and initial pH. Glycine oligopeptides up to 20 amino acids long were formed with very high monomer-to-oligomer conversion, and the majority of these products comprised three amino acid residues or more. Having established the formation of glycine homo-oligopeptides, we then demonstrated the co-condensation of glycine with eight other amino acids (Ala, Asp, Glu, His, Lys, Pro, Thr and Val), incorporating a range of side-chain functionality. Typically, in order to form large peptides, complex procedures or activating agents are required. Here, the authors show that simple aqueous conditions with dehydration-hydration cycles are sufficient for the oligomerization of amino acids into peptides (up to 20 amino acids long) in yields of up to 50%.
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