501
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Neelakandan PP, Jiménez A, Thoburn JD, Nitschke JR. An Autocatalytic System of Photooxidation-Driven Substitution Reactions on a FeII4L6Cage Framework. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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502
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Neelakandan PP, Jiménez A, Thoburn JD, Nitschke JR. An Autocatalytic System of Photooxidation-Driven Substitution Reactions on a Fe(II)4L6 Cage Framework. Angew Chem Int Ed Engl 2015; 54:14378-82. [PMID: 26437971 DOI: 10.1002/anie.201507045] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/15/2015] [Indexed: 12/11/2022]
Abstract
The functions of life are accomplished by systems exhibiting nonlinear kinetics: autocatalysis, in particular, is integral to the signal amplification that allows for biological information processing. Novel synthetic autocatalytic systems provide a foundation for the design of artificial chemical networks capable of carrying out complex functions. Here we report a set of Fe(II)4L6 cages containing BODIPY chromophores having tuneable photosensitizing properties. Electron-rich anilines were observed to displace electron-deficient anilines at the dynamic-covalent imine bonds of these cages. When iodoaniline residues were incorporated, heavy-atom effects led to enhanced (1)O2 production. The incorporation of (methylthio)aniline residues into a cage allowed for the design of an autocatalytic system: oxidation of the methylthio groups into sulfoxides make them electron-deficient and allows their displacement by iodoanilines, generating a better photocatalyst and accelerating the reaction.
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Affiliation(s)
- Prakash P Neelakandan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK).,Current address: Institute of Nano Science and Technology, Habitat Centre, Phase 10, Sector 64, Mohali 160062 (India)
| | - Azucena Jiménez
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK).,Current address: Department of Chemistry, University of Oviedo, Julian Clavería 8, Oviedo 33006 (Spain)
| | - John D Thoburn
- Department of Chemistry, Randolph-Macon College, Ashland, VA 23005 (USA)
| | - Jonathan R Nitschke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK).
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503
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Rao KVR, Caiveau N, David R, Shalayel I, Milet A, Vallée Y. Theoretical Study, Synthesis, and Reactivity of Five-Membered-Ring Acyl Sulfonium Cations. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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504
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Grochmal A, Prout L, Makin-Taylor R, Prohens R, Tomas S. Modulation of reactivity in the cavity of liposomes promotes the formation of peptide bonds. J Am Chem Soc 2015; 137:12269-75. [PMID: 26356087 DOI: 10.1021/jacs.5b06207] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In living cells, reactions take place in membrane-bound compartments, often in response to changes in the environment. Learning how the reactions are influenced by this compartmentalization will help us gain an optimal understanding of living organisms at the molecular level and, at the same time, will offer vital clues on the behavior of simple compartmentalized systems, such as prebiotic precursors of cells and cell-inspired artificial systems. In this work we show that a reactive building block (an activated amino acid derivative) trapped in the cavity of a liposome is protected against hydrolysis and reacts nearly quantitatively with another building block, which is membrane-permeable and free in solution, to form the dipeptide. By contrast, when the activated amino acid is found outside the liposome, hydrolysis is the prevalent reaction, showing that the cavity of the liposomes promotes the formation of peptide bonds. We attribute this result to the large lipid concentration in small compartments from the point of view of a membrane-impermeable molecule. Based on this result, we show how the outcome of the reaction can be predicted as a function of the size of the compartment. The implications of these results on the behavior of biomolecules in cell compartments, abiogenesis, and the design of artificial cell-inspired systems are considered.
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Affiliation(s)
- Anna Grochmal
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Luba Prout
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Robert Makin-Taylor
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Rafel Prohens
- CIRCE Crystal Engineering , 07121 Palma de Mallorca, Spain.,Unitat de Polimorfisme i Calorimetria, CCiT, Universitat de Barcelona , 08028 Barcelona, Spain
| | - Salvador Tomas
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
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505
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de la Escosura A, Briones C, Ruiz-Mirazo K. The systems perspective at the crossroads between chemistry and biology. J Theor Biol 2015; 381:11-22. [DOI: 10.1016/j.jtbi.2015.04.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/26/2015] [Indexed: 01/21/2023]
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506
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The enduring value of Gánti׳s chemoton model and life criteria: Heuristic pursuit of exact theoretical biology. J Theor Biol 2015; 381:23-8. [DOI: 10.1016/j.jtbi.2015.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/08/2015] [Indexed: 11/18/2022]
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507
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Nowak P, Colomb-Delsuc M, Otto S, Li J. Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library. J Am Chem Soc 2015; 137:10965-9. [PMID: 26192814 DOI: 10.1021/jacs.5b04380] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Self-assembly of a specific member of a dynamic combinatorial library (DCL) may lead to self-replication of this molecule. However, if the concentration of the potential replicator in the DCL fails to exceed its critical aggregation concentration (CAC), then self-replication will not occur. We now show how addition of a template can raise the concentration of a library member-template complex beyond its CAC, leading to the onset of self-replication. Once in existence, the replicator aggregates promote further replication also in the absence of the template that induced the initial emergence of the replicator.
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Affiliation(s)
- Piotr Nowak
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Mathieu Colomb-Delsuc
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jianwei Li
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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508
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Szekrenyi A, Garrabou X, Parella T, Joglar J, Bujons J, Clapés P. Asymmetric assembly of aldose carbohydrates from formaldehyde and glycolaldehyde by tandem biocatalytic aldol reactions. Nat Chem 2015; 7:724-9. [DOI: 10.1038/nchem.2321] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 07/08/2015] [Indexed: 01/11/2023]
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509
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Torbensen K, Rossi F, Pantani OL, Ristori S, Abou-Hassan A. Interaction of the Belousov–Zhabotinsky Reaction with Phospholipid Engineered Membranes. J Phys Chem B 2015; 119:10224-30. [DOI: 10.1021/acs.jpcb.5b04572] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Kristian Torbensen
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
| | - Federico Rossi
- Department
of Chemistry and Biology, University of Salerno, Via Giovanni
Paolo II 132, Fisciano (SA), Italy
| | - Ottorino L. Pantani
- Department
of Agrifood Production and Environmental Sciences, University of Florence, P.le delle Cascine 28, 50144 Firenze, Italy
| | - Sandra Ristori
- Department of Earth Sciences & CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Ali Abou-Hassan
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
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510
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Poust S, Piety J, Bar-Even A, Louw C, Baker D, Keasling JD, Siegel JB. Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction. Chembiochem 2015; 16:1950-1954. [PMID: 26109266 DOI: 10.1002/cbic.201500228] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 11/08/2022]
Abstract
An enzyme that catalyzes the formose reaction, termed "formolase", was recently engineered through a combination of computational protein design and directed evolution. We have investigated the kinetic role of the computationally designed residues and further characterized the enzyme's product profile. Kinetic studies illustrated that the computationally designed mutations were synergistic in their contributions towards enhancing activity. Mass spectrometry revealed that the engineered enzyme produces two products of the formose reaction-dihydroxyacetone and glycolaldehyde-with the product profile dependent on the formaldehyde concentration. We further explored the effects of this product profile on the thermodynamics and yield of the overall carbon assimilation from the formolase pathway to help guide future efforts to engineer this pathway.
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Affiliation(s)
- Sean Poust
- Department of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, Berkeley, CA 94720-1462 (USA).,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 (USA)
| | - James Piety
- Department of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, Berkeley, CA 94720-1462 (USA).,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 (USA)
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm (Germany)
| | - Catherine Louw
- Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195 (USA)
| | - David Baker
- Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195 (USA)
| | - Jay D Keasling
- Department of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, Berkeley, CA 94720-1462 (USA).,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 (USA)
| | - Justin B Siegel
- Departments of Chemistry and Biochemistry and Molecular Medicine, Genome Center, University of California, 451 Health Sciences Drive, Davis, CA 95616 (USA).,Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195 (USA)
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511
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Walde P, Umakoshi H, Stano P, Mavelli F. Emergent properties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators. Chem Commun (Camb) 2015; 50:10177-97. [PMID: 24921467 DOI: 10.1039/c4cc02812k] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article deals with artificial vesicles and their membranes as reaction promoters and regulators. Among the various molecular assemblies which can form in an aqueous medium from amphiphilic molecules, vesicle systems are unique. Vesicles compartmentalize the aqueous solution in which they exist, independent on whether the vesicles are biological vesicles (existing in living systems) or whether they are artificial vesicles (formed in vitro from natural or synthetic amphiphiles). After the formation of artificial vesicles, their aqueous interior (the endovesicular volume) may become - or may be made - chemically different from the external medium (the exovesicular solution), depending on how the vesicles are prepared. The existence of differences between endo- and exovesicular composition is one of the features on the basis of which biological vesicles contribute to the complex functioning of living organisms. Furthermore, artificial vesicles can be formed from mixtures of amphiphiles in such a way that the vesicle membranes become molecularly, compositionally and organizationally highly complex, similarly to the lipidic matrix of biological membranes. All the various properties of artificial vesicles as membranous compartment systems emerge from molecular assembly as these properties are not present in the individual molecules the system is composed of. One particular emergent property of vesicle membranes is their possible functioning as promoters and regulators of chemical reactions caused by the localization of reaction components, and possibly catalysts, within or on the surface of the membranes. This specific feature is reviewed and highlighted with a few selected examples which range from the promotion of decarboxylation reactions, the selective binding of DNA or RNA to suitable vesicle membranes, and the reactivation of fragmented enzymes to the regulation of the enzymatic synthesis of polymers. Such type of emergent properties of vesicle membranes may have been important for the prebiological evolution of protocells, the hypothetical compartment systems preceding the first cells in those chemical and physico-chemical processes that led to the origin of life.
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Affiliation(s)
- Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland.
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512
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Ajani OO, Isaac JT, Owoeye TF, Akinsiku AA. Exploration of the Chemistry and Biological Properties of Pyrimidine as a Privilege Pharmacophore in Therapeutics. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ijbc.2015.148.177] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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513
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Le Chevalier Isaad A, Carrara P, Stano P, Krishnakumar KS, Lafont D, Zamboulis A, Buchet R, Bouchu D, Albrieux F, Strazewski P. A hydrophobic disordered peptide spontaneously anchors a covalently bound RNA hairpin to giant lipidic vesicles. Org Biomol Chem 2015; 12:6363-73. [PMID: 24915577 DOI: 10.1039/c4ob00721b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The attraction of nucleic acids to lipidic compartments is the first step for carriers of potentially inheritable information to self-organise in functionalised synthetic cells. Confocal fluorescence imaging shows that a synthetic amphiphilic peptidyl RNA molecule spontaneously accumulates at the outer bilayer membranes of phospho- and glycolipidic giant vesicles. Cooperatively attractive interactions of -3.4 to -4.0 kcal mol(-1) between a random coil hydrophobic peptide and lipid membranes can thus pilot lipophobic RNA to its compartmentation. The separation of mixed lipid phases in the membranes further enhances the local concentration of anchored RNA.
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Affiliation(s)
- Alexandra Le Chevalier Isaad
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, Lyon, France.
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514
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Kimura J, Kitadai N. Polymerization of Building Blocks of Life on Europa and Other Icy Moons. ASTROBIOLOGY 2015; 15:430-41. [PMID: 26060981 PMCID: PMC4490594 DOI: 10.1089/ast.2015.1306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The outer Solar System may provide a potential habitat for extraterrestrial life. Remote sensing data from the Galileo spacecraft suggest that the jovian icy moons--Europa, Ganymede, and possibly Callisto--may harbor liquid water oceans underneath their icy crusts. Although compositional information required for the discussion of habitability is limited because of significantly restricted observation data, organic molecules are ubiquitous in the Universe. Recently, in situ spacecraft measurements and experiments suggest that amino acids can be formed abiotically on interstellar ices and comets. These amino acids could be continuously delivered by meteorite or comet impacts to icy moons. Here, we show that polymerization of organic monomers, in particular amino acids and nucleotides, could proceed spontaneously in the cold environment of icy moons, in particular the jovian icy moon Europa as a typical example, based on thermodynamic calculations, though kinetics of formation are not addressed. Observed surface temperature on Europa is 120 and 80 K in the equatorial region and polar region, respectively. At such low temperatures, Gibbs energies of polymerization become negative, and the estimated thermal structure of the icy crust should contain a shallow region (i.e., at a depth of only a few kilometers) favorable for polymerization. Investigation of the possibility of organic monomer polymerization on icy moons could provide good constraints on the origin and early evolution of extraterrestrial life.
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Affiliation(s)
- Jun Kimura
- Earth-Life Science Institute, Tokyo Institute of Technology , Tokyo, Japan
| | - Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology , Tokyo, Japan
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515
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Bissette AJ, Fletcher SP. Novel applications of physical autocatalysis. ORIGINS LIFE EVOL B 2015; 45:21-30. [PMID: 25716916 DOI: 10.1007/s11084-015-9404-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Abstract
The autocatalytic self-reproduction of micelles and vesicles has been studied for several decades. These systems are vital components of certain protocell models and some models for how life may have begun from mixtures of simple chemicals. Here we discuss our recently described autocatalytic systems where self-reproducing micelles are driven by bond-forming reactions. These systems generate increased complexity on both the molecular level, through covalent bond formation, and the supramolecular level, through spontaneous self-assembly into functional aggregates. This provides the conceptual basis for novel studies of the potential roles of self-reproducing lipid aggregates in the prebiotic world.
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Affiliation(s)
- Andrew J Bissette
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Rd, Oxford, OX1 3TA, UK
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516
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Kamimura A, Kaneko K. Transition to diversification by competition for multiple resources in catalytic reaction networks. ACTA ACUST UNITED AC 2015; 6:5. [PMID: 25960781 PMCID: PMC4412551 DOI: 10.1186/s13322-015-0010-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/17/2015] [Indexed: 11/10/2022]
Abstract
Background All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which the use of a great variety of components, and the coexistence of diverse cell-types with different compositions are achieved is as yet unknown. Results Here we show that coexistence of such diverse compositions and cell-types is the result of competitions for a variety of limited resources. We find that a transition to diversity occurs both in chemical compositions and in protocell types, as the resource supply is decreased, when the maximum inflow and consumption of resources are balanced. Conclusions Our results indicate that a simple physical principle of competition for a variety of limiting resources can be a strong driving force to diversify intracellular dynamics of a catalytic reaction network and to develop diverse protocell types in a primitive stage of life. Electronic supplementary material The online version of this article (doi:10.1186/s13322-015-0010-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Atsushi Kamimura
- Department of Basic Science, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, 153-8902 Tokyo Japan
| | - Kunihiko Kaneko
- Department of Basic Science, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, 153-8902 Tokyo Japan
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517
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518
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Andersen JL, Flamm C, Merkle D, Stadler PF. In silicoSupport for Eschenmoser’s Glyoxylate Scenario. Isr J Chem 2015. [DOI: 10.1002/ijch.201400187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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519
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Zhou P, Shi R, Yao JF, Sheng CF, Li H. Supramolecular self-assembly of nucleotide–metal coordination complexes: From simple molecules to nanomaterials. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.02.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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520
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Current Ideas about Prebiological Compartmentalization. Life (Basel) 2015; 5:1239-63. [PMID: 25867709 PMCID: PMC4500137 DOI: 10.3390/life5021239] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 01/17/2023] Open
Abstract
Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell's interior and the environment. Since such compartmentalization is a fundamental principle of all forms of life, scenarios have been elaborated about the emergence of prebiological compartments on early Earth, in particular about their likely structural characteristics and dynamic features. Chemical systems that consist of potentially prebiological compartments and chemical reaction networks have been designed to model pre-cellular systems. These systems are often referred to as "protocells". Past and current protocell model systems are presented and compared. Since the prebiotic formation of cell-like compartments is directly linked to the prebiotic availability of compartment building blocks, a few aspects on the likely chemical inventory on the early Earth are also summarized.
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521
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Gurevich L, Cohen-Luria R, Wagner N, Ashkenasy G. Robustness of synthetic circadian clocks to multiple environmental changes. Chem Commun (Camb) 2015; 51:5672-5. [PMID: 25714790 DOI: 10.1039/c5cc00098j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A molecular network that mimics circadian clocks from cyanobacteria is constructed in silico. Simulating its oscillatory behaviour under variable conditions reveals its robustness relative to networks of alternative topologies. The principles for synthetic chemical circadian networks to work properly are consequently highlighted.
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Affiliation(s)
- Lilia Gurevich
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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522
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523
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Fujihara A, Maeda N, Hayakawa S. EnantioselectivePhotolysis and Quantitative Chiral Analysis of Tryptophan Complexed With Alkali-Metalized L-Serine in the Gas Phase. Chirality 2015; 27:349-52. [DOI: 10.1002/chir.22442] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Akimasa Fujihara
- Department of Chemistry, Graduate School of Science; Osaka Prefecture University; Osaka Japan
| | - Naoto Maeda
- Department of Chemistry, Graduate School of Science; Osaka Prefecture University; Osaka Japan
| | - Shigeo Hayakawa
- Department of Chemistry, Graduate School of Science; Osaka Prefecture University; Osaka Japan
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524
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Strazewski P. Omne Vivum Ex Vivo … Omne? How to Feed an Inanimate Evolvable Chemical System so as to Let it Self-evolve into Increased Complexity and Life-like Behaviour. Isr J Chem 2015. [DOI: 10.1002/ijch.201400175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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525
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D'Aguanno E, Altamura E, Mavelli F, Fahr A, Stano P, Luisi PL. Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes. Life (Basel) 2015; 5:969-96. [PMID: 25793278 PMCID: PMC4390888 DOI: 10.3390/life5010969] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/10/2015] [Indexed: 01/18/2023] Open
Abstract
How did primitive living cells originate? The formation of early cells, which were probably solute-filled vesicles capable of performing a rudimentary metabolism (and possibly self-reproduction), is still one of the big unsolved questions in origin of life. We have recently used lipid vesicles (liposomes) as primitive cell models, aiming at the study of the physical mechanisms for macromolecules encapsulation. We have reported that proteins and ribosomes can be encapsulated very efficiently, against statistical expectations, inside a small number of liposomes. Moreover the transcription-translation mixture, which realistically mimics a sort of minimal metabolic network, can be functionally reconstituted in liposomes owing to a self-concentration mechanism. Here we firstly summarize the recent advancements in this research line, highlighting how these results open a new vista on the phenomena that could have been important for the formation of functional primitive cells. Then, we present new evidences on the non-random entrapment of macromolecules (proteins, dextrans) in phospholipid vesicle, and in particular we show how enzymatic reactions can be accelerated because of the enhancement of their concentration inside liposomes.
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Affiliation(s)
- Erica D'Aguanno
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Lessingstraße 8, D-07743 Jena, Germany.
| | - Emiliano Altamura
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70125 Bari, Italy.
| | - Fabio Mavelli
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70125 Bari, Italy.
| | - Alfred Fahr
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Lessingstraße 8, D-07743 Jena, Germany.
| | - Pasquale Stano
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
| | - Pier Luigi Luisi
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
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526
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Bukhryakov KV, Almahdali S, Rodionov VO. Amplification of chirality through self-replication of micellar aggregates in water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2931-2935. [PMID: 25740116 DOI: 10.1021/la504984j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe a system in which the self-replication of micellar aggregates results in a spontaneous amplification of chirality in the reaction products. In this system, amphiphiles are synthesized from two "clickable" fragments: a water-soluble "head" and a hydrophobic "tail". Under biphasic conditions, the reaction is autocatalytic, as aggregates facilitate the transfer of hydrophobic molecules to the aqueous phase. When chiral, partially enantioenriched surfactant heads are used, a strong nonlinear induction of chirality in the reaction products is observed. Preseeding the reaction mixture with an amphiphile of one chirality results in the amplification of this product and therefore information transfer between generations of self-replicating aggregates. Because our amphiphiles are capable of catalysis, information transfer, and self-assembly into bounded structures, they present a plausible model for prenucleic acid "lipid world" entities.
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Affiliation(s)
- Konstantin V Bukhryakov
- KAUST Catalysis Center and Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Sarah Almahdali
- KAUST Catalysis Center and Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Valentin O Rodionov
- KAUST Catalysis Center and Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
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527
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Atcher J, Moure A, Bujons J, Alfonso I. Salt-Induced Adaptation of a Dynamic Combinatorial Library of Pseudopeptidic Macrocycles: Unraveling the Electrostatic Effects in Mixed Aqueous Media. Chemistry 2015; 21:6869-78. [DOI: 10.1002/chem.201406155] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Joan Atcher
- Department of Biological Chemistry and Molecular Modeling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona (Spain)
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528
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Giri C, Sahoo PK, Puttreddy R, Rissanen K, Mal P. Solvent-Free Ball-Milling Subcomponent Synthesis of Metallosupramolecular Complexes. Chemistry 2015; 21:6390-3. [DOI: 10.1002/chem.201500734] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 11/08/2022]
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529
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Dragičević I, Barić D, Kovačević B, Golding BT, Smith DM. Non-enzymatic ribonucleotide reduction in the prebiotic context. Chemistry 2015; 21:6132-43. [PMID: 25754795 DOI: 10.1002/chem.201405741] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 02/02/2015] [Indexed: 12/14/2022]
Abstract
Model studies of prebiotic chemistry have revealed compelling routes for the formation of the building blocks of proteins and RNA, but not DNA. Today, deoxynucleotides required for the construction of DNA are produced by reduction of nucleotides catalysed by ribonucleotide reductases, which are radical enzymes. This study considers potential non-enzymatic routes via intermediate radicals for the ancient formation of deoxynucleotides. In this context, several mechanisms for ribonucleotide reduction, in a putative H2 S/HS(.) environment, are characterized using computational chemistry. A bio-inspired mechanistic cycle involving a keto intermediate and HSSH production is found to be potentially viable. An alternative pathway, proceeding through an enol intermediate is found to exhibit similar energetic requirements. Non-cyclical pathways, in which HSS(.) is generated in the final step instead of HS(.) , show a markedly increased thermodynamic driving force (ca. 70 kJ mol(-1) ) and thus warrant serious consideration in the context of the prebiotic ribonucleotide reduction.
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Affiliation(s)
- Ivan Dragičević
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb (Croatia); Department of Chemistry, Faculty of Science and Education, University of Mostar, Matice hrvatske bb, 88000 Mostar (Bosnia and Herzegovina)
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530
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531
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532
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Leonetti G, Otto S. Solvent composition dictates emergence in dynamic molecular networks containing competing replicators. J Am Chem Soc 2015; 137:2067-72. [PMID: 25584629 DOI: 10.1021/ja512644f] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In Darwinian evolution, species that are better adapted to their environment win the competition for common resources from less well-adapted competitors. Thus, in such scenarios the nature of the environment may dictate the outcome of the competition. We investigated to what degree these biological principles acting at the level of species extend to the molecular level into systems based on fully synthetic self-replicating molecules. We now report two systems in which two replicators compete for a common building block and where the environment dictates which of the two replicators wins. We observed that subtle changes in the environment can lead to dramatic differences in the outcome of the competition.
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Affiliation(s)
- Giulia Leonetti
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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533
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Uncertainty of prebiotic scenarios: the case of the non-enzymatic reverse tricarboxylic acid cycle. Sci Rep 2015; 5:8009. [PMID: 25620471 PMCID: PMC4306138 DOI: 10.1038/srep08009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/22/2014] [Indexed: 11/08/2022] Open
Abstract
We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended.
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534
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Stirling A, Rozgonyi T, Krack M, Bernasconi M. Pyrite in contact with supercritical water: the desolation of steam. Phys Chem Chem Phys 2015; 17:17375-9. [DOI: 10.1039/c5cp01146a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The supercritical water and pyrite interface has been studied by DFT calculations. A surprisingly dry surface has been found which points to a new reactivity under extreme conditions which has relevance in the iron–sulfur world prebiotic chemistry of the early Earth.
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Affiliation(s)
- András Stirling
- Institute of Organic Chemistry
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences
- Budapest
- Hungary
| | - Tamás Rozgonyi
- Institute of Materials and Environmental Chemistry
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences
- Budapest
- Hungary
| | - Matthias Krack
- Laboratory for Reactor Physics and Systems Behaviour
- Paul Scherrer Institute
- CH-5232 Villigen PSI
- Switzerland
| | - Marco Bernasconi
- Department of Materials Science
- University of Milano-Bicocca
- I-20125 Milano
- Italy
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535
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Feng Z, Castellarin Cudia C, Floreano L, Morgante A, Comelli G, Dri C, Cossaro A. A competitive amino-carboxylic hydrogen bond on a gold surface. Chem Commun (Camb) 2015; 51:5739-42. [DOI: 10.1039/c4cc10271a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel amino-carboxylic hetero-synthon is described, which drives the formation of a complex 2D hetero-organic architecture.
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Affiliation(s)
- Zhijing Feng
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | | | - Luca Floreano
- CNR-IOM Laboratorio Nazionale TASC
- I-34149 Trieste
- Italy
| | - Alberto Morgante
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | - Giovanni Comelli
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | - Carlo Dri
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
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536
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Deans RM, Chandrashaker V, Taniguchi M, Lindsey JS. Complexity in structure-directed prebiotic chemistry. Effect of a defective competing reactant in tetrapyrrole formation. NEW J CHEM 2015. [DOI: 10.1039/c5nj01474c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A reactive but defective pyrrole, derived from the simple β-diketone acetylacetone, terminates chain-growth in a quantitative combinatorial manner in tetrapyrrole formation.
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Affiliation(s)
- Richard M. Deans
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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537
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Niu L, Yang X, Zhu X, Yin Y, Qu W, Zhou J, Zhao M, Liang D. Dynamic assembly of DNA and polylysine mediated by electric energy. Chem Commun (Camb) 2015; 51:1506-9. [DOI: 10.1039/c4cc07537d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Under an electric field, the complex of DNA and PLL ejects daughter vehicles with mobility three times faster than free DNA.
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Affiliation(s)
- Lin Niu
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
| | - Xuyan Yang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- 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
- China
| | - Yudan Yin
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
| | - Wei Qu
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
| | - Jihan Zhou
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- 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
- China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
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538
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Alexy EJ, Hintz CW, Hughes HM, Taniguchi M, Lindsey JS. Paley's watchmaker analogy and prebiotic synthetic chemistry in surfactant assemblies. Formaldehyde scavenging by pyrroles leading to porphyrins as a case study. Org Biomol Chem 2015; 13:10025-31. [DOI: 10.1039/c5ob01409c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Facile exchange of micromolar dialkylpyrrolic constituents among a Poisson distribution of aqueous micelles overcomes immense statistical odds against reaction.
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Affiliation(s)
- Eric J. Alexy
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Carl W. Hintz
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Hubert M. Hughes
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
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539
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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540
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Liu Z, Beaufils D, Rossi JC, Pascal R. Evolutionary importance of the intramolecular pathways of hydrolysis of phosphate ester mixed anhydrides with amino acids and peptides. Sci Rep 2014; 4:7440. [PMID: 25501391 PMCID: PMC4262824 DOI: 10.1038/srep07440] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/21/2014] [Indexed: 01/31/2023] Open
Abstract
Aminoacyl adenylates (aa-AMPs) constitute essential intermediates of protein biosynthesis. Their polymerization in aqueous solution has often been claimed as a potential route to abiotic peptides in spite of a highly efficient CO2-promoted pathway of hydrolysis. Here we investigate the efficiency and relevance of this frequently overlooked pathway from model amino acid phosphate mixed anhydrides including aa-AMPs. Its predominance was demonstrated at CO2 concentrations matching that of physiological fluids or that of the present-day ocean, making a direct polymerization pathway unlikely. By contrast, the occurrence of the CO2-promoted pathway was observed to increase the efficiency of peptide bond formation owing to the high reactivity of the N-carboxyanhydride (NCA) intermediate. Even considering CO2 concentrations in early Earth liquid environments equivalent to present levels, mixed anhydrides would have polymerized predominantly through NCAs. The issue of a potential involvement of NCAs as biochemical metabolites could even be raised. The formation of peptide–phosphate mixed anhydrides from 5(4H)-oxazolones (transiently formed through prebiotically relevant peptide activation pathways) was also observed as well as the occurrence of the reverse cyclization process in the reactions of these mixed anhydrides. These processes constitute the core of a reaction network that could potentially have evolved towards the emergence of translation.
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Affiliation(s)
- Ziwei Liu
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
| | - Damien Beaufils
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
| | | | - Robert Pascal
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
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541
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Li J, Nowak P, Otto S. An Allosteric Receptor by Simultaneous “Casting” and “Molding” in a Dynamic Combinatorial Library. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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542
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Li J, Nowak P, Otto S. An allosteric receptor by simultaneous "casting" and "molding" in a dynamic combinatorial library. Angew Chem Int Ed Engl 2014; 54:833-7. [PMID: 25430978 DOI: 10.1002/anie.201408907] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/31/2014] [Indexed: 01/13/2023]
Abstract
Allosteric synthetic receptors are difficult to access by design. Herein we report a dynamic combinatorial strategy towards such systems based on the simultaneous use of two different templates. Through a process of simultaneous casting (the assembly of a library member around a template) and molding (the assembly of a library member inside the binding pocket of a template), a Russian-doll-like termolecular complex was obtained with remarkable selectivity. Analysis of the stepwise formation of the complex indicates that binding of the two partners by the central macrocycle exhibits significant positive cooperativity. Such allosteric systems represent hubs that may have considerable potential in systems chemistry.
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Affiliation(s)
- Jianwei Li
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.otto-lab.com
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543
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Könnyű B, Czárán T. Phenotype/genotype sequence complementarity and prebiotic replicator coexistence in the metabolically coupled replicator system. BMC Evol Biol 2014; 14:234. [PMID: 25421353 PMCID: PMC4256930 DOI: 10.1186/s12862-014-0234-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/06/2014] [Indexed: 12/11/2022] Open
Abstract
Background RNA or RNA-like polymers are the most likely candidates for having played the lead roles on the stage of the origin of life. RNA is known to feature two of the three essential functions of living entities (metabolism, heredity and membrane): it is capable of unlimited heredity and it has a proven capacity for catalysing very different chemical reactions which may form simple metabolic networks. The Metabolically Coupled Replicator System is a class of simulation models built on these two functions to show that an RNA World scenario for the origin of life is ecologically feasible, provided that it is played on mineral surfaces. The fact that RNA templates and their copies are of complementary base sequences has an obvious dynamical relevance: complementary strains may have very different structures and, consequently, functions – one may specialize for increasing enzymatic activity while the other takes the role of the gene of the enzyme. Results Incorporating the functional divergence of template and copy into the Metabolically Coupled Replicator System model framework we show that sequence complementarity 1) does not ruin the coexistence of a set of metabolically cooperating replicators; 2) the replicator system remains resistant to, but also tolerant with its parasites; 3) opens the way to the evolutionary differentiation of phenotype and genotype through a primitive version of phenotype amplification. Conclusions The functional asymmetry of complementary RNA strains results in a shift of phenotype/genotype (enzyme/gene) proportions in MCRS, favouring a slight genotype dominance. This asymmetry is expected to reverse due to the evolved trade-off of high “gene” replicability and high catalytic activity of the corresponding “enzyme” in expense of its replicability. This trade-off is the first evolutionary step towards the “division of labour” among enzymes and genes, which has concluded in the extreme form of phenotype amplification characteristic of our recent DNA-RNA-protein World. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0234-8) contains supplementary material, which is available to authorized users.
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544
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Thapaliya ER, Captain B, Raymo FM. Plasmonic Acceleration of a Photochemical Replicator. ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201402211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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545
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Kaiser RI, Maity S, Jones BM. Synthesis of Prebiotic Glycerol in Interstellar Ices. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ralf I. Kaiser
- Department of Chemistry, W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822 (USA)
| | - Surajit Maity
- Department of Chemistry, W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822 (USA)
| | - Brant M. Jones
- Department of Chemistry, W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822 (USA)
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546
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Kaiser RI, Maity S, Jones BM. Synthesis of prebiotic glycerol in interstellar ices. Angew Chem Int Ed Engl 2014; 54:195-200. [PMID: 25363714 DOI: 10.1002/anie.201408729] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 11/06/2022]
Abstract
Contemporary mechanisms for the spontaneous formation of glycerol have not been able to explain its existence on early Earth. The exogenous origin and delivery of organic molecules to early Earth presents an alternative route to their terrestrial in situ formation since biorelevant molecules like amino acids, carboxylic acids, and alkylphosphonic acids have been recovered from carbonaceous chondrites. Reported herein is the first in situ identification of glycerol, the key building block of all cellular membranes, formed by exposure of methanol-based - interstellar model ices to ionizing radiation in the form of energetic electrons. These results provide compelling evidence that the radiation-induced formation of glycerol in low-temperature interstellar model ices is facile. Synthesized on interstellar grains and eventually incorporated into the "building material" of solar systems, biorelevant molecules such as glycerol could have been dispensed to habitable planets such as early Earth by comets and meteorites.
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Affiliation(s)
- Ralf I Kaiser
- Department of Chemistry, W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822 (USA).
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547
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Dadon Z, Wagner N, Alasibi S, Samiappan M, Mukherjee R, Ashkenasy G. Competition and Cooperation in Dynamic Replication Networks. Chemistry 2014; 21:648-54. [DOI: 10.1002/chem.201405195] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Indexed: 11/09/2022]
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548
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Beaufils D, Danger G, Boiteau L, Rossi JC, Pascal R. Diastereoselectivity in prebiotically relevant 5(4H)-oxazolone-mediated peptide couplings. Chem Commun (Camb) 2014; 50:3100-2. [PMID: 24513651 DOI: 10.1039/c3cc49580a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A stereochemical study of a potentially prebiotic peptide-forming reaction was carried out as the first part of a systems chemistry investigation of potential paths for symmetry breaking. Substantial diastereomeric excesses result from a fast epimerization of the 5(4H)-oxazolone intermediate in aqueous solution.
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Affiliation(s)
- Damien Beaufils
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS-Université Montpellier 1 & Montpellier 2, CC17006, Place E. Bataillon, 34095 Montpellier, France.
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549
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Singh A, Kaur S, Kaur J, Singh P. Transformation of gas-phase amino acid clusters to dipeptides: a nice approach to demonstrate the formation of prebiotic peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2019-2023. [PMID: 25132302 DOI: 10.1002/rcm.6985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/08/2014] [Accepted: 07/13/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Exploring prebiotic developments is a fascinating area of research which is continually drawing the attention of the scientific community. It is probable that first the biomolecules were formed and then they became aggregated to generate life. Formation of one such biomolecules (peptide ions) is shown in the present experiments. METHODS All amino acid solutions for recording mass spectra 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 Bruker MicroTOF QII mass spectrometer. Before carrying out experiments in the collision cell, atmospheric pressure in-source fragmentations were also performed. The formation of different chemical species was detected with high-resolution mass spectrometry. RESULTS Here, we show experimentally the formation of amino acid cluster ions of varied populations, when a solution of an amino acid was injected into an electrospray ionization quadrupole time-of-flight (ESI-QTOF) mass spectrometer. During in-source fragmentation/collision cell fragmentation, the non-covalent interaction between two identical amino acids forms either the [M2 + H](+) dimer cluster ion and/or the [M2 + K](+) adduct ion which, by elimination of one molecule of water, form the covalent linked dipeptide. CONCLUSIONS After the formation of the amino acid cluster, it was established that the creation of the dipeptides, by a covalent bond resulting from the loss of a water molecule, was the initial step towards the formation of the primordial peptides.
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Affiliation(s)
- Amrinder Singh
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar, 143005, India
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550
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Thapaliya ER, Swaminathan S, Captain B, Raymo FM. Autocatalytic Fluorescence Photoactivation. J Am Chem Soc 2014; 136:13798-804. [DOI: 10.1021/ja5068383] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ek Raj Thapaliya
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Subramani Swaminathan
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Burjor Captain
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Françisco M. Raymo
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| |
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