1
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Samrout OE, Berlier G, Lambert JF. Amino Acid Polymerization on Silica Surfaces. Chempluschem 2024; 89:e202300642. [PMID: 38226922 DOI: 10.1002/cplu.202300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.
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Affiliation(s)
- Ola El Samrout
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Gloria Berlier
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, LRS, Sorbonne Université Place Jussieu, 75005, Paris, France
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2
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de Herrera AG, Markert T, Trixler F. Temporal nanofluid environments induce prebiotic condensation in water. Commun Chem 2023; 6:69. [PMID: 37059805 PMCID: PMC10104841 DOI: 10.1038/s42004-023-00872-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Water is a problem in understanding chemical evolution towards life's origins on Earth. Although all known life is being based on water key prebiotic reactions are inhibited by it. The prebiotic plausibility of current strategies to circumvent this paradox is questionable regarding the principle that evolution builds on existing pathways. Here, we report a straightforward way to overcome the water paradox in line with evolutionary conservatism. By utilising a molecular deposition method as a physicochemical probe, we uncovered a synergy between biomolecule assembly and temporal nanofluid conditions that emerge within transient nanoconfinements of water between suspended particles. Results from fluorometry, quantitative PCR, melting curve analysis, gel electrophoresis and computational modelling reveal that such conditions induce nonenzymatic polymerisation of nucleotides and promote basic cooperation between nucleotides and amino acids for RNA formation. Aqueous particle suspensions are a geochemical ubiquitous and thus prebiotic highly plausible setting. Harnessing nanofluid conditions in this setting for prebiotic syntheses is consistent with evolutionary conservatism, as living cells also work with temporal nanoconfined water for biosynthesis. Our findings add key insights required to understand the transition from geochemistry to biochemistry and open up systematic pathways to water-based green chemistry approaches in materials science and nanotechnology.
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Affiliation(s)
- Andrea Greiner de Herrera
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Theresienstraße 41, 80333, Munich, Germany
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- School of Education, Technical University of Munich and Deutsches Museum, Museumsinsel 1, 80538, Munich, Germany
| | - Thomas Markert
- Institute of Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank Trixler
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Theresienstraße 41, 80333, Munich, Germany.
- School of Education, Technical University of Munich and Deutsches Museum, Museumsinsel 1, 80538, Munich, Germany.
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Schellingtr. 4, 80799, Munich, Germany.
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3
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Fontecilla-Camps JC. Reflections on the Origin and Early Evolution of the Genetic Code. Chembiochem 2023; 24:e202300048. [PMID: 37052530 DOI: 10.1002/cbic.202300048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Indexed: 04/14/2023]
Abstract
Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.
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4
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El Samrout O, Fabbiani M, Berlier G, Lambert JF, Martra G. Emergence of Order in Origin-of-Life Scenarios on Mineral Surfaces: Polyglycine Chains on Silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15516-15525. [PMID: 36469018 PMCID: PMC9776562 DOI: 10.1021/acs.langmuir.2c02106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/21/2022] [Indexed: 06/17/2023]
Abstract
The polymerization of amino acids (AAs) to peptides on oxide surfaces has attracted interest owing to its high importance in biotechnology, prebiotic chemistry, and origin of life theories. However, its mechanism is still poorly understood. We tried to elucidate the reactivity of glycine (Gly) from the vapor phase on the surface of amorphous silica under controlled atmosphere at 160 °C. Infrared (IR) spectroscopy reveals that Gly functionalizes the silica surface through the formation of ester species, which represent, together with the weakly interacting silanols, crucial elements for monomers activation and polymerization. Once activated, β-turns start to form as initiators for the growth of long linear polypeptides (poly-Gly) chains, which elongate into ordered structures containing both β-sheet and helical conformations. The work also points to the role of water vapor in the formation of further self-assembled β-sheet structures that are highly resistant to hydrolysis.
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Affiliation(s)
- Ola El Samrout
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
- Laboratoire
de Réactivité de Surface, LRS, Sorbonne Université, Place Jussieu, 75005 Paris, France
| | - Marco Fabbiani
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Gloria Berlier
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Jean-François Lambert
- Laboratoire
de Réactivité de Surface, LRS, Sorbonne Université, Place Jussieu, 75005 Paris, France
| | - Gianmario Martra
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
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5
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Derbali I, Aroule O, Hoffmann G, Thissen R, Alcaraz C, Romanzin C, Zins EL. On the relevance of the electron density analysis for the study of micro-hydration and its impact on the formation of a peptide-like bond. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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6
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Brigiano FS, Gierada M, Tielens F, Pietrucci F. Mechanism and Free-Energy Landscape of Peptide Bond Formation at the Silica–Water Interface. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Flavio Siro Brigiano
- General Chemistry (ALGC), Materials Modeling Group, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Maciej Gierada
- General Chemistry (ALGC), Materials Modeling Group, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155 Kraków, Poland
| | - Frederik Tielens
- General Chemistry (ALGC), Materials Modeling Group, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d’Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, F-75005 Paris, France
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7
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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8
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Derbali I, Thissen R, Alcaraz C, Romanzin C, Zins EL. Study of the Reactivity of CH 3COOH +• and COOH + Ions with CH 3NH 2: Evidence of the Formation of New Peptide-like C(O)-N Bonds. J Phys Chem A 2021; 125:10006-10020. [PMID: 34761946 DOI: 10.1021/acs.jpca.1c06630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acetamide, a small organic compound containing a peptide bond, was observed in the interstellar medium, but reaction pathways leading to the formation of this prebiotic molecule remain uncertain. We investigated the possible formation of a peptide-like bond from the reaction between acetic acid (CH3-COOH) and methylamine (CH3-NH2) that were identified in the interstellar medium. From an experimental point of view, a quadrupole/octopole/quadrupole mass spectrometer was used in combination with synchrotron radiation as a tunable source of VUV photons for monitoring the reactivity of selected ions. Acetic acid was photoionized, and the reactivity of CH3COOH+• as well as COOH+ (produced from either acetic acid or formic acid) ions with neutral CH3NH2 was further studied. With no surprise, charge transfer, proton transfer, and concomitant dissociation processes were found to largely dominate the reactivity. However, a C(O)-N bond formation process between the two reactants was also evidenced, with a weak cross section reaction. From a theoretical point of view, results concerning reactivity and barrier heights were obtained using density functional theory, with the LC-ωPBE range-separated functional in combination with the 6-311++G(d,p) Pople basis set and are in perfect agreement with the experimental data.
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Affiliation(s)
- Imene Derbali
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, Sorbonne Université, CNRS, 75005 Paris, France
| | - Roland Thissen
- Institut de Chimie Physique, UMR 8000, Université Paris-Saclay, CNRS, Bât. 350, 91405 Orsay, France.,SOLEIL Synchrotron, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Christian Alcaraz
- Institut de Chimie Physique, UMR 8000, Université Paris-Saclay, CNRS, Bât. 350, 91405 Orsay, France.,SOLEIL Synchrotron, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Claire Romanzin
- Institut de Chimie Physique, UMR 8000, Université Paris-Saclay, CNRS, Bât. 350, 91405 Orsay, France.,SOLEIL Synchrotron, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Emilie-Laure Zins
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, Sorbonne Université, CNRS, 75005 Paris, France
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9
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Hühn A, Wisser D, Corral Valero M, Roy T, Rivallan M, Catita L, Lesage A, Michel C, Raybaud P. Structural Characterization of Phosphate Species Adsorbed on γ-Alumina by Combining DNP Surface Enhanced NMR Spectroscopy and DFT Calculations. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adrian Hühn
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Lyon F69342, France
| | - Dorothea Wisser
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, Solaize BP 3, 69360, France
| | - Manuel Corral Valero
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, Solaize BP 3, 69360, France
| | - Teddy Roy
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, Solaize BP 3, 69360, France
| | - Mickaël Rivallan
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, Solaize BP 3, 69360, France
| | - Leonor Catita
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, Solaize BP 3, 69360, France
| | - Anne Lesage
- Univ. Lyon, CNRS, ENS Lyon, Université Lyon1, High-Field NMR Center of Lyon, UMR 5082, Villeurbanne F-69100, France
| | - Carine Michel
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Lyon F69342, France
| | - Pascal Raybaud
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, Solaize BP 3, 69360, France
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Lyon F69342, France
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10
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Fontecilla-Camps JC. Primordial bioenergy sources: The two facets of adenosine triphosphate. J Inorg Biochem 2020; 216:111347. [PMID: 33450675 DOI: 10.1016/j.jinorgbio.2020.111347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H+ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.
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11
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Fan J, Kotov NA. Chiral Nanoceramics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1906738. [PMID: 32500963 DOI: 10.1002/adma.201906738] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/12/2019] [Accepted: 02/21/2020] [Indexed: 05/27/2023]
Abstract
The study of different chiral inorganic nanomaterials has been experiencing rapid growth during the past decade, with its primary focus on metals and semiconductors. Ceramic materials can substantially expand the range of mechanical, optical, chemical, electrical, magnetic, and biological properties of chiral nanostructures, further stimulating theoretical, synthetic, and applied research in this area. An ever-expanding toolbox of nanoscale engineering and self-organization provides a chirality-based methodology for engineering of hierarchically organized ceramic materials. However, fundamental discoveries and technological translations of chiral nanoceramics have received substantially smaller attention than counterparts from metals and semiconductors. Findings in this research area are scattered over a variety of sources and subfields. Here, the diversity of chemistries, geometries, and properties found in chiral ceramic nanostructures are summarized. They represent a compelling materials platform for realization of chirality transfer through multiple scales that can result in new forms of ceramic materials. Multiscale chiral geometries and the structural versatility of nanoceramics are complemented by their high chiroptical activity, enantioselectivity, catalytic activity, and biocompatibility. Future development in this field is likely to encompass chiral synthesis, biomedical applications, and optical/electronic devices. The implementation of computationally designed chiral nanoceramics for biomimetic catalysts and quantum information devices may also be expected.
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Affiliation(s)
- Jinchen Fan
- Department of Chemical Engineering and Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Shanghai Key Laboratory of Materials Protection and Advanced Materials in Electric Power, College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai, 200090, China
| | - Nicholas A Kotov
- Department of Chemical Engineering and Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
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12
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Huber MC, Schreiber A, Schiller SM. Minimalist Protocell Design: A Molecular System Based Solely on Proteins that Form Dynamic Vesicular Membranes Embedding Enzymatic Functions. Chembiochem 2019; 20:2618-2632. [PMID: 31183952 DOI: 10.1002/cbic.201900283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Life in its molecular context is characterized by the challenge of orchestrating structure, energy and information processes through compartmentalization and chemical transformations amenable to mimicry of protocell models. Here we present an alternative protocell model incorporating dynamic membranes based on amphiphilic elastin-like proteins (ELPs) rather than phospholipids. For the first time we demonstrate the feasibility of combining vesicular membrane formation and biocatalytic activity with molecular entities of a single class: proteins. The presented self-assembled protein-membrane-based compartments (PMBCs) accommodate either an anabolic reaction, based on free DNA ligase as an example of information transformation processes, or a catabolic process. We present a catabolic process based on a single molecular entity combining an amphiphilic protein with tobacco etch virus (TEV) protease as part of the enclosure of a reaction space and facilitating selective catalytic transformations. Combining compartmentalization and biocatalytic activity by utilizing an amphiphilic molecular building block with and without enzyme functionalization enables new strategies in bottom-up synthetic biology, regenerative medicine, pharmaceutical science and biotechnology.
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Affiliation(s)
- Matthias C Huber
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
| | - Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
| | - Stefan M Schiller
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
- IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany
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13
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Schreiber A, Huber MC, Schiller SM. Prebiotic Protocell Model Based on Dynamic Protein Membranes Accommodating Anabolic Reactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9593-9610. [PMID: 31287709 DOI: 10.1021/acs.langmuir.9b00445] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The nature of the first prebiotic compartments and their possible minimal molecular composition is of great importance in the origin of life scenarios. Current protocell model membranes are proposed to be lipid-based. This paradigm has several shortcomings such as limited membrane stability of monoacyl lipid-based membranes (e.g., fatty acids), missing pathways to synthesize protocell membrane components (e.g., phospholipids) under early earth conditions, and the requirement for different classes of molecules for the formation of compartments and the catalysis of reactions. Amino acids on the other hand are known to arise and persist with remarkable abundance under early earth conditions since the fundamental Miller-Urey experiments. They were also postulated early to form protocellular structures, for example, proteinoid capsules. Here, we present a protocell model constituted by membranes assembled from amphiphilic proteins based on prebiotic amino acids. Self-assembled dynamic protein membrane-based compartments (PMBCs) are impressively stable and compatible with prevalent cellular membrane constituents forming protein-only or protein-lipid hybrid membranes. They can embed processes essential for extant living cells, such as enclosure of molecules, membrane fusion, phase separation, and complex biosynthetic elements from modern cells demonstrating "upward" compatibility. Our findings suggest that prebiotic PMBCs represent a new type of protocell as a possible ancestor of current lipid-based cells. The presented prebiotic PMBC model can be used to design artificial cells, important for the study of structural, catalytic, and evolutionary pathways related to the emergence of life.
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Affiliation(s)
- Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA) , Albert-Ludwigs-Universität Freiburg , 7 Habsburgerstrasse 49 , D-79104 Freiburg , Germany
- Faculty of Biology , University of Freiburg , Schänzlestrasse 1 , D-79104 Freiburg , Germany
| | - Matthias C Huber
- Zentrum für Biosystemanalyse (ZBSA) , Albert-Ludwigs-Universität Freiburg , 7 Habsburgerstrasse 49 , D-79104 Freiburg , Germany
- Faculty of Biology , University of Freiburg , Schänzlestrasse 1 , D-79104 Freiburg , Germany
| | - Stefan M Schiller
- Zentrum für Biosystemanalyse (ZBSA) , Albert-Ludwigs-Universität Freiburg , 7 Habsburgerstrasse 49 , D-79104 Freiburg , Germany
- Faculty of Biology , University of Freiburg , Schänzlestrasse 1 , D-79104 Freiburg , Germany
- BIOSS Centre for Biological Signalling Studies , University of Freiburg , Schänzlestrasse 18 , D-79104 Freiburg , Germany
- IMTEK Department of Microsystems Engineering , University of Freiburg , Georges-Köhler-Allee 103 , D-79110 Freiburg , Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies , University of Freiburg , Georges-Köhler-Allee 105 , D-79110 Freiburg , Germany
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14
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Freza S. Water-assisted peptide bond formation between two double amino acid molecules in the gas phase. J Mol Model 2019; 25:184. [PMID: 31175466 DOI: 10.1007/s00894-019-4081-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/28/2019] [Indexed: 11/27/2022]
Abstract
The gas phase mechanism of the peptide bond formation between two double amino acid (DAA) molecules described by the (NH2)2C(COOH)2 formula is investigated in the presence of a water molecule. Formations of trans and cis DAA-DAA dipeptide products along both concerted and stepwise mechanisms have been studied at the CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ level. The results indicate that the activation energy barriers estimated for the water-assisted mechanisms are significantly reduced in comparison to the corresponding uncatalyzed reactions. The trans DAA-DAA isomer is expected to dominate in the final product due to its larger stability compared to the cis DAA-DAA product.
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Affiliation(s)
- Sylwia Freza
- Laboratory of Quantum Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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15
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Westall F, Hickman-Lewis K, Hinman N, Gautret P, Campbell KA, Bréhéret JG, Foucher F, Hubert A, Sorieul S, Dass AV, Kee TP, Georgelin T, Brack A. A Hydrothermal-Sedimentary Context for the Origin of Life. ASTROBIOLOGY 2018; 18:259-293. [PMID: 29489386 PMCID: PMC5867533 DOI: 10.1089/ast.2017.1680] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/07/2017] [Indexed: 05/02/2023]
Abstract
Critical to the origin of life are the ingredients of life, of course, but also the physical and chemical conditions in which prebiotic chemical reactions can take place. These factors place constraints on the types of Hadean environment in which life could have emerged. Many locations, ranging from hydrothermal vents and pumice rafts, through volcanic-hosted splash pools to continental springs and rivers, have been proposed for the emergence of life on Earth, each with respective advantages and certain disadvantages. However, there is another, hitherto unrecognized environment that, on the Hadean Earth (4.5-4.0 Ga), would have been more important than any other in terms of spatial and temporal scale: the sedimentary layer between oceanic crust and seawater. Using as an example sediments from the 3.5-3.33 Ga Barberton Greenstone Belt, South Africa, analogous at least on a local scale to those of the Hadean eon, we document constant permeation of the porous, carbonaceous, and reactive sedimentary layer by hydrothermal fluids emanating from the crust. This partially UV-protected, subaqueous sedimentary environment, characterized by physical and chemical gradients, represented a widespread system of miniature chemical reactors in which the production and complexification of prebiotic molecules could have led to the origin of life. Key Words: Origin of life-Hadean environment-Mineral surface reactions-Hydrothermal fluids-Archean volcanic sediments. Astrobiology 18, 259-293.
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Affiliation(s)
- F Westall
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - K Hickman-Lewis
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
- 2 Dipartmento di Scienze biologiche, geologiche e ambientale, Università di Bologna , Bologna, Italy
| | - N Hinman
- 3 Geosciences, University of Montana , Missoula, Montana, USA
| | - P Gautret
- 4 University of Orléans , ISTO, UMR 7327, Orléans, France, and CNRS, ISTO, UMR 7327, Orléans, France, and BRGM, ISTO, UMR 7327, Orléans, France
| | - K A Campbell
- 5 School of Environment, The University of Auckland , Auckland, New Zealand
| | - J G Bréhéret
- 6 GéoHydrosytèmes Continentaux, Faculté des Sciences et Techniques, Université François-Rabelais de Tours , Tours, France
| | - F Foucher
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - A Hubert
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - S Sorieul
- 7 University of Bordeaux , CNRS, IN2P3, CENBG, UMR5797, Gradignan, France
| | - A V Dass
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - T P Kee
- 8 School of Chemistry, University of Leeds , Leeds, UK
| | - T Georgelin
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
- 9 Sorbonne Universités , UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, Paris, France
| | - A Brack
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
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Dalai P, Pleyer HL, Strasdeit H, Fox S. The Influence of Mineral Matrices on the Thermal Behavior of Glycine. ORIGINS LIFE EVOL B 2017; 47:427-452. [PMID: 27757771 DOI: 10.1007/s11084-016-9523-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 08/27/2016] [Indexed: 10/20/2022]
Abstract
On the Hadean-Early Archean Earth, the first islands must have provided hot and dry environments for abiotically formed organic molecules. The heat sources, mainly volcanism and meteorite impacts, were also available on Mars during the Noachian period. In recent work simulating this scenario, we have shown that neat glycine forms a black, sparingly water-soluble polymer ("thermomelanoid") when dry-heated at 200 °C under pure nitrogen. The present study explores whether relevant minerals and mineral mixtures can change this thermal behavior. Most experiments were conducted at 200 or 250 °C for 2 or 7 days. The mineral matrices used were phyllosilicates (Ca-montmorillonites SAz-1 and STx-1, Na-montmorillonite SAz-1-Na, nontronite NAu-1, kaolinite KGa-1), salts (NaCl, NaCl-KCl, CaCl2, artificial sea salt, gypsum, magnesite), picritic basalt, and three Martian regolith simulants (P-MRS, S-MRS, JSC Mars-1A). The main analytical method employed was high-performance liquid chromatography (HPLC). Glycine intercalated in SAz-1 and SAz-1-Na was well protected against thermomelanoid formation and sublimation at 200 °C: after 2 days, 95 and 79 %, respectively, had either survived unaltered or been transformed into the cyclic dipeptide (DKP) and linear peptides up to Gly6. The glycine survival rate followed the order SAz-1 > SAz-1-Na > STx-1 ≈ NAu-1 > KGa-1. Very good protection was also provided by artificial sea salt (84 % unaltered glycine after 200 °C for 7 days). P-MRS promoted the condensation up to Gly6, consistent with its high phyllosilicate content. The remaining matrices were less effective in preserving glycine as such or as peptides.
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Affiliation(s)
- Punam Dalai
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Hannes Lukas Pleyer
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Henry Strasdeit
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
| | - Stefan Fox
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
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17
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Chemical Transformations in Proto-Cytoplasmic Media. Phosphorus Coupling in the Silica Hydrogel Phase. Life (Basel) 2017; 7:life7040045. [PMID: 29156594 PMCID: PMC5745558 DOI: 10.3390/life7040045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/12/2017] [Accepted: 10/27/2017] [Indexed: 01/03/2023] Open
Abstract
It has been proposed that prebiotic chemical studies on the emergence of primitive life would be most relevant when performed in a hydrogel, rather than an aqueous, environment. In this paper we describe the ambient temperature coupling of phosphorus oxyacids [Pi] mediated by Fe(II) under aerobic conditions within a silica hydrogel (SHG) environment. We have chosen to examine SHGs as they have considerable geological precedence as key phases in silicification en route to rock formation. Following a description of the preparation and characterization studies on our SHG formulations, coupling experiments between Pi species are described across multiple permutations of (i) Pi compound; (ii) gel formulation; (iii) metal salt additive; and (iv) pH-modifying agent. The results suggest that successful Pi coupling, indicated by observation of pyrophosphate [PPi(V)] via 31P-NMR spectroscopy, takes place when the following components are present: (i) a mixture of mixture of Pi(III) and Pi(V) or pure PPi(III– V); (ii) Fe(II); (iii) acetic or formic acid (not hydrochloric acid); (iv) aerobic conditions or the presence of H2O2 as an oxidant; and (v) the presence of a gel system. On the basis of these, and aqueous control reactions, we suggest mechanistic possibilities.
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18
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Heredia A, Colín-García M, Puig TPI, Alba-Aldave L, Meléndez A, Cruz-Castañeda JA, Basiuk VA, Ramos-Bernal S, Mendoza AN. Computer simulation and experimental self-assembly of irradiated glycine amino acid under magnetic fields: Its possible significance in prebiotic chemistry. Biosystems 2017; 162:66-74. [PMID: 28851657 DOI: 10.1016/j.biosystems.2017.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/18/2017] [Accepted: 08/21/2017] [Indexed: 10/19/2022]
Abstract
Ionizing radiation may have played a relevant role in chemical reactions for prebiotic biomolecule formation on ancient Earth. Environmental conditions such as the presence of water and magnetic fields were possibly relevant in the formation of organic compounds such as amino acids. ATR-FTIR, Raman, EPR and X-ray spectroscopies provide valuable information about molecular organization of different glycine polymorphs under static magnetic fields. γ-glycine polymorph formation increases in irradiated samples interacting with static magnetic fields. The increase in γ-glycine polymorph agrees with the computer simulations. The AM1 semi-empirical simulations show a change in the catalyst behavior and dipole moment values in α and γ-glycine interaction with the static magnetic field. The simulated crystal lattice energy in α-glycine is also affected by the free radicals under the magnetic field, which decreases its stability. Therefore, solid α and γ-glycine containing free radicals under static magnetic fields might have affected the prebiotic scenario on ancient Earth by causing the oligomerization of glycine in prebiotic reactions.
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Affiliation(s)
- Alejandro Heredia
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico.
| | - María Colín-García
- Instituto de Geología, Universidad Nacional Autónoma de México, Instituto de Geología, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico
| | - Teresa Pi I Puig
- Instituto de Geología, Universidad Nacional Autónoma de México, Instituto de Geología, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico
| | - Leticia Alba-Aldave
- Instituto de Geología, Universidad Nacional Autónoma de México, Instituto de Geología, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico
| | - Adriana Meléndez
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico; Posgrado en Ciencias Químicas, Universidad Nacional Autónoma de México, Mexico
| | - Jorge A Cruz-Castañeda
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico; Posgrado en Ciencias Químicas, Universidad Nacional Autónoma de México, Mexico
| | - Vladimir A Basiuk
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico
| | - Sergio Ramos-Bernal
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico
| | - Alicia Negrón Mendoza
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico
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19
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Kitadai N, Oonishi H, Umemoto K, Usui T, Fukushi K, Nakashima S. Glycine Polymerization on Oxide Minerals. ORIGINS LIFE EVOL B 2017; 47:123-143. [PMID: 27473494 DOI: 10.1007/s11084-016-9516-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 11/24/2022]
Abstract
It has long been suggested that mineral surfaces played an important role in peptide bond formation on the primitive Earth. However, it remains unclear which mineral species was key to the prebiotic processes. This is because great discrepancies exist among the reported catalytic efficiencies of minerals for amino acid polymerizations, owing to mutually different experimental conditions. This study examined polymerization of glycine (Gly) on nine oxide minerals (amorphous silica, quartz, α-alumina and γ-alumina, anatase, rutile, hematite, magnetite, and forsterite) using identical preparation, heating, and analytical procedures. Results showed that a rutile surface is the most effective site for Gly polymerization in terms of both amounts and lengths of Gly polymers synthesized. The catalytic efficiency decreased as rutile > anatase > γ-alumina > forsterite > α- alumina > magnetite > hematite > quartz > amorphous silica. Based on reported molecular-level information for adsorption of Gly on these minerals, polymerization activation was inferred to have arisen from deprotonation of the NH3+ group of adsorbed Gly to the nucleophilic NH2 group, and from withdrawal of electron density from the carboxyl carbon to the surface metal ions. The orientation of adsorbed Gly on minerals is also a factor influencing the Gly reactivity. The examination of Gly-mineral interactions under identical experimental conditions has enabled the direct comparison of various minerals' catalytic efficiencies and has made discussion of polymerization mechanisms and their relative influences possible Further systematic investigations using the approach reported herein (which are expected to be fruitful) combined with future microscopic surface analyses will elucidate the role of minerals in the process of abiotic peptide bond formation.
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Affiliation(s)
- Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Hiroyuki Oonishi
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Koichiro Umemoto
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tomohiro Usui
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Keisuke Fukushi
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Satoru Nakashima
- Department of Earth and Space Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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20
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Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702633] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Akouche M, Jaber M, Maurel MC, Lambert JF, Georgelin T. Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017; 56:7920-7923. [PMID: 28558156 DOI: 10.1002/anie.201702633] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/15/2017] [Indexed: 11/07/2022]
Abstract
In this contribution, we report the formation under prebiotic conditions of phosphoribosyl pyrophosphate (PRPP) as a molecular precursor in the one-pot synthesis of a canonical nucleotide, namely adenosine monophosphate (AMP) from its building blocks (KH2 PO4 or Pi , adenine, and d-ribose), on a fumed silica surface. The on-the-rocks approach has been successfully applied to the simultaneous phosphorylation and glycosylation of ribose. The one-pot formation mechanism of AMP involves a two-step pathway via an activated intermediate, namely PRPP, obtained by multiple ribose phosphorylations upon mild thermal activation.
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Affiliation(s)
- Mariame Akouche
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Maguy Jaber
- Sorbonne Universités, UPMC Paris06, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, 75005, Paris, France
| | | | - Jean-Francois Lambert
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Thomas Georgelin
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
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22
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Fuchida S, Naraoka H, Masuda H. Formation of Diastereoisomeric Piperazine-2,5-dione from DL-Alanine in the Presence of Olivine and Water. ORIGINS LIFE EVOL B 2017; 47:83-92. [PMID: 27072833 DOI: 10.1007/s11084-016-9500-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
Abstract
DL-Alanine (Ala) was heated with/without powdered olivine and water at 120 °C for 8 days to investigate the formation of the diastereoisomers of piperazine-2,5-dione (diketopiperazine, DKP). When only DL-Ala was heated with a small amount of water, 3.0 % of DL-Ala changed to cis- and trans-DKP after 8 days. DKPs were not detected after heating when no water was added. The presence of a small amount of water is important factor controlling peptide production rates under thermal conditions. When DL-Ala was heated with olivine powder for 8 days, the yields of cis- and trans-DKP were 6.8 and 4.9 %, respectively. The high yield of cis-DKP compared with trans-DKP was attributed to greater thermal stability of cis-DKP. After heating for 8 days, the diastereoisomeric excess of cis-DKP without olivine was 7.3 %, whereas a much higher value of 16.3 % was obtained in the presence of olivine. Taken together, these results show that olivine is not only an efficient catalyst for the formation of DKPs but that it also play a significant role in determining the diastereoisomer selectivity of these cyclic dipeptides.
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Affiliation(s)
- Shigeshi Fuchida
- Department of Geoscience, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan.
- Marine Environment Section, Center for Regional Environmental Research, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.
| | - Hiroshi Naraoka
- Department of Earth and Planetary Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Harue Masuda
- Department of Geoscience, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
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23
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Iron(III) Oxide Nanoparticles as Catalysts for the Formation of Linear Glycine Peptides. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601296] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Akouche M, Jaber M, Zins EL, Maurel MC, Lambert JF, Georgelin T. Thermal Behavior of d-Ribose Adsorbed on Silica: Effect of Inorganic Salt Coadsorption and Significance for Prebiotic Chemistry. Chemistry 2016; 22:15834-15846. [PMID: 27624284 DOI: 10.1002/chem.201601418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 12/13/2022]
Abstract
Understanding ribose reactivity is a crucial step in the "RNA world" scenario because this molecule is a component of all extant nucleotides that make up RNA. In solution, ribose is unstable and susceptible to thermal destruction. We examined how ribose behaves upon thermal activation when adsorbed on silica, either alone or with the coadsorption of inorganic salts (MgCl2 , CaCl2 , SrCl2 , CuCl2 , FeCl2 , FeCl3 , ZnCl2 ). A combination of 13 C NMR, in situ IR, and TGA analyses revealed a variety of phenomena. When adsorbed alone, ribose remains stable up to 150 °C, at which point ring opening is observed, together with minor oxidation to a lactone. All the metal salts studied showed specific interactions with ribose after dehydration, resulting in the formation of polydentate metal ion complexes. Anomeric equilibria were affected, generally favoring ribofuranoses. Zn2+ stabilized ribose up to higher temperatures than bare silica (180 to 200 °C). Most other cations had an adverse effect on ribose stability, with ring opening already upon drying at 70 °C. In addition, alkaline earth cations catalyzed the dehydration of ribose to furfural and, to variable degrees, its further decarbonylation to furan. Transition-metal ions with open d-shells took part in redox reactions with ribose, either as reagents or as catalysts. These results allow the likelihood of prebiotic chemistry scenarios to be evaluated, and may also be of interest for the valorization of biomass-derived carbohydrates by heterogeneous catalysis.
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Affiliation(s)
- Mariame Akouche
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 7197, LRS case courrier 178, UPMC 4 Pl. Jussieu, 75252, PARIS CEDEX 05, France
| | - Maguy Jaber
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 8220, LAMS, case courrier 225, UPMC 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Emilie-Laure Zins
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 8233, MONARIS, case courrier, UPMC 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | | | - Jean-Francois Lambert
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 7197, LRS case courrier 178, UPMC 4 Pl. Jussieu, 75252, PARIS CEDEX 05, France.
| | - Thomas Georgelin
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 7197, LRS case courrier 178, UPMC 4 Pl. Jussieu, 75252, PARIS CEDEX 05, France.
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25
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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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26
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27
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Fox S, Dalai P, Lambert JF, Strasdeit H. Hypercondensation of an amino acid: synthesis and characterization of a black glycine polymer. Chemistry 2015; 21:8897-904. [PMID: 25933438 DOI: 10.1002/chem.201500820] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Indexed: 12/24/2022]
Abstract
A granular material was obtained by thermal polymerization of glycine at 200 °C. It has been named "thermomelanoid" because of its strikingly deep-black color. The polymerization process is mainly a dehydration condensation leading to conventional amide bonds, and also CC double bonds that are formed from CO and CH2 groups ("hypercondensation"). Spectroscopic data, in particular from (13) C and (15) N solid-state cross-polarization magic angle spinning (CP-MAS) NMR spectra, suggest that the black color is due to (cross-)conjugated CC, CO, and NH groups. Small glycine peptides, especially triglycine, appear to be key intermediates in the formation of the thermomelanoid. This has been concluded by comparing the thermal behavior of glyn homopeptides (n=2-6) and glycine. The glycine polymerization was accompanied by the formation of small amounts of byproducts. Notably, a few percent of alanine and aspartic acid could be detected in the polymer. By using (13) C-labeled glycine, it was shown that these two amino acids formed through a common pathway, namely CαCα bond formation between glycine molecules. The thermomelanoid is hydrolyzed by strong acids and bases at room temperature, forming brown solutions.
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Affiliation(s)
- Stefan Fox
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Punam Dalai
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75252 Paris Cedex 05 (France)
| | - Henry Strasdeit
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany).
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28
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Block KA, Trusiak A, Katz A, Alimova A, Wei H, Gottlieb P, Steiner JC. Exfoliation and intercalation of montmorillonite by small peptides. APPLIED CLAY SCIENCE 2015; 107:173-181. [PMID: 25825549 PMCID: PMC4375959 DOI: 10.1016/j.clay.2015.01.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding structural changes in clay minerals induced by complexation with organic matter is relevant to soil science and agricultural applications. In this study, the effect of peptide storage in montmorillonite and the thermal stability of peptide-clay complexes was examined through characterization by X-ray diffraction (XRD), electron microscopy, UV absorption, and thermogravimetric analysis (TGA). XRD analysis of small peptide-montmorillonite clay complexes produced profiles consisting of reflections associated with the smectite 001 reflection and related peaks similar to that produced by a mixed layer clay mineral structure. Shifts in higher order diffraction maxima were attributed to disorder caused by the intercalation with the peptides. Increasing peptide concentrations resulted in greater shifts towards smaller 2θ from 6.37° (1.39 nm) to 5.45° (1.62 nm) as the interlayer space expanded. The expansion was accompanied by broadening of the 001 reflection (FWHM increases from 0.51 to 1.22° 2θ). The XRD line broadening was interpreted as caused by poorer crystallinity resulting from intercalation and tactoid exfoliation. SEM images revealed montmorillonite platelets with upwardly rolled edges that tend toward cylindrical structures with the production of tubules. High-resolution TEM images revealed bending of montmorillonite platelets, confirming exfoliation. The distribution of basal spacings in the micrographs was determined from the spatial frequencies obtained by Fourier analysis of density profiles. The distribution indicated the presence of discrete coherent crystallite domains. XRD and TGA results indicated that higher peptide concentrations resulted in a greater fraction of intercalated peptides and that surface adsorption of peptides mediated intercalation. Therefore, higher peptide concentration led to more stable organoclay complexes. However, UV absorption and TGA found that peptide adsorption onto montmorillonite had a finite limit at approximately 16% by weight.
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Affiliation(s)
- Karin A. Block
- Department of Earth and Atmospheric Sciences, The City College of New York, 160 Convent Ave, New York, NY, 10031
| | - Adrianna Trusiak
- Department of Earth and Atmospheric Sciences, The City College of New York, 160 Convent Ave, New York, NY, 10031
| | - Al Katz
- Department of Physics, The City College of New York, 160 Convent Ave, New York, NY, 10031
| | - Alexandra Alimova
- Sophie Davis School of Biomedical Education, The City College of New York, 160 Convent Ave, New York, NY, 10031
| | - Hui Wei
- Sophie Davis School of Biomedical Education, The City College of New York, 160 Convent Ave, New York, NY, 10031
| | - Paul Gottlieb
- Sophie Davis School of Biomedical Education, The City College of New York, 160 Convent Ave, New York, NY, 10031
| | - Jeffrey C. Steiner
- Department of Earth and Atmospheric Sciences, The City College of New York, 160 Convent Ave, New York, NY, 10031
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Feuillie C, Sverjensky DA, Hazen RM. Attachment of ribonucleotides on α-alumina as a function of pH, ionic strength, and surface loading. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:240-248. [PMID: 25469864 DOI: 10.1021/la504034k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The interactions between nucleic acids and mineral surfaces have been the focus of many studies in environmental sciences, in biomedicine, as well as in origin of life studies for the prebiotic formation of biopolymers. However, few studies have focused on a wide range of environmental conditions and the likely modes of attachment. Here we investigated the adsorption of ribonucleotides onto α-alumina surfaces over a wide range of pH, ionic strength, and ligand-to-solid ratio, by both an experimental and a theoretical approach. The adsorption of ribonucleotides is strongly affected by pH, with a maximum adsorption at pH values around 5. Alumina adsorbs high amounts of nucleotides >2 μmol/m(2). We used the extended triple-layer model (ETLM) to predict the speciation of the surface complexes formed as well as the stoichiometry and equilibrium constants. We propose the formation of two surface species: a monodentate inner-sphere complex, dominant at pH <7, and a bidentate outer-sphere complex, dominant at higher pH. Both complexes would involve interactions between the negatively charged phosphate group and the positively charged surface of alumina. Our results provide a better understanding of how nucleic acids attach to mineral surfaces under varying environmental conditions. Moreover, the predicted configuration of nucleotide surface species, bound via the phosphate group, could have implications for the abiotic formation of nucleic acids in the context of the origin of life.
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Affiliation(s)
- Cécile Feuillie
- Geophysical Laboratory, Carnegie Institution of Washington , 5251 Broad Branch Road North West, Washington, DC 20015, United States
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