1
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Moreno A, Bonduelle C. New Insights on the Chemical Origin of Life: The Role of Aqueous Polymerization of N-carboxyanhydrides (NCA). Chempluschem 2024; 89:e202300492. [PMID: 38264807 DOI: 10.1002/cplu.202300492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/29/2023] [Indexed: 01/25/2024]
Abstract
At the origin, the emergence of proteins was based on crucial prebiotic stages in which simple amino acids-based building blocks spontaneously evolved from the prebiotic soup into random proto-polymers called protoproteins. Despite advances in modern peptide synthesis, these prebiotic chemical routes to protoproteins remain puzzling. We discuss in this perspective how polymer science and systems chemistry are reaching a point of convergence in which simple monomers called N-carboxyanhydrides would be able to form such protoproteins via the emergence of a protometabolic cycle involving aqueous polymerization and featuring macromolecular Darwinism behavior.
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Affiliation(s)
- Abel Moreno
- Instituto de Quimica, UNAM, Ciudad Universitaria, Coyoacan, 04510, Mexico DF
| | - Colin Bonduelle
- CNRS, Bordeaux INP, LCPO UMR5629, Univ. Bordeaux, 33600, Pessac, France
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2
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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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3
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Zhang L, Ying J. Amino acid analogues provide multiple plausible pathways to prebiotic peptides. J R Soc Interface 2024; 21:20240014. [PMID: 38715323 PMCID: PMC11077012 DOI: 10.1098/rsif.2024.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Prebiotic peptide synthesis has consistently been a prominent topic within the field of the origin of life. While research predominantly centres on the 20 classical amino acids, the synthesis process encounters significant thermodynamic barriers. Consequently, amino acid analogues are being explored as potential building blocks for prebiotic peptide synthesis. This review delves into the pathway of polypeptide formation, identifying specific amino acid analogues that might have existed on early Earth, potentially participating in peptide synthesis and chemical evolution. Moreover, considering the complexity and variability of the environment on early Earth, we propose the plausibility of coevolution between amino acids and their analogues.
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Affiliation(s)
- Li Zhang
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
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4
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Fairchild J, Islam S, Singh J, Bučar DK, Powner MW. Prebiotically plausible chemoselective pantetheine synthesis in water. Science 2024; 383:911-918. [PMID: 38386754 DOI: 10.1126/science.adk4432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Coenzyme A (CoA) is essential to all life on Earth, and its functional subunit, pantetheine, is important in many origin-of-life scenarios, but how pantetheine emerged on the early Earth remains a mystery. Earlier attempts to selectively synthesize pantetheine failed, leading to suggestions that "simpler" thiols must have preceded pantetheine at the origin of life. In this work, we report high-yielding and selective prebiotic syntheses of pantetheine in water. Chemoselective multicomponent aldol, iminolactone, and aminonitrile reactions delivered spontaneous differentiation of pantoic acid and proteinogenic amino acid syntheses, as well as the dihydroxyl, gem-dimethyl, and β-alanine-amide moieties of pantetheine in dilute water. Our results are consistent with a role for canonical pantetheine at the outset of life on Earth.
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Affiliation(s)
- Jasper Fairchild
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Saidul Islam
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Department of Chemistry and Centre for the Physical Science of Life, King's College London, London SE1 1DB, UK
| | - Jyoti Singh
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | | | - Matthew W Powner
- Department of Chemistry, University College London, London WC1H 0AJ, UK
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5
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Dai K, Pol MD, Saile L, Sharma A, Liu B, Thomann R, Trefs JL, Qiu D, Moser S, Wiesler S, Balzer BN, Hugel T, Jessen HJ, Pappas CG. Spontaneous and Selective Peptide Elongation in Water Driven by Aminoacyl Phosphate Esters and Phase Changes. J Am Chem Soc 2023; 145:26086-26094. [PMID: 37992133 DOI: 10.1021/jacs.3c07918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Nature chose phosphates to activate amino acids, where reactive intermediates and complex machinery drive the construction of polyamides. Outside of biology, the pathways and mechanisms that allow spontaneous and selective peptide elongation in aqueous abiotic systems remain unclear. Herein we work to uncover those pathways by following the systems chemistry of aminoacyl phosphate esters, synthetic counterparts of aminoacyl adenylates. The phosphate esters act as solubility tags, making hydrophobic amino acids and their oligomers soluble in water and enabling selective elongation and different pathways to emerge. Thus, oligomers up to dodecamers were synthesized in one flask and on the minute time scale, where consecutive additions activated autonomous phase changes. Depending on the pathway, the resulting phases initially carry nonpolar peptides and amphiphilic oligomers containing phosphate esters. During elongation and phosphate release, shorter oligomers dominate in solution, while the aggregated phase favors the presence of longer oligomers due to their self-assembly propensity. Furthermore we demonstrated that the solution phases can be isolated and act as a new environment for continuous elongation, by adding various phosphate esters. These findings suggest that the systems chemistry of aminoacyl phosphate esters can activate a selection mechanism for peptide bond formation by merging aqueous synthesis and self-assembly.
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Affiliation(s)
- Kun Dai
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Mahesh D Pol
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Lenard Saile
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Arti Sharma
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bin Liu
- College of Materials and Chemical Engineering, China Three Gorges University, Yichang, Hubei 443002, China
| | - Ralf Thomann
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
| | - Johanna L Trefs
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Sandra Moser
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Stefan Wiesler
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Bizan N Balzer
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Thorsten Hugel
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Henning J Jessen
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Charalampos G Pappas
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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6
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Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett 2023; 597:2879-2896. [PMID: 37884438 DOI: 10.1002/1873-3468.14766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.
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Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Sarah Fisher
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Cesar Menor-Salvan
- Department of Biología de Sistemas, Universidad de Alcalá, Madrid, Spain
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
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7
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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8
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Harold SE, Warf SL, Shields GC. Prebiotic dimer and trimer peptide formation in gas-phase atmospheric nanoclusters of water. Phys Chem Chem Phys 2023; 25:28517-28532. [PMID: 37847315 DOI: 10.1039/d3cp02915h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Insight into the origin of prebiotic molecules is key to our understanding of how living systems evolved into the complex network of biological processes on Earth. By modelling diglycine and triglycine peptide formation in the prebiotic atmosphere, we provide a plausible pathway for peptide growth. By examining different transition states (TSs), we conclude that the formation of diglycine and triglycine in atmospheric nanoclusters of water in the prebiotic atmosphere kinetically favors peptide growth by an N-to-C synthesis of glycines through a trans conformation. Addition of water stabilizes the TS structures and lowers the Gibbs free activation energies. At temperatures that model the prebiotic atmosphere, the free energies of activation with a six water nanocluster as part of the TS are predicted to be 16 kcal mol-1 relative to the prereactive complex. Examination of the trans vs. cis six water transition states reveals that a homodromic water network that maximizes the acceptor/donor nature of the six waters is responsible for enhanced kinetic favorability of the trans N-to-C pathway. Compared to the non-hydrated trans TS, the trans six-water TS accelerates the reaction of diglycine and glycine to form triglycine by 13 orders of magnitude at 217 K. Nature uses the trans N-to-C pathway to synthesize proteins in the ribosome, and we note the similarities in hydrogen bond stabilization between the transition state for peptide synthesis in the ribosome and the transition states formed in nanoclusters of water in the same pathway. These results support the hypothesis that small oligomers formed in the prebiotic atmosphere and rained onto earth's surface.
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Affiliation(s)
- Shannon E Harold
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - Skyler L Warf
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
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9
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Shalayel I, Leqraa N, Blandin V, Vallée Y. Straightforward Creation of Possibly Prebiotic Complex Mixtures of Thiol-Rich Peptides. Life (Basel) 2023; 13:life13040983. [PMID: 37109512 PMCID: PMC10145665 DOI: 10.3390/life13040983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/07/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
At the origin of life, extremely diverse mixtures of oligomers and polymers could be obtained from relatively simple molecular bricks. Here, we present an example of the polymerization of two amidonitriles derived from cysteine, Cys-Ala-CN and Cys-Met-CN. The thiol function in a molecule adds onto the nitrile group of another one, allowing efficient condensation reactions and making available an extensive range of polymers containing amide bonds and/or five-membered heterocycles, namely thiazolines. Macrocycles were also identified, the biggest one containing sixteen residues (cyclo(Cys-Met)8). MALDI-TOF mass spectrometry was used to identify all the present species. What these examples show is that complex mixtures are likely to have formed on the primitive Earth and that, ultimately, the selection that must have followed may have been an even more crucial step towards life than the synthesis of the pre-biological species themselves.
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Affiliation(s)
- Ibrahim Shalayel
- Université Grenoble Alpes, TIMC-IMAG, CNRS, F-38000 Grenoble, France
| | - Naoual Leqraa
- Université Grenoble Alpes, DCM, CNRS, F-38000 Grenoble, France
| | | | - Yannick Vallée
- Université Grenoble Alpes, DCM, CNRS, F-38000 Grenoble, France
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10
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Boigenzahn H, Yin J. Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments. ORIGINS LIFE EVOL B 2022; 52:249-261. [DOI: 10.1007/s11084-022-09634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022]
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11
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Abstract
α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic ChemistryLeibniz University HannoverSchneiderberg 1B30167HannoverGermany
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12
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Cuccu F, De Luca L, Delogu F, Colacino E, Solin N, Mocci R, Porcheddu A. Mechanochemistry: New Tools to Navigate the Uncharted Territory of "Impossible" Reactions. CHEMSUSCHEM 2022; 15:e202200362. [PMID: 35867602 PMCID: PMC9542358 DOI: 10.1002/cssc.202200362] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/01/2022] [Indexed: 05/10/2023]
Abstract
Mechanochemical transformations have made chemists enter unknown territories, forcing a different chemistry perspective. While questioning or revisiting familiar concepts belonging to solution chemistry, mechanochemistry has broken new ground, especially in the panorama of organic synthesis. Not only does it foster new "thinking outside the box", but it also has opened new reaction paths, allowing to overcome the weaknesses of traditional chemistry exactly where the use of well-established solution-based methodologies rules out progress. In this Review, the reader is introduced to an intriguing research subject not yet fully explored and waiting for improved understanding. Indeed, the study is mainly focused on organic transformations that, although impossible in solution, become possible under mechanochemical processing conditions, simultaneously entailing innovation and expanding the chemical space.
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Affiliation(s)
- Federico Cuccu
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042, Monserrato, Cagliari, Italy
| | - Lidia De Luca
- Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, via Vienna 2, 07100, Sassari, Italy
| | - Francesco Delogu
- Dipartimento di Ingegneria Meccanica, Chimica e dei Materiali, Università degli Studi di Cagliari, Via Marengo 2, 09123, Cagliari, Italy
| | | | - Niclas Solin
- Department of Physics, Chemistry and Biology (IFM), Electronic and Photonic Materials (EFM), Building Fysikhuset, Room M319, Campus, Valla, Sweden
| | - Rita Mocci
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042, Monserrato, Cagliari, Italy
| | - Andrea Porcheddu
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042, Monserrato, Cagliari, Italy
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13
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Bready CJ, Vanovac S, Odbadrakh TT, Shields GC. Amino Acids Compete with Ammonia in Sulfuric Acid-Based Atmospheric Aerosol Prenucleation: The Case of Glycine and Serine. J Phys Chem A 2022; 126:5195-5206. [PMID: 35896016 DOI: 10.1021/acs.jpca.2c03539] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a computational investigation of the sulfuric acid, glycine, serine, ammonia, and water system to understand if this system can form prenucleation clusters, which are precursors to larger aerosols in the atmosphere. We have performed a comprehensive configurational search of all possible clusters in this system, starting with the four different monomers and zero to five waters. Accurate Gibbs free energies of formation have been calculated with the DLPNO-CCSD(T)/complete basis set (CBS) method on ωb97xd/6-31++G** geometries. For the dry dimers of sulfuric acid, the weakest base, serine, is found to form the most stable complex, which is a consequence of the strong di-ionic complex formed between the bisulfate ion and the protonated serine cation. For the dry dimers without sulfuric acid, the glycine-serine complex is more stable than the glycine-ammonia or serine-ammonia complexes, stemming from the detailed structure and not related to base strength. For the larger complexes, sulfuric acid deprotonates and the proton is shifted to glycine, serine, or ammonia. The two amino acids and ammonia are almost interchangeable and there is no easy way to predict which molecule will be protonated without the calculated results. Assuming reasonable starting concentrations and a closed system of sulfuric acid, glycine, serine, ammonia, and five waters, we predict the concentrations of all possible complexes at two temperatures spanning the troposphere. The most negative ΔG° values are a function of the detailed molecular interactions of these clusters. These details are more important than the base strength of ammonia, glycine, and serine.
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Affiliation(s)
- Conor J Bready
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sara Vanovac
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Tuguldur T Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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14
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Janzen E, Shen Y, Vázquez-Salazar A, Liu Z, Blanco C, Kenchel J, Chen IA. Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes. Nat Commun 2022; 13:3631. [PMID: 35752631 PMCID: PMC9233669 DOI: 10.1038/s41467-022-31387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 06/16/2022] [Indexed: 11/24/2022] Open
Abstract
Systems of catalytic RNAs presumably gave rise to important evolutionary innovations, such as the genetic code. Such systems may exhibit particular tolerance to errors (error minimization) as well as coding specificity. While often assumed to result from natural selection, error minimization may instead be an emergent by-product. In an RNA world, a system of self-aminoacylating ribozymes could enforce the mapping of amino acids to anticodons. We measured the activity of thousands of ribozyme mutants on alternative substrates (activated analogs for tryptophan, phenylalanine, leucine, isoleucine, valine, and methionine). Related ribozymes exhibited shared preferences for substrates, indicating that adoption of additional amino acids by existing ribozymes would itself lead to error minimization. Furthermore, ribozyme activity was positively correlated with specificity, indicating that selection for increased activity would also lead to increased specificity. These results demonstrate that by-products of ribozyme evolution could lead to adaptive value in specificity and error tolerance.
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Affiliation(s)
- Evan Janzen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Yuning Shen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Celia Blanco
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Josh Kenchel
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Irene A Chen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA. .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA. .,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
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15
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Abstract
The RNA world concept1 is one of the most fundamental pillars of the origin of life theory2–4. It predicts that life evolved from increasingly complex self-replicating RNA molecules1,2,4. The question of how this RNA world then advanced to the next stage, in which proteins became the catalysts of life and RNA reduced its function predominantly to information storage, is one of the most mysterious chicken-and-egg conundrums in evolution3–5. Here we show that non-canonical RNA bases, which are found today in transfer and ribosomal RNAs6,7, and which are considered to be relics of the RNA world8–12, are able to establish peptide synthesis directly on RNA. The discovered chemistry creates complex peptide-decorated RNA chimeric molecules, which suggests the early existence of an RNA–peptide world13 from which ribosomal peptide synthesis14 may have emerged15,16. The ability to grow peptides on RNA with the help of non-canonical vestige nucleosides offers the possibility of an early co-evolution of covalently connected RNAs and peptides13,17,18, which then could have dissociated at a higher level of sophistication to create the dualistic nucleic acid–protein world that is the hallmark of all life on Earth. Peptide synthesis can take place directly on RNA, which suggests how a nucleic acid–protein world might have originated on early Earth.
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16
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Angle KJ, Nowak CM, Davasam A, Dommer AC, Wauer NA, Amaro RE, Grassian VH. Amino Acids Are Driven to the Interface by Salts and Acidic Environments. J Phys Chem Lett 2022; 13:2824-2829. [PMID: 35324217 DOI: 10.1021/acs.jpclett.2c00231] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amino acids (AAs), the building blocks of proteins, are enriched by several orders of magnitude in sea spray aerosols compared to ocean waters. This suggests that AAs may reside at the air-water interface and be highly surface active. Using surface tension measurements, infrared reflection-absorption spectroscopy, and molecular dynamics simulations, we show that AAs are surface active and that salts and low-pH environments are drivers of surface activity. At typical sea spray salt concentrations and pH values, we determine that the surface coverage of hydrophobic AAs increases by approximately 1 order of magnitude. Additionally, divalent cations such as Ca2+ and Mg2+ can further increase AA surface propensity, particularly at neutral pH. Overall, these results indicate that AAs are likely to be found at increased concentrations at the surface of sea spray aerosols, where they can impact the cloud activation properties of the aerosol and enhance peptide formation under certain conditions.
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Affiliation(s)
- Kyle J Angle
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Christopher M Nowak
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Aakash Davasam
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Abigail C Dommer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Nicholas A Wauer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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17
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New Signatures of Bio-Molecular Complexity in the Hypervelocity Impact Ejecta of Icy Moon Analogues. Life (Basel) 2022; 12:life12040508. [PMID: 35454999 PMCID: PMC9026792 DOI: 10.3390/life12040508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 01/05/2023] Open
Abstract
Impact delivery of prebiotic compounds to the early Earth from an impacting comet is considered to be one of the possible ways by which prebiotic molecules arrived on the Earth. Given the ubiquity of impact features observed on all planetary bodies, bolide impacts may be a common source of organics on other planetary bodies both in our own and other solar systems. Biomolecules such as amino acids have been detected on comets and are known to be synthesized due to impact-induced shock processing. Here we report the results of a set of hypervelocity impact experiments where we shocked icy mixtures of amino acids mimicking the icy surface of planetary bodies with high-speed projectiles using a two-stage light gas gun and analyzed the ejecta material after impact. Electron microscopic observations of the ejecta have shown the presence of macroscale structures with long polypeptide chains revealed from LCMS analysis. These results suggest a pathway in which impact on cometary ices containing building blocks of life can lead to the synthesis of material architectures that could have played a role in the emergence of life on the Earth and which may be applied to other planetary bodies as well.
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18
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Dong Y, Zhang S, Zhao L. Unraveling the Structural Development of
Peptide‐Coordinated Iron‐Sulfur
Clusters: Prebiotic Evolution and Biosynthetic Strategies. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yijun Dong
- School of Life Sciences, Tsinghua University Beijing 100084 China
| | - Siqi Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
| | - Liang Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
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19
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Experimental identification of aminomethanol (NH 2CH 2OH)-the key intermediate in the Strecker Synthesis. Nat Commun 2022; 13:375. [PMID: 35046418 PMCID: PMC8770675 DOI: 10.1038/s41467-022-27963-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022] Open
Abstract
The Strecker Synthesis of (a)chiral α-amino acids from simple organic compounds, such as ammonia (NH3), aldehydes (RCHO), and hydrogen cyanide (HCN) has been recognized as a viable route to amino acids on primordial earth. However, preparation and isolation of the simplest hemiaminal intermediate – the aminomethanol (NH2CH2OH)– formed in the Strecker Synthesis to even the simplest amino acid glycine (H2NCH2COOH) has been elusive. Here, we report the identification of aminomethanol prepared in low-temperature methylamine (CH3NH2) – oxygen (O2) ices upon exposure to energetic electrons. Isomer-selective photoionization time-of-flight mass spectrometry (PI-ReTOF-MS) facilitated the gas phase detection of aminomethanol during the temperature program desorption (TPD) phase of the reaction products. The preparation and observation of the key transient aminomethanol changes our perception of the synthetic pathways to amino acids and the unexpected kinetic stability in extreme environments. The Strecker synthesis is considered a viable route to amino acids formation on the primordial Earth. Here the authors succeed in observing its elusive intermediate aminomethanol, formed by insertion of an electronically excited oxygen atom in methylamine and stabilized by an icy matrix, using isomer-selective photoionization time-of-flight mass spectrometry during thermal desorption of the ice mixture.
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20
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Chiarinelli J, Barreiro-Lage D, Bolognesi P, RICHTER R, Zettergren H, Stockett MH, Díaz-Tendero S, Avaldi L. Electron and ion spectroscopy of the cyclo-alanine-alanine dipeptide. Phys Chem Chem Phys 2022; 24:5855-5867. [DOI: 10.1039/d1cp05811h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The VUV photoionisation and photofragmentation of cyclo-alanine-alanine (cAA) has been studiedin a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron-photoion coincidence (PEPICO) measurements, which enable a control...
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21
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From amino acid mixtures to peptides in liquid sulphur dioxide on early Earth. Nat Commun 2021; 12:7182. [PMID: 34893619 PMCID: PMC8664857 DOI: 10.1038/s41467-021-27527-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
The formation of peptide bonds is one of the most important biochemical reaction steps. Without the development of structurally and catalytically active polymers, there would be no life on our planet. However, the formation of large, complex oligomer systems is prevented by the high thermodynamic barrier of peptide condensation in aqueous solution. Liquid sulphur dioxide proves to be a superior alternative for copper-catalyzed peptide condensations. Compared to water, amino acids are activated in sulphur dioxide, leading to the incorporation of all 20 proteinogenic amino acids into proteins. Strikingly, even extremely low initial reactant concentrations of only 50 mM are sufficient for extensive peptide formation, yielding up to 2.9% of dialanine in 7 days. The reactions carried out at room temperature and the successful use of the Hadean mineral covellite (CuS) as a catalyst, suggest a volcanic environment for the formation of the peptide world on early Earth. Peptide bond formation is one of the key biochemical reactions needed for the formation of life, but is thermodynamically unfavoured in water. Here, the authors report on the possibility of complex oligomer formation in liquid sulphur dioxide which may have existed on early Earth at the emergence of life.
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22
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Molteni E, Mattioli G, Alippi P, Avaldi L, Bolognesi P, Carlini L, Vismarra F, Wu Y, Varillas RB, Nisoli M, Singh M, Valadan M, Altucci C, Richter R, Sangalli D. A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase. Phys Chem Chem Phys 2021; 23:26793-26805. [PMID: 34816853 DOI: 10.1039/d1cp04050b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.
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Affiliation(s)
- Elena Molteni
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
| | - Giuseppe Mattioli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Alippi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Bolognesi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Laura Carlini
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Federico Vismarra
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Yingxuan Wu
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | | | - Mauro Nisoli
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Manjot Singh
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy
| | - Mohammadhassan Valadan
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Robert Richter
- Sincrotrone Trieste, Area Science Park, Basovizza, Trieste, Italy
| | - Davide Sangalli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
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23
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Barreiro-Lage D, Bolognesi P, Chiarinelli J, Richter R, Zettergren H, Stockett MH, Carlini L, Diaz-Tendero S, Avaldi L. "Smart Decomposition" of Cyclic Alanine-Alanine Dipeptide by VUV Radiation: A Seed for the Synthesis of Biologically Relevant Species. J Phys Chem Lett 2021; 12:7379-7386. [PMID: 34324354 DOI: 10.1021/acs.jpclett.1c01788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A combined experimental and theoretical study shows how the interaction of VUV radiation with cyclo-(alanine-alanine), one of the 2,5-diketopiperazines (DKPs), produces reactive oxazolidinone intermediates. The theoretical simulations reveal that the interaction of these intermediates with other neutral and charged fragments, released in the molecular decomposition, leads either to the reconstruction of the cyclic dipeptide or to the formation of longer linear peptide chains. These results may explain how DKPs could have, on one hand, survived hostile chemical environments and, on the other, provided the seed for amino acid polymerization. Shedding light on the mechanisms of production of such prebiotic building blocks is of paramount importance to understanding the abiotic synthesis of relevant biologically active compounds.
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Affiliation(s)
- Darío Barreiro-Lage
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Paola Bolognesi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Jacopo Chiarinelli
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Robert Richter
- Elettra Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | | | - Mark H Stockett
- Department of Physics, Stockholm University, Se-10691 Stockholm, Sweden
| | - Laura Carlini
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
| | - Sergio Diaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Science (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lorenzo Avaldi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo, Italy
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24
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Ma JT, Wang LS, Chai Z, Chen XF, Tang BC, Chen XL, He C, Wu YD, Wu AX. Access to 2-arylquinazolines via catabolism/reconstruction of amino acids with the insertion of dimethyl sulfoxide. Chem Commun (Camb) 2021; 57:5414-5417. [PMID: 33949486 DOI: 10.1039/d1cc00623a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quinazoline skeletons are synthesized by amino acid catabolism/reconstruction combined with the insertion/cyclization of dimethyl sulfoxide for the first time. The amino acid acts as a carbon and nitrogen source through HI-mediated catabolism and is then reconstructed using aromatic amines and dimethyl sulfoxide (DMSO) as a one-carbon synthon. This protocol is of great significance for the further study of the conversion of amino acids.
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Affiliation(s)
- Jin-Tian Ma
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Li-Sheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Zhi Chai
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Xin-Feng Chen
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Bo-Cheng Tang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Xiang-Long Chen
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Cai He
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Yan-Dong Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - An-Xin Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
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25
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Ying J, Ding R, Liu Y, Zhao Y. Prebiotic Chemistry in Aqueous Environment: A Review of Peptide Synthesis and Its Relationship with Genetic Code. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianxi Ying
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Yan Liu
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
| | - Yufen Zhao
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
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26
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Guo Y, Ying J, Sun D, Zhang Y, Zheng M, Ding R, Liu Y, Zhao Y. Cyclic Dipeptides Formation From Linear Dipeptides Under Potentially Prebiotic Earth Conditions. Front Chem 2021; 9:675821. [PMID: 34262893 PMCID: PMC8273163 DOI: 10.3389/fchem.2021.675821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/14/2021] [Indexed: 11/30/2022] Open
Abstract
Cyclic dipeptides (DKPs) are peptide precursors and chiral catalysts in the prebiotic process. This study reports proline-containing DKPs that were spontaneously obtained from linear dipeptides under an aqueous solution. Significantly, the yields of DKPs were affected by the sequence of linear dipeptides and whether the reaction contains trimetaphosphate. These findings provide the possibility that DKPs might play a key role in the origin of life.
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Affiliation(s)
- Yeting Guo
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Yumeng Zhang
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Minyang Zheng
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Yan Liu
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China.,Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.,Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
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27
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation*. Angew Chem Int Ed Engl 2021; 60:12727-12731. [PMID: 33769680 DOI: 10.1002/anie.202100806] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. Prebiotically plausible pathways to peptides from inactivated amino acids are still unclear as most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Now, a combination of prebiotically plausible minerals and mechanochemical activation enables the oligomerization of glycine at ambient temperature in the absence of water. Raising the reaction temperature increases the degree of oligomerization concomitantly with the formation of a commonly unwanted cyclic glycine dimer (DKP). However, DKP is a productive intermediate in the mechanochemical oligomerization of glycine. The findings of this research show that mechanochemical peptide bond formation is a dynamic process that provides alternative routes towards oligopeptides and establishes new synthetic approaches for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Nikola Cindro
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - José G Hernández
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
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28
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Nikola Cindro
- Department of Organic Chemistry Faculty of Science University of Zagreb Horvatovac 102a 10000 Zagreb Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - José G. Hernández
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
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29
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Affiliation(s)
- Dragana Despotovic
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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30
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Sibilska-Kaminski IK, Yin J. Toward Molecular Cooperation by De Novo Peptides. ORIGINS LIFE EVOL B 2021; 51:71-82. [PMID: 33566281 PMCID: PMC8212187 DOI: 10.1007/s11084-021-09603-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
Theoretical models of the chemical origins of life depend on self-replication or autocatalysis, processes that arise from molecular interactions, recruitment, and cooperation. Such models often lack details about the molecules and reactions involved, giving little guidance to those seeking to detect signs of interaction, recruitment, or cooperation in the laboratory. Here, we develop minimal mathematical models of reactions involving specific chemical entities: amino acids and their condensation reactions to form de novo peptides. Reactions between two amino acids form a dipeptide product, which enriches linearly in time; subsequent recruitment of such products to form longer peptides exhibit super-linear growth. Such recruitment can be reciprocated: a peptide contributes to and benefits from the formation of one or more other peptides; in this manner, peptides can cooperate and thereby exhibit autocatalytic or exponential growth. We have started to test these predictions by quantitative analysis of de novo peptide synthesis conducted by wet-dry cycling of a five-amino acid mixture over 21 days. Using high-performance liquid chromatography, we tracked abundance changes for >60 unique peptide species. Some species were highly transient, with the emergence of up to 17 new species and the extinction of nine species between samplings, while other species persisted across many cycles. Of the persisting species, most exhibited super-linear growth, a sign of recruitment anticipated by our models. This work shows how mathematical modeling and quantitative analysis of kinetic data can guide the search for prebiotic chemistries that have the potential to cooperate and replicate.
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Affiliation(s)
- Izabela K Sibilska-Kaminski
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery , University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery , University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA.
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31
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Bonfio C. The curious case of peptide-coordinated iron-sulfur clusters: prebiotic and biomimetic insights. Dalton Trans 2021; 50:801-807. [PMID: 33351009 DOI: 10.1039/d0dt03947k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-sulfur clusters are among the most ancient biological cofactors and are thought to have had an ancient role in mediating the chemical reactions that led to life. Two different, yet complementary approaches, based on bioinorganic chemistry and prebiotic chemistry, have already provided important clues for the formation and activity of biomimetic iron-sulfur analogues in aqueous solution. This frontier article discusses the efforts spent in the last 50 years in the context of peptide-coordinated iron-sulfur clusters, with a particular emphasis on insightful contributions from recent prebiotic chemistry research.
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Affiliation(s)
- Claudia Bonfio
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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32
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Wu LF, Liu Z, Sutherland JD. pH-Dependent peptide bond formation by the selective coupling of α-amino acids in water. Chem Commun (Camb) 2021; 57:73-76. [PMID: 33242043 PMCID: PMC7808311 DOI: 10.1039/d0cc06042a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Selective peptide elongation chemistry by coupling α-amino acids via mixed anhydride intermediates in water.
A novel mechanism enabling selective peptide elongation by coupling α-amino acids over other potentially competing prebiotic amines under acidic aqueous condition is suggested. It proceeds via the generation of a carboxylic acid anhydride intermediate with subsequent intramolecular formation of the amide bond.
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Affiliation(s)
- Long-Fei Wu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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33
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Affiliation(s)
- Kamila B Muchowska
- University of Strasbourg, Centre National de la Recherche Scientifique, Institut de Science et d'Ingénierie Supramoléculaires, 67000 Strasbourg, France
| | - Joseph Moran
- University of Strasbourg, Centre National de la Recherche Scientifique, Institut de Science et d'Ingénierie Supramoléculaires, 67000 Strasbourg, France.
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34
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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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35
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Steele BA, Goldman N, Kuo IFW, Kroonblawd MP. Mechanochemical synthesis of glycine oligomers in a virtual rotational diamond anvil cell. Chem Sci 2020; 11:7760-7771. [PMID: 34123069 PMCID: PMC8163322 DOI: 10.1039/d0sc00755b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/11/2020] [Indexed: 01/18/2023] Open
Abstract
Mechanochemistry of glycine under compression and shear at room temperature is predicted using quantum-based molecular dynamics (QMD) and a simulation design based on rotational diamond anvil cell (RDAC) experiments. Ensembles of high throughput semiempirical density functional tight binding (DFTB) simulations are used to identify chemical trends and bounds for glycine chemistry during rapid shear under compressive loads of up to 15.6 GPa. Significant chemistry is found to occur during compressive shear above 10 GPa. Recovered products consist of small molecules such as water, structural analogs to glycine, heterocyclic molecules, large oligomers, and polypeptides including the simplest polypeptide glycylglycine at up to 4% mass fraction. The population and size of oligomers generally increases with pressure. A number of oligomeric polypeptide precursors and intermediates are also identified that consist of two or three glycine monomers linked together through C-C, C-N, and/or C-O bridges. Even larger oligomers also form that contain peptide C-N bonds and exhibit branched structures. Many of the product molecules exhibit one or more chiral centers. Our simulations demonstrate that athermal mechanical compressive shearing of glycine is a plausible prebiotic route to forming polypeptides.
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Affiliation(s)
- Brad A Steele
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - I-Feng W Kuo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
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36
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Usabiaga I, Camiruaga A, Calabrese C, Veloso A, D'mello VC, Wategaonkar S, Fernández JA. Exploration of the theobromine-water dimer: comparison with DNA microhydration. Phys Chem Chem Phys 2020; 22:15759-15768. [PMID: 32627788 DOI: 10.1039/d0cp02397c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding the molecular basis of the appearance of life on Earth is an exciting research field. Many factors may have influenced the election of the molecules used by living beings and evolution may have modified those original compounds. In an attempt to understand the role played by intermolecular interactions in the election of CGAT as the alphabet of life, we present here a thorough experimental and computational study on the interaction of theobromine with water. Theobromine is a xanthine derivative, structurally related to the nucleobases, and also present in many living beings. The experimental results demonstrate that the most stable isomer of theobromine-water was formed and detected in supersonic expansions. This isomer very well resembles the structure of the dimers between nucleobases and water, offering similar values of binding energy. A comparison between the results obtained for theobromine-water with those reported in the literature for monohydrates of nucleobases is also offered.
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Affiliation(s)
- Imanol Usabiaga
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48940, Leioa, Spain.
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do Nascimento Vieira A, Kleinermanns K, Martin WF, Preiner M. The ambivalent role of water at the origins of life. FEBS Lett 2020; 594:2717-2733. [PMID: 32416624 DOI: 10.1002/1873-3468.13815] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022]
Abstract
Life as we know it would not exist without water. However, water molecules not only serve as a solvent and reactant but can also promote hydrolysis, which counteracts the formation of essential organic molecules. This conundrum constitutes one of the central issues in origin of life. Hydrolysis is an important part of energy metabolism for all living organisms but only because, inside cells, it is a controlled reaction. How could hydrolysis have been regulated under prebiotic settings? Lower water activities possibly provide an answer: geochemical sites with less free and more bound water can supply the necessary conditions for protometabolic reactions. Such conditions occur in serpentinising systems, hydrothermal sites that synthesise hydrogen gas via rock-water interactions. Here, we summarise the parallels between biotic and abiotic means of controlling hydrolysis in order to narrow the gap between biochemical and geochemical reactions and briefly outline how hydrolysis could even have played a constructive role at the origin of molecular self-organisation.
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Affiliation(s)
| | | | - William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, Germany
| | - Martina Preiner
- Institute for Molecular Evolution, University of Düsseldorf, Germany
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38
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The kinetics and mechanisms of reactions in the flow systems glycine-sodium trimetaphosphate-imidazoles: the crucial role of imidazoles in prebiotic peptide syntheses. Amino Acids 2020; 52:811-821. [PMID: 32372392 DOI: 10.1007/s00726-020-02854-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/30/2020] [Indexed: 12/12/2022]
Abstract
The kinetics of oligopeptides formation in the flow systems glycine-sodium trimetaphosphate-imidazole/N-methylimidazole at thermocyclic regime has been investigated by HPLC and 31P NMR methods in the ranges of temperature from 45 to 90 °C and pH from 8.5 to 11.5. Detailed reaction mechanisms have been proposed and justified by quantum chemical calculations using DFT method at the CAM-B3LYP/TZVP level with accounting solvent effect by the C-PCM model. A new imidazole catalysis mechanism by which imidazole reacts with cyclic N,O-phosphoryl glycine giving N-imidazolyl-O-glycyl phosphate as a key intermediate was proposed and validated. It is emphasized that while in the absence of imidazoles, prebiotic activation of amino acids occurs at the N-terminus, in the presence of imidazoles it shifts to the O-terminus. This means that in the peptide elongation N-imidazolyl-O-aminoacyl phosphates play in prebiotic systems the outstanding role similar to that of aminoacyl adenylates formed at the ATP and aminoacyl-tRNA synthetases presence in biosystems. The new crucial role of imidazoles in prebiotic evolution has been noticed. The systems used and modes of their conversion can be good models for prebiotic peptide syntheses in a flow thermocyclic regime.
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39
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Gale AG, Odbadrakh TT, Ball BT, Shields GC. Water-Mediated Peptide Bond Formation in the Gas Phase: A Model Prebiotic Reaction. J Phys Chem A 2020; 124:4150-4159. [DOI: 10.1021/acs.jpca.0c02906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ariel G. Gale
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Tuguldur T. Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Benjamin T. Ball
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - George C. Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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40
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Kleinsmann AJ, Nachtsheim BJ. A minimalistic hydrolase based on co-assembled cyclic dipeptides. Org Biomol Chem 2020; 18:102-107. [PMID: 31799587 DOI: 10.1039/c9ob02198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.
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Affiliation(s)
- Alexander J Kleinsmann
- Institut für Organische Chemie Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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41
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Jash B, Richert C. Templates direct the sequence-specific anchoring of the C-terminus of peptido RNAs. Chem Sci 2020; 11:3487-3494. [PMID: 34109020 PMCID: PMC8152794 DOI: 10.1039/c9sc05958j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/28/2020] [Indexed: 02/02/2023] Open
Abstract
When amino acids and ribonucleotides react in aqueous condensation buffer, they form peptido RNA with a phosphoramidate bond between the N-terminus of the peptide and the 5'-terminal phosphate of a ribonucleotide. If peptido RNA was the product of spontaneous reactions of amino acids and nucleotides, there must have been a transition to peptidyl tRNAs, where the C-terminus of the peptide is ester-linked to the 2',3'-terminus of an oligonucleotide. Here we report how short peptido RNAs react with the 3'-terminus of oligodeoxynucleotides, templated by RNA strands. In our model system, the rate and yield of the anchoring of the C-terminus of the dipeptido dinucleotides to an amino group was found to depend on the sequence of the peptide, the 5'-terminal nucleotide of the dinucleotide and the RNA template. In all cases tested, highest yields were found for dinucleotides hybridizing next to the primer terminus. For the most reactive species, GlyPro-AA, anchoring yields ranged from 8-99%, depending on the template. When LeuLeu-AA, PhePhe-AA and GlyGly-AA were allowed to compete for anchoring on 3'-UUC-5' as templating sequence, they gave a product ratio of 1 : 2 : 6, and this selectivity was almost independent of the terminal base of the primer. Our results show the control that a simple duplex context has over the covalent anchoring of peptido RNAs at a position known from peptidyl tRNAs. Processes of this type may have bridged the gap between untemplated condensation reactions and the highly specific processes of ribosomal protein synthesis.
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Affiliation(s)
- Biswarup Jash
- Institute of Organic Chemistry, University of Stuttgart 70569 Stuttgart Germany +49 711 608 64321 +49 711 608 64311
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart 70569 Stuttgart Germany +49 711 608 64321 +49 711 608 64311
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42
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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43
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Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry. Life (Basel) 2020; 10:life10010006. [PMID: 31963928 PMCID: PMC7175156 DOI: 10.3390/life10010006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/22/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.
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44
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Sun Y, Frenkel-Pinter M, Liotta CL, Grover MA. The pH dependent mechanisms of non-enzymatic peptide bond cleavage reactions. Phys Chem Chem Phys 2020; 22:107-113. [DOI: 10.1039/c9cp05240b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide cleavage can occur through scission and backbiting, depending on the pH.
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Affiliation(s)
- Yi Sun
- School of Chemical & Biomolecular Engineering
- Georgia Institute of Technology
- Atlanta
- USA
- NSF/NASA Center for Chemical Evolution
| | - Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry & Biochemistry
- Georgia Institute of Technology
- Atlanta
| | - Charles L. Liotta
- School of Chemical & Biomolecular Engineering
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry & Biochemistry
| | - Martha A. Grover
- School of Chemical & Biomolecular Engineering
- Georgia Institute of Technology
- Atlanta
- USA
- NSF/NASA Center for Chemical Evolution
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45
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Abstract
Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.
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46
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Calles J, Justice I, Brinkley D, Garcia A, Endy D. Fail-safe genetic codes designed to intrinsically contain engineered organisms. Nucleic Acids Res 2019; 47:10439-10451. [PMID: 31511890 PMCID: PMC6821295 DOI: 10.1093/nar/gkz745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022] Open
Abstract
One challenge in engineering organisms is taking responsibility for their behavior over many generations. Spontaneous mutations arising before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such that point mutations in protein-coding sequences are selected against. Synthetic genetic systems so-encoded should fail more safely in response to most spontaneous mutations. We designed fail-safe codes and simulated their expected effects on the evolution of so-encoded proteins. We predict fail-safe codes supporting expression of 20 or 15 amino acids could slow protein evolution to ∼30% or 0% the rate of standard-encoded proteins, respectively. We also designed quadruplet-codon codes that should ensure all single point mutations in protein-coding sequences are selected against while maintaining expression of 20 or more amino acids. We demonstrate experimentally that a reduced set of 21 tRNAs is capable of expressing a protein encoded by only 20 sense codons, whereas a standard 64-codon encoding is not expressed. Our work suggests that biological systems using rationally depleted but otherwise natural translation systems should evolve more slowly and that such hypoevolvable organisms may be less likely to invade new niches or outcompete native populations.
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Affiliation(s)
- Jonathan Calles
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Isaac Justice
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Detravious Brinkley
- Department of Mathematics and Computer Science, Claflin University, Orangeburg, SC 29115, USA
| | - Alexa Garcia
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Drew Endy
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
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47
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Li Z, Li L, McKenna KR, Schmidt M, Pollet P, Gelbaum L, Fernández FM, Krishnamurthy R, Liotta CL. The Oligomerization of Glucose Under Plausible Prebiotic Conditions. ORIGINS LIFE EVOL B 2019; 49:225-240. [PMID: 31792744 DOI: 10.1007/s11084-019-09588-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023]
Abstract
The prebiotic origin of polysaccharides, the largest class of biopolymers by mass in extant biology, has seldom been investigated experimentally. Herein, we report on the acid-catalyzed condensation of aqueous solutions of glucose, a model monosaccharide, under plausible prebiotic conditions employing a wet-dry (night-day) protocol with 0.01 M HCl at 50 °C. This protocol leads to the formation of oligosaccharides containing up to eight monomeric units identified by high resolution mass spectrometry. The regio- and stereochemistry of the oligomeric acetal linkages, as well as the quantitative analysis of glucose conversion, are elucidated by combining 1H, 13C and 2D NMR spectroscopy. Ten out of eleven possible acetal linkages, including α- and β- anomers, have been identified with the α- and β- 1,6-acetals being the dominant linkages observed. In addition, the acid-catalyzed oligomerization of several glucose disaccharides such as cellobiose, maltose, and gentiobiose are presented along with an accompanying comparison with the corresponding oligomerization of glucose.
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Affiliation(s)
- Zhao Li
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA
| | - Li Li
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA
| | - Kristin R McKenna
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA
| | - Merranda Schmidt
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA
- Department of Chemistry, Ripon College, Ripon, WI, 54971, USA
| | - Pamela Pollet
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA
| | - Leslie Gelbaum
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA.
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA.
| | - Charles L Liotta
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- NSF/NASA Center for Chemical Evolution, Alexandria, GA, 30332, USA.
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48
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Huang H, Yang S, Liu Y, Yang Y, Li H, McLeod JA, Ding G, Huang J, Kang Z. Photocatalytic Polymerization from Amino Acid to Protein by Carbon Dots at Room Temperature. ACS APPLIED BIO MATERIALS 2019; 2:5144-5153. [DOI: 10.1021/acsabm.9b00805] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Siwei Yang
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | | | - Yucheng Yang
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | | | | | - Guqiao Ding
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
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49
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Campbell TD, Febrian R, McCarthy JT, Kleinschmidt HE, Forsythe JG, Bracher PJ. Prebiotic condensation through wet-dry cycling regulated by deliquescence. Nat Commun 2019; 10:4508. [PMID: 31586058 PMCID: PMC6778215 DOI: 10.1038/s41467-019-11834-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
Wet-dry cycling is widely regarded as a means of driving condensation reactions under prebiotic conditions to generate mixtures of prospective biopolymers. A criticism of this model is its reliance on unpredictable rehydration events, like rainstorms. Here, we report the ability of deliquescent minerals to mediate the oligomerization of glycine during iterative wet-dry cycles. The reaction mixtures evaporate to dryness at high temperatures and spontaneously reacquire water vapor to form aqueous solutions at low temperatures. Deliquescent mixtures can foster yields of oligomerization over ten-fold higher than non-deliquescent controls. The deliquescent mixtures tightly regulate their moisture content, which is crucial, as too little water precludes dissolution of the reactants while too much water favors hydrolysis over condensation. The model also suggests a potential reason why life evolved to favor the enrichment of potassium: so living systems could acquire and retain sufficient water to serve as a solvent for biochemical reactions.
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Affiliation(s)
- Thomas D Campbell
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Rio Febrian
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Jack T McCarthy
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Holly E Kleinschmidt
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Jay G Forsythe
- Department of Chemistry and Biochemistry, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Paul J Bracher
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA.
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50
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Das T, Ghule S, Vanka K. Insights Into the Origin of Life: Did It Begin from HCN and H 2O? ACS CENTRAL SCIENCE 2019; 5:1532-1540. [PMID: 31572780 PMCID: PMC6764159 DOI: 10.1021/acscentsci.9b00520] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 05/14/2023]
Abstract
The seminal Urey-Miller experiments showed that molecules crucial to life such as HCN could have formed in the reducing atmosphere of the Hadean Earth and then dissolved in the oceans. Subsequent proponents of the "RNA World" hypothesis have shown aqueous HCN to be the starting point for the formation of the precursors of RNA and proteins. However, the conditions of early Earth suggest that aqueous HCN would have had to react under a significant number of constraints. Therefore, given the limiting conditions, could RNA and protein precursors still have formed from aqueous HCN? If so, what mechanistic routes would have been followed? The current computational study, with the aid of the ab initio nanoreactor (AINR), a powerful new tool in computational chemistry, addresses these crucial questions. Gratifyingly, not only do the results from the AINR approach show that aqueous HCN could indeed have been the source of RNA and protein precursors, but they also indicate that just the interaction of HCN with water would have sufficed to begin a series of reactions leading to the precursors. The current work therefore provides important missing links in the story of prebiotic chemistry and charts the road from aqueous HCN to the precursors of RNA and proteins.
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Affiliation(s)
- Tamal Das
- Physical and Materials Chemistry Division,
CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha
Road, Pashan, Pune 411008, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
| | - Siddharth Ghule
- Physical and Materials Chemistry Division,
CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha
Road, Pashan, Pune 411008, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
| | - Kumar Vanka
- Physical and Materials Chemistry Division,
CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha
Road, Pashan, Pune 411008, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
- E-mail:
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