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Edri R, Williams LD, Frenkel-Pinter M. From Catalysis of Evolution to Evolution of Catalysis. Acc Chem Res 2024. [PMID: 39373892 DOI: 10.1021/acs.accounts.4c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
ConspectusThe mystery of the origins of life is one of the most difficult yet intriguing challenges to which humanity has grappled. How did biopolymers emerge in the absence of enzymes (evolved biocatalysts), and how did long-lasting chemical evolution find a path to the highly selective complex biology that we observe today? In this paper, we discuss a chemical framework that explores the very roots of catalysis, demonstrating how standard catalytic activity based on chemical and physical principles can evolve into complex machineries. We provide several examples of how prebiotic catalysis by small molecules can be exploited to facilitate polymerization, which in biology has transformed the nature of catalysis. Thus, catalysis evolved, and evolution was catalyzed, during the transformation of prebiotic chemistry to biochemistry. Traditionally, a catalyst is defined as a substance that (i) speeds up a chemical reaction by lowering activation energy through different chemical mechanisms and (ii) is not consumed during the course of the reaction. However, considering prebiotic chemistry, which involved a highly diverse chemical space (i.e., high number of potential reactants and products) and constantly changing environment that lacked highly sophisticated catalytic machinery, we stress here that a more primitive, broader definition should be considered. Here, we consider a catalyst as any chemical species that lowers activation energy. We further discuss various demonstrations of how simple prebiotic molecules such as hydroxy acids and mercaptoacids promote the formation of peptide bonds via energetically favored exchange reactions. Even though the small molecules are partially regenerated and partially retained within the resulting oligomers, these prebiotic catalysts fulfill their primary role. Catalysis by metal ions and in complex chemical mixtures is also highlighted. We underline how chemical evolution is primarily dictated by kinetics rather than thermodynamics and demonstrate a novel concept to support this notion. Moreover, we propose a new perspective on the role of water in prebiotic catalysis. The role of water as simply a "medium" obscures its importance as an active participant in the chemistry of life, specifically as a very efficient catalyst and as a participant in many chemical transformations. Here we highlight the unusual contribution of water to increasing complexification over the course of chemical evolution. We discuss possible pathways by which prebiotic catalysis promoted chemical selection and complexification. Taken together, this Account draws a connection line between prebiotic catalysis and contemporary biocatalysis and demonstrates that the fundamental elements of chemical catalysis are embedded within today's biocatalysts. This Account illustrates how the evolution of catalysis was intertwined with chemical evolution from the very beginning.
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Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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2
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Lévêque P, Queffelec C, Sotin C, Afonso C, Bollengier O, Clouet A, Le Menn E, Marrocchi Y, Schmitz I, Bujoli B. Effect of Nitrogen on the Structure and Composition of Primordial Organic Matter Analogs. ACS EARTH & SPACE CHEMISTRY 2024; 8:1281-1295. [PMID: 39045227 PMCID: PMC11261614 DOI: 10.1021/acsearthspacechem.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 07/25/2024]
Abstract
Organic molecules are ubiquitous in primitive solar system bodies such as comets and asteroids. These primordial organic compounds may have formed in the interstellar medium and in protoplanetary disks (PPDs) before being accreted and further transformed in the parent bodies of meteorites, icy moons, and dwarf planets. The present study describes the composition of primordial organics analogs produced in a laboratory simulator of the PPD (the Nebulotron experiment at the CRPG laboratory) with nitrogen contents varying from N/C < 0.01 to N/C = 0.63. We present the first Fourier transform ion cyclotron resonance mass spectrometry analysis of these analogs. Several thousands of molecules with masses between m/z 100 and 500 are characterized. The mass spectra show a Gaussian shape with maxima around m/z 250. Highly condensed polyaromatic hydrocarbons (PAH) are the most common compounds identified in the samples with lower nitrogen contents. As the amount of nitrogen increases, a dramatic increase of the chemical diversity is observed. Nitrogen-bearing compounds are also dominated by polyaromatic hydrocarbons (PANH) made of 5- and 6-membered rings containing up to four nitrogen atoms, including triazine and pyrazole rings. Such N-rich aromatic species are expected to decompose easily in the presence of water at higher temperatures. Pure carbon molecules are also observed for samples with relatively small fractions of nitrogen. MS peaks compatible with the presence of amino acids and nucleobases, or their isomers, are detected. When comparing these Nebulotron samples with the insoluble fraction of the Paris meteorite organic matter, we observe that the samples with intermediate N/C ratios bracketing that of the Paris insoluble organic matter (IOM) display relative proportions of the CH, CHO, CHN, and CHNO chemical families also bracketing those of the Paris IOM. Our results support that Nebulotron samples are relevant laboratory analogs of primitive chondritic organic matter.
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Affiliation(s)
- Pauline Lévêque
- Nantes
Université, Univ. Angers, Le Mans Université, CNRS,
Laboratoire de Planétologie et Géosciences, LPG UMR
6112, Nantes 44000, France
- CEISAM,
Nantes Université, UMR-CNRS 6230, Nantes F-44000, France
| | | | - Christophe Sotin
- Nantes
Université, Univ. Angers, Le Mans Université, CNRS,
Laboratoire de Planétologie et Géosciences, LPG UMR
6112, Nantes 44000, France
| | - Carlos Afonso
- Normandie
Université, COBRA, UMR 6014, FR 3038, Université de
Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan 76821 Mont-Saint-Aignan Cedex, France
| | - Olivier Bollengier
- Nantes
Université, Univ. Angers, Le Mans Université, CNRS,
Laboratoire de Planétologie et Géosciences, LPG UMR
6112, Nantes 44000, France
| | - Adriana Clouet
- Nantes
Université, Univ. Angers, Le Mans Université, CNRS,
Laboratoire de Planétologie et Géosciences, LPG UMR
6112, Nantes 44000, France
| | - Erwan Le Menn
- Nantes
Université, Univ. Angers, Le Mans Université, CNRS,
Laboratoire de Planétologie et Géosciences, LPG UMR
6112, Nantes 44000, France
| | - Yves Marrocchi
- Centre
de Recherches Pétrographiques et Géochimiques, UMR 7358
CNRS-Université de Lorraine, Vandoeuvre-lès-Nancy F-54501, France
| | - Isabelle Schmitz
- Normandie
Université, COBRA, UMR 6014, FR 3038, Université de
Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan 76821 Mont-Saint-Aignan Cedex, France
| | - Bruno Bujoli
- CEISAM,
Nantes Université, UMR-CNRS 6230, Nantes F-44000, France
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3
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Cohen ZR, Todd ZR, Maibaum L, Catling DC, Black RA. Stabilization of Prebiotic Vesicles by Peptides Depends on Sequence and Chirality: A Mechanism for Selection of Protocell-Associated Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8971-8980. [PMID: 38629792 DOI: 10.1021/acs.langmuir.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Cells require oligonucleotides and polypeptides with specific, homochiral sequences to perform essential functions, but it is unclear how such oligomers were selected from random sequences at the origin of life. Cells were probably preceded by simple compartments such as fatty acid vesicles, and oligomers that increased the stability, growth, or division of vesicles could have thereby increased in frequency. We therefore tested whether prebiotic peptides alter the stability or growth of vesicles composed of a prebiotic fatty acid. We find that three of 15 dipeptides tested reduce salt-induced flocculation of vesicles. All three contain leucine, and increasing their length increases the efficacy. Also, leucine-leucine but not alanine-alanine increases the size of vesicles grown by multiple additions of micelles. In a molecular simulation, leucine-leucine docks to the membrane, with the side chains inserted into the hydrophobic core of the bilayer, while alanine-alanine fails to dock. Finally, the heterochiral forms of leucine-leucine, at a high concentration, rapidly shrink the vesicles and make them leakier and less stable to high pH than the homochiral forms do. Thus, prebiotic peptide-membrane interactions influence the flocculation, growth, size, leakiness, and pH stability of prebiotic vesicles, with differential effects due to sequence, length, and chirality. These differences could lead to a population of vesicles enriched for peptides with beneficial sequence and chirality, beginning selection for the functional oligomers that underpin life.
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Affiliation(s)
- Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R Todd
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David C Catling
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Ishikawa A, Kebukawa Y, Kobayashi K, Yoda I. Gamma-Ray-Induced Amino Acid Formation during Aqueous Alteration in Small Bodies: The Effects of Compositions of Starting Solutions. Life (Basel) 2024; 14:103. [PMID: 38255718 PMCID: PMC10817335 DOI: 10.3390/life14010103] [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: 10/20/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Organic compounds, such as amino acids, are essential for the origin of life, and they may have been delivered to the prebiotic Earth from extra-terrestrial sources, such as carbonaceous chondrites. In the parent bodies of carbonaceous chondrites, the radioactive decays of short-lived radionuclides, such as 26Al, cause the melting of ice, and aqueous alteration occurs in the early stages of solar system formation. Many experimental studies have shown that complex organic matter, including amino acids and high-molecular-weight organic compounds, is produced by such hydrothermal processes. On the other hand, radiation, particularly gamma rays from radionuclides, can contribute to the formation of amino acids from simple molecules such as formaldehyde and ammonia. In this study, we investigated the details of gamma-ray-induced amino acid formation, focusing on the effects of different starting materials on aqueous solutions of formaldehyde, ammonia, methanol, and glycolaldehyde with various compositions, as well as hexamethylenetetramine. Alanine and glycine were the most abundantly formed amino acids after acid hydrolysis of gamma-ray-irradiated products. Amino acid formation increased with increasing gamma-ray irradiation doses. Lower amounts of ammonia relative to formaldehyde produced more amino acids. Glycolaldehyde significantly increased amino acid yields. Our results indicated that glycolaldehyde formation from formaldehyde enhanced by gamma rays is key for the subsequent production of amino acids.
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Affiliation(s)
- Akari Ishikawa
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan (K.K.)
| | - Yoko Kebukawa
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan (K.K.)
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Kensei Kobayashi
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan (K.K.)
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Isao Yoda
- Co60 Irradiation Facility, Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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5
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Li Y, Kurokawa H, Sekine Y, Kebukawa Y, Nakano Y, Kitadai N, Zhang N, Zang X, Ueno Y, Fujimori G, Nakamura R, Fujishima K, Isa J. Aqueous breakdown of aspartate and glutamate to n-ω-amino acids on the parent bodies of carbonaceous chondrites and asteroid Ryugu. SCIENCE ADVANCES 2023; 9:eadh7845. [PMID: 38100590 PMCID: PMC10848742 DOI: 10.1126/sciadv.adh7845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Amino acids in carbonaceous chondrites may have seeded the origin of life on Earth and possibly elsewhere. Recently, the return samples from a C-type asteroid Ryugu were found to contain amino acids with a similar distribution to Ivuna-type CI chondrites, suggesting the potential of amino acid abundances as molecular descriptors of parent body geochemistry. However, the chemical mechanisms responsible for the amino acid distributions remain to be elucidated particularly at low temperatures (<50°C). Here, we report that two representative proteinogenic amino acids, aspartic acid and glutamic acid, decompose to β-alanine and γ-aminobutyric acid, respectively, under simulated geoelectrochemical conditions at 25°C. This low-temperature conversion provides a plausible explanation for the enrichment of these two n-ω-amino acids compared to their precursors in heavily aqueously altered CI chondrites and Ryugu's return samples. The results suggest that these heavily aqueously altered samples originated from the water-rich mantle of their water/rock differentiated parent planetesimals where protein α-amino acids were decomposed.
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Affiliation(s)
- Yamei Li
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroyuki Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Earth Science and Astronomy, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yasuhito Sekine
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Institute of Nature and Environmental Technology, Japan Kanazawa University, Ishikawa, Kanazawa, Kakumachi 920-1192, Japan
- Planetary Plasma and Atmospheric Research Center, Tohoku University, Aramaki-aza-Aoba 6-3, Aoba, Sendai, Miyagi 980-8578, Japan
| | - Yoko Kebukawa
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogayaku, Yokohama 240-8501, Japan
| | - Yuko Nakano
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Norio Kitadai
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Naizhong Zhang
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Xiaofeng Zang
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Gen Fujimori
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogayaku, Yokohama 240-8501, Japan
| | - Ryuhei Nakamura
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa 252-0882, Japan
| | - Junko Isa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Planetary Exploration Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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6
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Sharma A. Sequential Amplification of Amino Acid Enantiomeric Excess by Conglomerate and Racemic Compound: Plausible Prebiotic Route Towards Homochirality. ORIGINS LIFE EVOL B 2023; 53:175-185. [PMID: 37831272 DOI: 10.1007/s11084-023-09642-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Some amino acids can crystallize from aqueous solution both as conglomerates and racemic compounds: under high supersaturation following rapid evaporation, dissolved amino acids draining over porous sand-bars behave like conglomerates whereas in the resulting deeper pool of water, amino acid solution switches to the more common racemic-compound system. We show how the two forms might have sequentially combined under prebiotic conditions to form the basis of homochirality. The paper is a quantitative analysis of enantiomeric excess (EE) this dual behavior of amino acids is capable of producing in tandem: Initial amplification by preferential crystallization (PC) in conglomerate system (CS) followed by further amplification in the racemic compound system (RCS). Using aspartic acid as a model system, ternary phase diagram shows that a minimum supersaturation of 1.65 is required in the CS for the solution-EE to reach its maximum value of 50% at the RCS eutectic point. A relationship is derived for the dependence of this threshold supersaturation on the eutectic solubilities of CS and RCS. For given supersaturation in CS, a relation is also derived for minimum solution-EE that must be produced by PC before CS switches to RCS. Required PC-induced threshold solution-EE of 0.194, 0.070, 0.033 is calculated for supersaturation of 2, 5, 10 respectively in aspartic acid. Switching from CS to RCS further amplifies solution-EE, resulting in an overall growth of aspartic acid solution EE from near-zero in CS to around 50% in RCS.
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Affiliation(s)
- A Sharma
- Department of Physics, Alabama A&M University, Huntsville, AL, 35762, USA.
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7
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [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: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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8
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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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9
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Fox AC, Boettger JD, Berger EL, Burton AS. The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations. Life (Basel) 2023; 13:1796. [PMID: 37763200 PMCID: PMC10532638 DOI: 10.3390/life13091796] [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: 07/18/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated-neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl-amino acid complexes for both the positive-neutral and neutral-neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction.
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Affiliation(s)
- Allison C. Fox
- NASA Postdoctoral Program, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Jason D. Boettger
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, TX 79968, USA;
| | - Eve L. Berger
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
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10
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Gamalero E, Lingua G, Glick BR. Ethylene, ACC, and the Plant Growth-Promoting Enzyme ACC Deaminase. BIOLOGY 2023; 12:1043. [PMID: 37626930 PMCID: PMC10452086 DOI: 10.3390/biology12081043] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023]
Abstract
Here, a brief summary of the biosynthesis of 1-aminocyclopropane-1-carboxylate (ACC) and ethylene in plants, as well as overviews of how ACC and ethylene act as signaling molecules in plants, is presented. Next, how the bacterial enzyme ACC deaminase cleaves plant-produced ACC and thereby decreases or prevents the ethylene or ACC modulation of plant gene expression is considered. A detailed model of ACC deaminase functioning, including the role of indoleacetic acid (IAA), is presented. Given that ACC is a signaling molecule under some circumstances, this suggests that ACC, which appears to have evolved prior to ethylene, may have been a major signaling molecule in primitive plants prior to the evolution of ethylene and ethylene signaling. Due to their involvement in stimulating ethylene production, the role of D-amino acids in plants is then considered. The enzyme D-cysteine desulfhydrase, which is structurally very similar to ACC deaminase, is briefly discussed and the possibility that ACC deaminase arose as a variant of D-cysteine desulfhydrase is suggested.
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Affiliation(s)
- Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
| | - Guido Lingua
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
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11
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Garcia A, Serra C, Remaury QB, Garcia AD, Righezza M, Meinert C, Poinot P, Danger G. Gas chromatography coupled-to Fourier transform orbitrap mass spectrometer for enantioselective amino acid analyses: Application to pre-cometary organic analog. J Chromatogr A 2023; 1704:464118. [PMID: 37315448 DOI: 10.1016/j.chroma.2023.464118] [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: 02/10/2023] [Revised: 05/17/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
Gas chromatography (GC) is a separation technique commonly developed for targeted in situ analyses in planetary space missions. It is coupled with low-resolution mass spectrometry to obtain additional structural information and allow compound identification. However, ground-based analyses of extraterrestrial samples have shown the presence of large molecular diversities. For future targeted in situ analyses, it is therefore essential to develop new technologies. High resolution mass spectrometry (HRMS) is currently being spatialized using FT-orbitrap-MS technology. In this contribution, the coupling of gas chromatography with FT-orbitrap-MS is studied for targeted amino acid analyses. The method for enantioselective separation of amino acids was optimized on a standard mixture comprising 47 amino acid enantiomers. Different ionization modes were optimized, chemical ionization with three different reactive gasses (NH3, CH4 and NH3/CH4) and electron impact ionization at different electron energies. Single ion and full scan monitoring modes were compared, and detection and quantification limits were estimated by internal calibration under the optimized conditions. The GC-FT-orbitrap-MS demonstrated its ability to separate 47 amino acid enantiomers with minimal co-elution. Furthermore, due to the high mass resolution and accuracy of FT-orbitrap-MS, with mass extraction, the S/N is close to zero, allowing average LOD values of 10⁻7 M, orders of magnitude lower than conventional GC-MS techniques. Finally, these conditions were tested for enantioselective analysis of amino acids on an analog of a pre-cometary organic material showing similarities to that of extraterrestrial materials.
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Affiliation(s)
- A Garcia
- Aix-Marseille Université, CNRS, Institut Origines, Laboratoire PIIM, Marseille, France
| | - C Serra
- Aix-Marseille Université, CNRS, Institut Origines, Laboratoire PIIM, Marseille, France; UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), E.BiCoM Team, University of Poitiers, 4 rue Michel-Brunet, TSA 51106, 86073, Poitiers, Cedex 9, France
| | - Q Blancart Remaury
- UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), E.BiCoM Team, University of Poitiers, 4 rue Michel-Brunet, TSA 51106, 86073, Poitiers, Cedex 9, France
| | - A D Garcia
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272 CNRS, F-06108 Nice, France
| | - M Righezza
- Aix-Marseille Université, CNRS, Institut Origines, Laboratoire PIIM, Marseille, France
| | - C Meinert
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272 CNRS, F-06108 Nice, France
| | - P Poinot
- UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), E.BiCoM Team, University of Poitiers, 4 rue Michel-Brunet, TSA 51106, 86073, Poitiers, Cedex 9, France
| | - G Danger
- Aix-Marseille Université, CNRS, Institut Origines, Laboratoire PIIM, Marseille, France; Institut Universitaire de France (IUF), France.
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12
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Sharma A. Magnetic Circular Dichroism in Archean Stratospheric Oxygen: Enantiomeric Excess of Amino Acids Produced in Volcanic Plumes. ORIGINS LIFE EVOL B 2023; 53:71-86. [PMID: 37278960 DOI: 10.1007/s11084-023-09637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023]
Abstract
While there is consensus that Archean atmosphere was anoxic with O2 pressure, p(O2) <10-6 PAL (present atmospheric level) at sea-level, evidence suggests that p(O2) at stratospheric altitudes of 10-50 km was orders of magnitude higher, a result of photodissociation of CO2 by UVC sunlight and incomplete mixing of O2 with other gases. Molecular O2 is paramagnetic due to triplet ground state. Magnetic circular dichroism (MCD) by stratospheric O2 is examined in earth's magnetic field and shows maximum circular polarization │(I+ - I-)│ at altitude of 15-30 km (I+/I- is intensity of left/right circularly polarized light). While (I+ - I-)/(I+ + I-) is small (~10-10), it is an unexplored source of enantiomeric excess (EE) by asymmetric photolysis of amino acid precursors produced in volcanic eruptions. The precursors reside in stratosphere for periods of over a year due to relative absence of vertical transport. Due to negligible thermal gradient across equator, they are trapped in the hemisphere where they are produced, with interhemispheric exchange time of over a year. The precursors diffuse through altitudes of maximum circular polarization before getting hydrolyzed on ground to amino acids. Enantiomeric excess of ~10-12 is calculated for precursors and amino acids. While small, this EE is orders of magnitude higher than predicted (~10-18) by parity violating energy differences (PVED) and could be the seed for growth of biological homochirality. Preferential crystallization (PC) is described as a plausible mechanism for amplification of solution EE of some amino acids from 10-12 to 10-2, for period of several days.
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Affiliation(s)
- A Sharma
- Department of Physics, Alabama A&M University, Huntsville, AL, 35762, USA.
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13
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Fontecilla-Camps JC. Reflections on the Origin and Early Evolution of the Genetic Code. Chembiochem 2023; 24:e202300048. [PMID: 37052530 DOI: 10.1002/cbic.202300048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Indexed: 04/14/2023]
Abstract
Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.
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14
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Shoji M, Kitazawa Y, Sato A, Watanabe N, Boero M, Shigeta Y, Umemura M. Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids. J Phys Chem Lett 2023; 14:3243-3248. [PMID: 36975120 PMCID: PMC10084466 DOI: 10.1021/acs.jpclett.2c03862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 05/16/2023]
Abstract
High enantiomeric excesses (ee's) of l-amino acids, including non-proteinogenic amino acid isovaline (Iva), were discovered in the Murchison meteorite, but the detailed molecular mechanism responsible for the observed ee of amino acids remains elusive and inconsistent, because Iva has an inverted circular dichroism (CD) spectrum with respect to α-H amino acids, e.g., alanine. To address this issue, we resort to accurate ab initio calculations for amino acids and their precursors in the Strecker synthesis. We evaluated their photolysis-induced ee in the range 5-11 eV including the Lyman alpha emission line (Lyα), the typical intensive 10.2 eV radiation ascribed to the early phase of galactic evolution. We show that only the aminonitrile precursors are characterized by positive ee in the Lyα region, explaining why right-handed circularly polarized Lyα (R-CP-Lyα) induces homologous l-amino acids. This study shows that the homochirality of amino acids is produced at the aminonitrile precursors stage.
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Affiliation(s)
- Mitsuo Shoji
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuya Kitazawa
- Graduate
School of Pure and Applied Sciences, University
of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Akimasa Sato
- Graduate
School of Pure and Applied Sciences, University
of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Natsuki Watanabe
- Graduate
School of Pure and Applied Sciences, University
of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Mauro Boero
- University
of Strasbourg, Institut de Physique
et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504, 23 rue du Loess, Strasbourg F-67034, France
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Masayuki Umemura
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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15
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Distinguishing Biotic vs. Abiotic Origins of ‘Bio’signatures: Clues from Messy Prebiotic Chemistry for Detection of Life in the Universe. Life (Basel) 2023; 13:life13030766. [PMID: 36983921 PMCID: PMC10058490 DOI: 10.3390/life13030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/04/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
It is not a stretch to say that the search for extraterrestrial life is possibly the biggest of the cosmic endeavors that humankind has embarked upon. With the continued discovery of several Earth-like exoplanets, the hope of detecting potential biosignatures is multiplying amongst researchers in the astrobiology community. However, to be able to discern these signatures as being truly of biological origin, we also need to consider their probable abiotic origin. The field of prebiotic chemistry, which is aimed at understanding enzyme-free chemical syntheses of biologically relevant molecules, could particularly aid in this regard. Specifically, certain peculiar characteristics of prebiotically pertinent messy chemical reactions, including diverse and racemic product yields and lower synthesis efficiencies, can be utilized in analyzing whether a perceived ‘signature of life’ could possibly have chemical origins. The knowledge gathered from understanding the transition from chemistry to biology during the origin of life could be used for creating a library of abiotically synthesized biologically relevant organic molecules. This can then be employed in designing, standardizing, and testing mission-specific instruments/analysis systems, while also enabling the effective targeting of exoplanets with potentially ‘ongoing’ molecular evolutionary processes for robust detection of life in future explorative endeavors.
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16
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Kebukawa Y, Asano S, Tani A, Yoda I, Kobayashi K. Gamma-Ray-Induced Amino Acid Formation in Aqueous Small Bodies in the Early Solar System. ACS CENTRAL SCIENCE 2022; 8:1664-1671. [PMID: 36589881 PMCID: PMC9801502 DOI: 10.1021/acscentsci.2c00588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 06/01/2023]
Abstract
Carbonaceous chondrites contain life's essential building blocks, including amino acids, and their delivery of organic compounds would have played a key role in life's emergence on Earth. Aqueous alteration of carbonaceous chondrites is a widespread process induced by the heat produced by radioactive decay of nuclides like 26Al. Simple ubiquitous molecules like formaldehyde and ammonia could produce various organic compounds, including amino acids and complex organic macromolecules. However, the effects of radiation on such organic chemistry are unknown. Hence, the effects of gamma rays from radioactive decays on the formation of amino acids in meteorite parent bodies are demonstrated here. We discovered that gamma-ray irradiation of aqueous formaldehyde and ammonia solutions afforded a variety of amino acids. The amino acid yields had a linear relationship with the total gamma-ray dose but were unaffected by the irradiation dose rates. Given the gamma-ray production rates in the meteorite parent bodies, we estimated that the production rates were reasonable compared to amino acid abundances in carbonaceous chondrites. Our findings indicate that gamma rays may contribute to amino acid formation in parent bodies during aqueous alteration. In this paper, we propose a new prebiotic amino acid formation pathway that contributes to life's origin.
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Affiliation(s)
- Yoko Kebukawa
- Department
of Chemistry and Life Science, Yokohama
National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa240-8501, Japan
| | - Shinya Asano
- Department
of Chemistry and Life Science, Yokohama
National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa240-8501, Japan
| | - Atsushi Tani
- Graduate
School of Human Development and Environment, Kobe University, 3-11
Tsurukabuto, Nada-ku, Kobe, Hyogo657-8501, Japan
| | - Isao Yoda
- Co60
irradiation facility, Laboratory for Zero-Carbon Energy, Institute
of Innovative Research, Tokyo Institute
of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kensei Kobayashi
- Department
of Chemistry and Life Science, Yokohama
National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa240-8501, Japan
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17
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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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18
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Shoji M, Watanabe N, Hori Y, Furuya K, Umemura M, Boero M, Shigeta Y. Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses. ASTROBIOLOGY 2022; 22:1129-1142. [PMID: 35951031 DOI: 10.1089/ast.2022.0011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Enantiomeric excesses of l-amino acids have been detected in meteorites; however, their molecular mechanism and prebiotic syntheses are still a matter of debate. To elucidate the origin of homochirality, alanine and the chiral precursors formed in prebiotic processes were investigated with regard to their stabilities among their isomers by employing the minimum energy principle, namely, the abundancy of a molecule in the interstellar medium is directly correlated to the stability among isomers. To facilitate the search for possible isomers, we developed a new isomer search algorithm, the random connection method, and performed a thorough search for all the stable isomers within a given chemical formula. We found that alanine and most of its precursors are located at higher energy by more than 5.7 kcal mol-1, with respect to the most stable isomer that consists of a linear-chain structure, whereas only the 2-aminopropanenitrile is the most stable isomer among all others possible. The inherent stability of the α-amino nitrile suggests that the 2-aminopropanenitrile is the dominant contribution in the formation of the common enantiomeric excess over α-amino acids.
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
- JST-PRESTO, Kawaguchi, Japan
| | - Natsuki Watanabe
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuta Hori
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kenji Furuya
- National Astronomical Observatory of Japan, Mitaka, Japan
| | - Masayuki Umemura
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mauro Boero
- University of Strasbourg, Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504, Strasbourg, France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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19
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Li Y, Kitadai N, Sekine Y, Kurokawa H, Nakano Y, Johnson-Finn K. Geoelectrochemistry-driven alteration of amino acids to derivative organics in carbonaceous chondrite parent bodies. Nat Commun 2022; 13:4893. [PMID: 35986003 PMCID: PMC9391434 DOI: 10.1038/s41467-022-32596-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
A long-standing question regarding carbonaceous chondrites (CCs) is how the CCs' organics were sourced and converted before and after the accretion of their parent bodies. Growing evidence shows that amino acid abundances in CCs decrease with an elongated aqueous alteration. However, the underlying chemical processes are unclear. If CCs' parent bodies were water-rock differentiated, pH and redox gradients can drive electrochemical reactions by using H2 as an electron source. Here, we simulate such redox conditions and demonstrate that α-amino acids are electrochemically altered to monoamines and α-hydroxy acids on FeS and NiS catalysts at 25 °C. This conversion is consistent with their enrichment compared to amino acid analogs in heavily altered CCs. Our results thus suggest that H2 can be an important driver for organic evolution in water-rock differentiated CC parent bodies as well as the Solar System icy bodies that might possess similar pH and redox gradients.
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Affiliation(s)
- Yamei Li
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, Japan.
| | - Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yasuhito Sekine
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, Japan
- Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa, Japan
| | - Hiroyuki Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, Japan
| | - Yuko Nakano
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, Japan
| | - Kristin Johnson-Finn
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, Japan
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
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20
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A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet. J Mol Evol 2022; 90:307-323. [PMID: 35666290 DOI: 10.1007/s00239-022-10061-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
Recent findings, in vitro and in silico, are strengthening the idea of a simpler, earlier stage of genetically encoded proteins which used amino acids produced by prebiotic chemistry. These findings motivate a re-examination of prior work which has identified unusual properties of the set of twenty amino acids found within the full genetic code, while leaving it unclear whether similar patterns also characterize the subset of prebiotically plausible amino acids. We have suggested previously that this ambiguity may result from the low number of amino acids recognized by the definition of prebiotic plausibility used for the analysis. Here, we test this hypothesis using significantly updated data for organic material detected within meteorites, which contain several coded and non-coded amino acids absent from prior studies. In addition to confirming the well-established idea that "late" arriving amino acids expanded the chemistry space encoded by genetic material, we find that a prebiotically plausible subset of coded amino acids generally emulates the patterns found in the full set of 20, namely an exceptionally broad and even distribution of volumes and an exceptionally even distribution of hydrophobicities (quantified as logP) over a narrow range. However, the strength of this pattern varies depending on both the size and composition the library used to create a background (null model) for a random alphabet, and the precise definition of exactly which amino acids were present in a simpler, earlier code. Findings support the idea that a small sample size of amino acids caused previous ambiguous results, and further improvements in meteorite analysis, and/or prebiotic simulations will further clarify the nature and extent of unusual properties. We discuss the case of sulfur-containing amino acids as a specific and clear example and conclude by reviewing the potential impact of better understanding the chemical "logic" of a smaller forerunner to the standard amino acid alphabet.
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21
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Iglesias-Groth S, Cataldo F. Integrated Molar Absorptivity of Mid- and Far-Infrared Spectra of Alanine and a Selection of Other Five Amino Acids of Astrobiological Relevance. ASTROBIOLOGY 2022; 22:462-480. [PMID: 35133882 DOI: 10.1089/ast.2021.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Alanine and other five proteinogeninc amino acids produced quite easily in exogenous and/or endogenous prebiotic processes, that is, valine, serine, proline, glutamic acid, and aspartic acid (Ala, Val, Ser, Pro, Glu, and Asp, respectively) were studied in the mid- and far-infrared spectral range. This work is an extension of the previous one where other proteinogenic amino acids glycine, isoleucine, phenylalanine, tyrosine, and tryptophan (Gly, Ile, Phe, Tyr, and Trp, respectively) were studied in the mid-infrared and in the far-infrared with the purpose to facilitate the search and identification of these astrobiological and astrochemical relevant molecules in space environments. The molar extinction coefficients (ɛ) of all mid- and far-infrared bands were determined as well as the integrated molar absorptivities (ψ). The mid-infrared spectra of Ala, Val, Ser, Pro, Glu, and Asp were recorded also at three different temperatures from -180°C to nearly ambient temperature and at 200°C. With the reported values of ɛ and ψ, it will be possible to estimate the relative abundance of these molecules in space environments.
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22
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Giese CC, ten Kate IL, van den Ende MPA, Wolthers M, Aponte JC, Camprubi E, Dworkin JP, Elsila JE, Hangx S, King HE, Mclain HL, Plümper O, Tielens AGG. Experimental and Theoretical Constraints on Amino Acid Formation from PAHs in Asteroidal Settings. ACS EARTH & SPACE CHEMISTRY 2022; 6:468-481. [PMID: 35330631 PMCID: PMC8935471 DOI: 10.1021/acsearthspacechem.1c00329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Amino acids and polycyclic aromatic hydrocarbons (PAHs) belong to the range of organic compounds detected in meteorites. In this study, we tested empirically and theoretically if PAHs are precursors for amino acids in carbonaceous chondrites, as previously suggested. We conducted experiments to synthesize amino acids from fluoranthene (PAH), with ammonium bicarbonate as a source for ammonia and carbon dioxide under mimicked asteroidal conditions. In our thermodynamic calculations, we extended our analysis to additional PAH-amino acid combinations. We explored 36 reactions involving the PAHs naphthalene, anthracene, fluoranthene, pyrene, triphenylene, and coronene and the amino acids glycine, alanine, valine, leucine, phenylalanine, and tyrosine. Our experiments do not show the formation of amino acids, whereas our theoretical results hint that PAHs could be precursors of amino acids in carbonaceous chondrites at low temperatures.
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Affiliation(s)
- Claudia-Corina Giese
- Leiden
Observatory, Faculty of Science, Leiden
University, 2300 RA Leiden, The Netherlands
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Inge Loes ten Kate
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | | | - Mariette Wolthers
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - José C. Aponte
- Solar
System Exploration Division, NASA Goddard
Space Flight Center, Greenbelt, Maryland 20771, United States
- Department
of Physics, The Catholic University of America, Washington D. C. 20064, United States
- Center for
Research and Exploration in Space Science and Technology, NASA/GSFC, Greenbelt, Maryland 20771, United States
| | - Eloi Camprubi
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Jason P. Dworkin
- Solar
System Exploration Division, NASA Goddard
Space Flight Center, Greenbelt, Maryland 20771, United States
| | - Jamie E. Elsila
- Solar
System Exploration Division, NASA Goddard
Space Flight Center, Greenbelt, Maryland 20771, United States
| | - Suzanne Hangx
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Helen E. King
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Hannah L. Mclain
- Solar
System Exploration Division, NASA Goddard
Space Flight Center, Greenbelt, Maryland 20771, United States
- Department
of Physics, The Catholic University of America, Washington D. C. 20064, United States
- Center for
Research and Exploration in Space Science and Technology, NASA/GSFC, Greenbelt, Maryland 20771, United States
| | - Oliver Plümper
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
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23
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Focused ultrasound extraction versus microwave-assisted extraction for extraterrestrial objects analysis. Anal Bioanal Chem 2022; 414:3643-3651. [PMID: 35267058 DOI: 10.1007/s00216-022-04004-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/01/2022]
Abstract
Search for organic bioindicators in the solar system is a fundamental challenge for the space research community. If tremendous improvements have been achieved in detection, little or no research has been dedicated to extraction of the targets from the studied mineral matrices. Apart from thermodesorption, no extraction step was ever performed in situ within the context of biomarker detection experiments. This work presents an extraction protocol compatible with in situ space constraints. Two extraction methods, i.e., microwave-assisted extraction (MAE) and focused ultrasonic extraction (FUSE), were optimized with the aim of extracting molecules having an astrobiological interest (amino acids, nucleobases, polyaromatic carboxylic acids) and that are included in mineral matrices representative of the Martian soil. Higher efficiency was obtained with the FUSE method (20 kHz, amplitude 80%, pulse and relaxation 1 s each, for 10 min) with yields ranging from 30 to 95%. It was then applied on an Atacama Desert soil sample and Aguas Zarcas meteorite fragment. Both water-soluble and organic-soluble compounds present at trace levels were extracted using this short extraction time, and small amounts of sample and solvent compliant with in situ requirements (50 mg, 500 μL). This unique FUSE/derivatization-GC-MS approach gave similar yields to usual 24 h hot water extraction and increased the recovery of the target molecules compared to the derivatization-GC-MS method already used for in situ space experiments by a factor from 2 to 8. The data highlighted the suitability of a focused ultrasonic method for the extraction of trace organic compounds from extraterrestrial samples.
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Kaiser K, Schulz F, Maillard JF, Hermann F, Pozo I, Peña D, Cleaves HJ, Burton AS, Danger G, Afonso C, Sandford S, Gross L. Visualization and identification of single meteoritic organic molecules by atomic force microscopy. METEORITICS & PLANETARY SCIENCE 2022; 57:644-656. [PMID: 35912284 PMCID: PMC9305854 DOI: 10.1111/maps.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/16/2021] [Indexed: 06/15/2023]
Abstract
Using high-resolution atomic force microscopy (AFM) with CO-functionalized tips, we atomically resolved individual molecules from Murchison meteorite samples. We analyzed powdered Murchison meteorite material directly, as well as processed extracts that we prepared to facilitate characterization by AFM. From the untreated Murchison sample, we resolved very few molecules, as the sample contained mostly small molecules that could not be identified by AFM. By contrast, using a procedure based on several trituration and extraction steps with organic solvents, we isolated a fraction enriched in larger organic compounds. The treatment increased the fraction of molecules that could be resolved by AFM, allowing us to identify organic constituents and molecular moieties, such as polycyclic aromatic hydrocarbons and aliphatic chains. The AFM measurements are complemented by high-resolution mass spectrometry analysis of Murchison fractions. We provide a proof of principle that AFM can be used to image and identify individual organic molecules from meteorites and propose a method for extracting and preparing meteorite samples for their investigation by AFM. We discuss the challenges and prospects of this approach to study extraterrestrial samples based on single-molecule identification.
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Affiliation(s)
| | - Fabian Schulz
- IBM Research—ZurichRüschlikon8003Switzerland
- Present address:
Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Julien F. Maillard
- Normandie UnivCOBRAUMR 6014 et FR 3038 Univ RouenINSA RouenCNRS IRCOF1 Rue TesnièreMont‐Saint‐Aignan Cedex76821France
| | | | - Iago Pozo
- Departamento de Química OrgánicaCentro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)Universidade de Santiago de CompostelaSantiago de Compostela15782Spain
| | - Diego Peña
- Departamento de Química OrgánicaCentro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)Universidade de Santiago de CompostelaSantiago de Compostela15782Spain
| | - H. James Cleaves
- Earth‐Life Science InstituteTokyo Institute of Technology2‑12‑1‑IE‑1 Ookayama, Meguro‑kuTokyo152‑8550Japan
- Blue Marble Space Institute for Science1001 4th Ave, Suite 3201SeattleWashington98154USA
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science DivisionNASA Johnson Space CenterMS XI‐3HoustonTexas77058USA
| | - Gregoire Danger
- Laboratoire de Physique des Interactions Ioniques et Moléculaires (PIIM)CNRSAix‐Marseille UniversitéMarseilleFrance
- CNRSCNESLAMAix‐Marseille UniversitéMarseilleFrance
- Institut Universitaire de FranceParisFrance
| | - Carlos Afonso
- Normandie UnivCOBRAUMR 6014 et FR 3038 Univ RouenINSA RouenCNRS IRCOF1 Rue TesnièreMont‐Saint‐Aignan Cedex76821France
| | - Scott Sandford
- Space Science DivisionNASA Ames Research CenterMS 245‐6Moffett FieldCalifornia94035USA
| | - Leo Gross
- IBM Research—ZurichRüschlikon8003Switzerland
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25
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Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030460] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.
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26
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Frenkel-Pinter M, Jacobson KC, Eskew-Martin J, Forsythe JG, Grover MA, Williams LD, Hud NV. Differential Oligomerization of Alpha versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions. Life (Basel) 2022; 12:265. [PMID: 35207553 PMCID: PMC8876357 DOI: 10.3390/life12020265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
The origin of biopolymers is a central question in origins of life research. In extant life, proteins are coded linear polymers made of a fixed set of twenty alpha-L-amino acids. It is likely that the prebiotic forerunners of proteins, or protopeptides, were more heterogenous polymers with a greater diversity of building blocks and linkage stereochemistry. To investigate a possible chemical selection for alpha versus beta amino acids in abiotic polymerization reactions, we subjected mixtures of alpha and beta hydroxy and amino acids to single-step dry-down or wet-dry cycling conditions. The resulting model protopeptide mixtures were analyzed by a variety of analytical techniques, including mass spectrometry and NMR spectroscopy. We observed that amino acids typically exhibited a higher extent of polymerization in reactions that also contained alpha hydroxy acids over beta hydroxy acids, whereas the extent of polymerization by beta amino acids was higher compared to their alpha amino acid analogs. Our results suggest that a variety of heterogenous protopeptide backbones existed during the prebiotic epoch, and that selection towards alpha backbones occurred later as a result of polymer evolution.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Kaitlin C. Jacobson
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jonathan Eskew-Martin
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA
| | - Jay G. Forsythe
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA
| | - Martha A. Grover
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V. Hud
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Kobayashi K, Mita H, Kebukawa Y, Nakagawa K, Kaneko T, Obayashi Y, Sato T, Yokoo T, Minematsu S, Fukuda H, Oguri Y, Yoda I, Yoshida S, Kanda K, Imai E, Yano H, Hashimoto H, Yokobori SI, Yamagishi A. Space Exposure of Amino Acids and Their Precursors during the Tanpopo Mission. ASTROBIOLOGY 2021; 21:1479-1493. [PMID: 34793260 DOI: 10.1089/ast.2021.0027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Amino acids have been detected in extraterrestrial bodies such as carbonaceous chondrites (CCs), which suggests that extraterrestrial organics could be the source of the first life on Earth, and interplanetary dust particles (IDPs) or micrometeorites (MMs) are promising carriers of extraterrestrial organic carbon. Some amino acids found in CCs are amino acid precursors, but these have not been well characterized. The Tanpopo mission was conducted in Earth orbit from 2015 to 2019, and the stability of glycine (Gly), hydantoin (Hyd), isovaline (Ival), 5-ethyl-5-methylhydantoin (EMHyd), and complex organics formed by proton irradiation from CO, NH3, and H2O (CAW) in space were analyzed by high-performance liquid chromatography and/or gas chromatography/mass spectrometry. The target substances showed a logarithmic decomposition over 1-3 years upon space exposure. Recoveries of Gly and CAW were higher than those of Hyd, Ival, and EMHyd. Ground simulation experiments showed different results: Hyd was more stable than Gly. Solar ultraviolet light was fatal to all organics, and they required protection when carried by IDPs/MMs. Thus, complex amino acid precursors (such as CAW) were possibly more robust than simple precursors during transportation to primitive Earth. The Tanpopo 2 mission is currently being conducted to expose organics to more probable space conditions.
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Affiliation(s)
- Kensei Kobayashi
- Department of Chemistry, Yokohama National University, Hodogaya-ku, Yokohama, Japan
| | - Hajime Mita
- Department of Life, Environment and Applied Chemistry, Faculty of Engineering, Higashi-ku, Fukuoka Institute of Technology, Fukuoka, Japan
| | - Yoko Kebukawa
- Department of Chemistry, Yokohama National University, Hodogaya-ku, Yokohama, Japan
| | - Kazumichi Nakagawa
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Takeo Kaneko
- Department of Chemistry, Yokohama National University, Hodogaya-ku, Yokohama, Japan
| | - Yumiko Obayashi
- Department of Chemistry, Yokohama National University, Hodogaya-ku, Yokohama, Japan
| | - Tomohito Sato
- Department of Chemistry, Yokohama National University, Hodogaya-ku, Yokohama, Japan
| | - Takuya Yokoo
- Department of Chemistry, Yokohama National University, Hodogaya-ku, Yokohama, Japan
| | - Saaya Minematsu
- Department of Life, Environment and Applied Chemistry, Faculty of Engineering, Higashi-ku, Fukuoka Institute of Technology, Fukuoka, Japan
| | | | | | - Isao Yoda
- Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Satoshi Yoshida
- National Institute for Quantum and Radiological Science and Technology, Inage-ku, Chiba, Japan
| | - Kazuhiro Kanda
- University of Hyogo, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Eiichi Imai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Hajime Yano
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (ISAS/JAXA), Sagamihara, Kanagawa, Japan
| | - Hirofumi Hashimoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (ISAS/JAXA), Sagamihara, Kanagawa, Japan
| | - Shin-Ichi Yokobori
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Akihiko Yamagishi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (ISAS/JAXA), Sagamihara, Kanagawa, Japan
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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28
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Engineering a cationic supramolecular charge switch for facile amino acids enantiodiscrimination based on extended-gate field effect transistors. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.11.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Abstract
The origin of life, based on the homochirality of biomolecules, is a persistent mystery. Did life begin by using both forms of chirality, and then one of the forms disappeared? Or did the choice of homochirality precede the formation of biomolecules that could ensure replication and information transfer? Is the natural choice of L-amino acids and D-sugars on which life is based deterministic or random? Is the handedness present in/of the Universe from its beginning? The whole biosystem on the Earth, all living creatures are chiral. Many theories try to explain the origin of life and chirality on the Earth: e.g., the panspermia hypothesis, the primordial soup hypothesis, theory of parity violation in weak interactions. Additionally, heavy neutrinos and the impact of the fact that only left-handed particles decay, and even dark matter, all have to be considered.
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30
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Sheng M, Silvestrini F, Biczysko M, Puzzarini C. Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case. J Phys Chem A 2021; 125:9099-9114. [PMID: 34623165 DOI: 10.1021/acs.jpca.1c06993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
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Affiliation(s)
- Mingzhu Sheng
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Filippo Silvestrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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31
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Thompson SP, Kennedy H, Butler BM, Day SJ, Safi E, Evans A. Laboratory exploration of mineral precipitates from Europa's subsurface ocean. J Appl Crystallogr 2021; 54:1455-1479. [PMID: 34667451 PMCID: PMC8493616 DOI: 10.1107/s1600576721008554] [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: 05/19/2021] [Accepted: 08/17/2021] [Indexed: 11/10/2022] Open
Abstract
The precipitation of hydrated phases from a chondrite-like Na-Mg-Ca-SO4-Cl solution is studied using in situ synchrotron X-ray powder diffraction, under rapid- (360 K h-1, T = 250-80 K, t = 3 h) and ultra-slow-freezing (0.3 K day-1, T = 273-245 K, t = 242 days) conditions. The precipitation sequence under slow cooling initially follows the predictions of equilibrium thermodynamics models. However, after ∼50 days at 245 K, the formation of the highly hydrated sulfate phase Na2Mg(SO4)2·16H2O, a relatively recent discovery in the Na2Mg(SO4)2-H2O system, was observed. Rapid freezing, on the other hand, produced an assemblage of multiple phases which formed within a very short timescale (≤4 min, ΔT = 2 K) and, although remaining present throughout, varied in their relative proportions with decreasing temperature. Mirabilite and meridianiite were the major phases, with pentahydrite, epsomite, hydrohalite, gypsum, blödite, konyaite and loweite also observed. Na2Mg(SO4)2·16H2O was again found to be present and increased in proportion relative to other phases as the temperature decreased. The results are discussed in relation to possible implications for life on Europa and application to other icy ocean worlds.
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Affiliation(s)
- Stephen P. Thompson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Hilary Kennedy
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, United Kingdom
| | - Benjamin M. Butler
- Environmental and Biochemical Sciences, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, United Kingdom
| | - Sarah J. Day
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Emmal Safi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Astrophysics Group, Lennard-Jones Laboratories, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Aneurin Evans
- Astrophysics Group, Lennard-Jones Laboratories, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
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32
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Exploring the enantiomeric 13C position-specific isotope fractionation: challenges and anisotropic NMR-based analytical strategy. Anal Bioanal Chem 2021; 413:6379-6392. [PMID: 34498104 DOI: 10.1007/s00216-021-03599-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/27/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
Trying to answer the intriguing and fundamental question related to chiral induction/amplification at the origin of homochirality in Nature: "Is there a relationship between enantiomeric and isotopic fractionation of carbon 13 in chiral molecules?" is a difficult but stimulating challenge. Although isotropic 13C-PSIA NMR is a promising tool for the determination of (13C/12C) ratios capable of providing key 13C isotopic data for understanding the reaction mechanisms of biological processes or artificial transformations, this method does not provide access to any enantiomeric 13C isotopic data unless mirror-image isomers are first physically separated. Interestingly, 13C spectral enantiodiscriminations can be potentially performed in situ in the presence of enantiopure entities as chiral-europium complexes or chiral liquid crystals (CLCs). In this work, we explored for the first time the capabilities of the anisotropic 13C-{1H} NMR using PBLG-based lyotropic CLCs as enantiodiscriminating media in the context of the enantiomeric position-specific 13C isotope fractionation (EPSIF), within the requested precision of the order of the permil. As enantiomeric NMR signals are discriminated on the basis of a difference of 13C residual chemical shift anisotropy (13C-RCSA) prior to being deconvoluted, analysis of enantiomeric mixtures becomes possible. The analytical potential of this approach when using poly-γ-benzyl-L-glutamate (PBLG) is presented, and the preliminary quantitative results on small model chiral molecules obtained at 17.5 T with a cryogenic NMR probe are reported and discussed. A promising analytical approach based on anisotropic irm-13C-NMR spectrometry to potentially reveal the natural 13C/12C isotopic enantiofractionation effects in organic chiral molecules is proposed and discussed.
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33
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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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34
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Iglesias-Groth S, Cataldo F. Integrated Molar Absorptivity of Mid- and Far-Infrared Spectra of Glycine and Other Selected Amino Acids. ASTROBIOLOGY 2021; 21:526-540. [PMID: 33956490 DOI: 10.1089/ast.2020.2307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A selection of five proteinogenic amino acids-glycine, isoleucine, phenylalanine, tyrosine, and tryptophan-were studied in the mid-infrared and in the far-infrared with the purpose to facilitate the search and identification of these astrobiologically and astrochemically relevant molecules in space environments. The molar extinction coefficients (ɛ) of all mid- and far-infrared bands were determined as well as the integrated molar absorptivities (ψ). The mid-infrared spectra of the five selected amino acids were recorded also at three different temperatures from -180°C to ambient temperature to +200°C. We measured the wavelength shift of the infrared bands caused by temperature; and for the most relevant or temperature-sensitive infrared bands, a series of linear equations were determined relating wavelength position with temperature. Such equations may provide estimates of the temperature of these molecules once detected in astrophysical objects; and with the reported values of ɛ and ψ, it will be possible to estimate the relative abundance of these molecules in space environments.
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35
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Chu XY, Zhang HY. Protein Homochirality May Be Derived from Primitive Peptide Synthesis by RNA. ASTROBIOLOGY 2021; 21:628-635. [PMID: 33600215 DOI: 10.1089/ast.2020.2324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Homochirality is a feature of life, but its origin is still disputed. Recent theories indicate that the origin of homochirality coincided with that of the RNA world, but proteins have not yet been incorporated into the story. Ribosome is considered a living fossil that survived the RNA world and records the oldest interaction between RNA and proteins. Inspired by several ribosome-related findings, we propose a hypothesis as follows: the substrate chirality preference of some primitive peptide synthesis ribozymes can mediate the chirality transmission from RNA to protein. In return, the chiral preference of protective peptide-RNA interaction can bring these ribozymes an evolutionary advantage and facilitate the expansion of enantiomeric excess in peptides. Monte Carlo simulation results show that this system's chemistry model is plausible. This model can be further tested through investigation of the chirality preference for the interactions between d/l-ribose-composed rRNA homologs and l/d-amino acid-composed peptides.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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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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Fujiya W, Furukawa Y, Sugahara H, Koike M, Bajo KI, Chabot NL, Miura YN, Moynier F, Russell SS, Tachibana S, Takano Y, Usui T, Zolensky ME. Analytical protocols for Phobos regolith samples returned by the Martian Moons eXploration (MMX) mission. EARTH, PLANETS, AND SPACE : EPS 2021; 73:120. [PMID: 34776735 PMCID: PMC8550573 DOI: 10.1186/s40623-021-01438-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/10/2021] [Indexed: 05/12/2023]
Abstract
Japan Aerospace Exploration Agency (JAXA) will launch a spacecraft in 2024 for a sample return mission from Phobos (Martian Moons eXploration: MMX). Touchdown operations are planned to be performed twice at different landing sites on the Phobos surface to collect > 10 g of the Phobos surface materials with coring and pneumatic sampling systems on board. The Sample Analysis Working Team (SAWT) of MMX is now designing analytical protocols of the returned Phobos samples to shed light on the origin of the Martian moons as well as the evolution of the Mars-moon system. Observations of petrology and mineralogy, and measurements of bulk chemical compositions and stable isotopic ratios of, e.g., O, Cr, Ti, and Zn can provide crucial information about the origin of Phobos. If Phobos is a captured asteroid composed of primitive chondritic materials, as inferred from its reflectance spectra, geochemical data including the nature of organic matter as well as bulk H and N isotopic compositions characterize the volatile materials in the samples and constrain the type of the captured asteroid. Cosmogenic and solar wind components, most pronounced in noble gas isotopic compositions, can reveal surface processes on Phobos. Long- and short-lived radionuclide chronometry such as 53Mn-53Cr and 87Rb-87Sr systematics can date pivotal events like impacts, thermal metamorphism, and aqueous alteration on Phobos. It should be noted that the Phobos regolith is expected to contain a small amount of materials delivered from Mars, which may be physically and chemically different from any Martian meteorites in our collection and thus are particularly precious. The analysis plan will be designed to detect such Martian materials, if any, from the returned samples dominated by the endogenous Phobos materials in curation procedures at JAXA before they are processed for further analyses.
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Affiliation(s)
- Wataru Fujiya
- Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512 Japan
| | - Yoshihiro Furukawa
- Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578 Japan
| | - Haruna Sugahara
- Institute of Space and Astronautical Science, JAXA, 3-1-1 Yoshinodai, Sagamihara, Kanagawa 252-5210 Japan
| | - Mizuho Koike
- Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8526 Japan
| | - Ken-ichi Bajo
- Department of Earth and Planetary Sciences, Hokkaido University, N10W8 Kita-ku, Sapporo, 060-0810 Japan
| | - Nancy L. Chabot
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd, Laurel, MD 20723 USA
| | - Yayoi N. Miura
- Earthquake Research Institute, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
| | - Frederic Moynier
- Institut de Physique du Globe de Paris, CNRS, University of Paris, Paris, France
| | - Sara S. Russell
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Shogo Tachibana
- Institute of Space and Astronautical Science, JAXA, 3-1-1 Yoshinodai, Sagamihara, Kanagawa 252-5210 Japan
- UTOPS, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yoshinori Takano
- Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, 237-0061 Japan
| | - Tomohiro Usui
- Institute of Space and Astronautical Science, JAXA, 3-1-1 Yoshinodai, Sagamihara, Kanagawa 252-5210 Japan
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A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids. Symmetry (Basel) 2020. [DOI: 10.3390/sym12122046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules. Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them. However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization, or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. The main goal of these experiments is to show that using minerals it is possible, at least, to obtain peptides whose composition includes a high quantity of L-amino acids and protein amino acids (PAAs). These experiments should be performed using hydrothermal environments and wet/dry cycles. In addition, for hydrothermal environment experiments, it is very important to use one of the suggested artificial seawaters, and for wet/dry environments, it is important to perform the experiments in distilled water and diluted salt solutions. Finally, from these experiments, we suggest that, without an RNA world or even a pre genetic world, a small peptide set could emerge that better resembles modern proteins.
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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Aponte JC, Elsila JE, Hein JE, Dworkin JP, Glavin DP, McLain HL, Parker ET, Cao T, Berger EL, Burton AS. Analysis of amino acids, hydroxy acids, and amines in CR chondrites. METEORITICS & PLANETARY SCIENCE 2020; 55:2422-2439. [PMID: 33536738 PMCID: PMC7839561 DOI: 10.1111/maps.13586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/23/2020] [Indexed: 05/20/2023]
Abstract
The abundances, relative distributions, and enantiomeric and isotopic compositions of amines, amino acids, and hydroxy acids in Miller Range (MIL) 090001 and MIL 090657 meteorites were determined. Chiral distributions and isotopic compositions confirmed that most of the compounds detected were indigenous to the meteorites and not the result of terrestrial contamination. Combined with data in the literature, suites of these compounds have now been analyzed in a set of six CR chondrites, spanning aqueous alteration types 2.0-2.8. Amino acid abundances ranged from 17 to 3300 nmol g-1 across the six CRs; hydroxy acid abundances ranged from 180 to 1800 nmol g-1; and amine abundances ranged from 40 to 2100 nmol g-1. For amino acids and amines, the weakly altered chondrites contained the highest abundances, whereas hydroxy acids were most abundant in the more altered CR2.0 chondrite. Because water contents in the meteorites are orders of magnitude greater than soluble organics, synthesis of hydroxy acids, which requires water, may be less affected by aqueous alteration than amines and amino acids that require nitrogen-bearing precursors. Two chiral amino acids that were plausibly extraterrestrial in origin were present with slight enantiomeric excesses: L-isovaline (~10% excess) and D-β-amino-n-butyric acid (~9% excess); further studies are needed to verify that the chiral excess in the latter compound is truly extraterrestrial in origin. The isotopic compositions of compounds reported here did not reveal definitive links between the different compound classes such as common synthetic precursors, but will provide a framework for further future in-depth analyses.
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Affiliation(s)
- José C. Aponte
- Department of ChemistryCatholic University of AmericaWashingtonDistrict of Columbia20064USA
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Jamie E. Elsila
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Jason E. Hein
- University of British ColumbiaBritish ColumbiaV6T 1Z2Canada
| | - Jason P. Dworkin
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Daniel P. Glavin
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Hannah L. McLain
- Department of ChemistryCatholic University of AmericaWashingtonDistrict of Columbia20064USA
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Eric T. Parker
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Timothy Cao
- Department of ChemistryUniversity of CaliforniaMercedCalifornia95343USA
| | - Eve L. Berger
- Astromaterials Research and Exploration Science DivisionTexas State University / Jacobs JETS ContractNASA Johnson Space CenterHoustonTexas77058USA
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science DivisionNASA Johnson Space CenterHoustonTexas77058USA
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41
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Chien CY, Yu SS. Ester-mediated peptide formation promoted by deep eutectic solvents: a facile pathway to proto-peptides. Chem Commun (Camb) 2020; 56:11949-11952. [PMID: 32929424 DOI: 10.1039/d0cc03319g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ester-amide exchange reaction enables spontaneous formation of prebiotic proto-peptides under mild conditions. However, this reaction also leads to oligomers with a vast sequence diversity of ester and amide linkages. Here, we demonstrate using deep eutectic solvents as a universal strategy to regulate the reaction pathways and promote the formation of amino acid-enriched oligomers with peptide backbones.
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Affiliation(s)
- Chen-Yu Chien
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City, 70101, Taiwan, Republic of China.
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42
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Zhao G, Samanta SS, Michieletto J, Roche SP. A Broad Substrate Scope of Aza-Friedel-Crafts Alkylation for the Synthesis of Quaternary α-Amino Esters. Org Lett 2020; 22:5822-5827. [PMID: 32649206 PMCID: PMC7654210 DOI: 10.1021/acs.orglett.0c01895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A versatile synthetic protocol of aza-Friedel-Crafts alkylation has been developed for the synthesis of quaternary α-amino esters. This operationally simple alkylation proceeds under ambient conditions with high efficiency, regioselectivity, and an exceptionally broad scope of arene nucleophiles. A key feature of this alkylation is the role associated with the silver(I) salt counteranions liberated during the reaction. Taking advantage of a phase-transfer counteranion/Brønsted acid pair mechanism, we also report a catalytic enantioselective example of the reaction.
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Affiliation(s)
- Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Shyam S Samanta
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Jessica Michieletto
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
- Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33458, United States
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Schaefer K, Dambuza IM, Dall’Angelo S, Yuecel R, Jaspars M, Trembleau L, Zanda M, Brown GD, Netea MG, Gow NAR. A Weakened Immune Response to Synthetic Exo-Peptides Predicts a Potential Biosecurity Risk in the Retrieval of Exo-Microorganisms. Microorganisms 2020; 8:microorganisms8071066. [PMID: 32708909 PMCID: PMC7409182 DOI: 10.3390/microorganisms8071066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 11/25/2022] Open
Abstract
Simple Summary We tested the immune response of T cells of the mammalian immune system towards protein antigens that includes the unusual amino acids isovaline and α-aminoisobutyric. Those amino acids have been found in high abundance on carbonaceous meteorites but are extremely rare in proteomes of earth organisms. We hypothesised that proteins of non-terrestrial alien life forms might contain such amino acids and tested whether chemically synthesised “exopeptides” that contain these amino acids could be detected by the immune system. Our assays, based on the responses of CD8+ T cells to these exopeptides, indicated that antigen cleavage, processing, and subsequent T cell activation still occurred, but were less efficient than the response to control peptides that lacked these amino acids. We therefore speculate that the encounter of putative exo-microorganisms of an unusual antigenic repertoire might pose an immunological risk for space missions aiming to retrieve potentially biotic samples from exoplanets and moons. Abstract The discovery of liquid water at several locations in the solar system raises the possibility that microbial life may have evolved outside Earth and as such could be accidently introduced into the Earth’s ecosystem. Unusual sugars or amino acids, like non-proteinogenic isovaline and α-aminoisobutyric acid that are vanishingly rare or absent from life forms on Earth, have been found in high abundance on non-terrestrial carbonaceous meteorites. It is therefore conceivable that exo-microorganisms might contain proteins that include these rare amino acids. We therefore asked whether the mammalian immune system would be able to recognize and induce appropriate immune responses to putative proteinaceous antigens that include these rare amino acids. To address this, we synthesised peptide antigens based on a backbone of ovalbumin and introduced isovaline and α-aminoisobutyric acid residues and demonstrated that these peptides can promote naïve OT-I cell activation and proliferation, but did so less efficiently than the canonical peptides. This is relevant to the biosecurity of missions that may retrieve samples from exoplanets and moons that have conditions that may be permissive for life, suggesting that accidental contamination and exposure to exo-microorganisms with such distinct proteomes might pose an immunological challenge.
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Affiliation(s)
- Katja Schaefer
- The Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (I.M.D.); (G.D.B.); (N.A.R.G.)
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- Correspondence:
| | - Ivy M. Dambuza
- The Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (I.M.D.); (G.D.B.); (N.A.R.G.)
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Sergio Dall’Angelo
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK; (S.D.); (M.Z.)
| | - Raif Yuecel
- Iain Fraser Cytometry Centre (IFCC), University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK;
- Centre for Cytomics, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (M.J.); (L.T.)
| | - Laurent Trembleau
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (M.J.); (L.T.)
| | - Matteo Zanda
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK; (S.D.); (M.Z.)
- Sir David Davies Building, Centre for Imaging Science, School of Science, Loughborough University, Loughborough LE11 3TU, UK
| | - Gordon D. Brown
- The Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (I.M.D.); (G.D.B.); (N.A.R.G.)
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Neil A. R. Gow
- The Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (I.M.D.); (G.D.B.); (N.A.R.G.)
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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Chan QHS, Stroud R, Martins Z, Yabuta H. Concerns of Organic Contamination for Sample Return Space Missions. SPACE SCIENCE REVIEWS 2020; 216:56. [PMID: 32624626 PMCID: PMC7319412 DOI: 10.1007/s11214-020-00678-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Analysis of organic matter has been one of the major motivations behind solar system exploration missions. It addresses questions related to the organic inventory of our solar system and its implication for the origin of life on Earth. Sample return missions aim at returning scientifically valuable samples from target celestial bodies to Earth. By analysing the samples with the use of state-of-the-art analytical techniques in laboratories here on Earth, researchers can address extremely complicated aspects of extra-terrestrial organic matter. This level of detailed sample characterisation provides the range and depth in organic analysis that are restricted in spacecraft-based exploration missions, due to the limitations of the on-board in-situ instrumentation capabilities. So far, there are four completed and in-process sample return missions with an explicit mandate to collect organic matter: Stardust and OSIRIS-REx missions of NASA, and Hayabusa and Hayabusa2 missions of JAXA. Regardless of the target body, all sample return missions dedicate to minimise terrestrial organic contamination of the returned samples, by applying various degrees or strategies of organic contamination mitigation methods. Despite the dedicated efforts in the design and execution of contamination control, it is impossible to completely eliminate sources of organic contamination. This paper aims at providing an overview of the successes and lessons learned with regards to the identification of indigenous organic matter of the returned samples vs terrestrial contamination.
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Affiliation(s)
- Queenie Hoi Shan Chan
- Planetary and Space Sciences, School of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
- Present Address: Department of Earth Sciences, Royal Holloway University of London, Egham Surrey, TW20 0EX UK
| | - Rhonda Stroud
- Code 6360, Naval Research Laboratory, Washington, DC 20375 USA
| | - Zita Martins
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico (IST), Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - Hikaru Yabuta
- Department of Earth and Planetary Systems Science, Hiroshima University, 1-3-1 Kagamiyama, Hiroshima, 739-8526 Japan
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45
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Alteration and Stability of Complex Macromolecular Amino Acid Precursors in Hydrothermal Environments. ORIGINS LIFE EVOL B 2020; 50:15-33. [PMID: 32314306 DOI: 10.1007/s11084-020-09593-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
Abstract
The early Solar System comprised a broad area of abiotically created organic compounds, including interstellar organics which were integrated into planetesimals and parent bodies of meteorites, and eventually delivered to the early Earth. In this study, we simulated interstellar complex organic compounds synthesized by proton irradiation of a gas mixture of CO, NH3, and H2O, which are known to release amino acids after acid hydrolysis on the basis of Kobayashi et al. (1999) who reported that at the first stage of chemical evolution, the main compounds formed abiotically are complex organic compounds with high molecular weights. We examined their possible hydrothermal alteration and stabilities as amino acid precursors under high temperature and pressure conditions simulating parent bodies of meteorites by using an autoclave. We reported that all samples treated at 200-300 °C predominantly released glycine and alanine, followed by α-aminobutyric acid, and serine. After heating, amino acid concentrations decreased in general; however, the recovery ratios of γ-aminobutyric acid increased with temperature. The interstellar complex organic analog could maintain as amino acid precursors after being treated at high temperature (200-300 °C) and pressure (8-14 MPa). However, the molecular structures were altered during heating to form organic compounds that are more stable and can survive in elevated hydrothermal conditions.
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46
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Neeman EM, León I, Alonso ER, Mata S, Alonso JL. Gas-Phase Conformational Map of the Amino Acid Isovaline. Chemphyschem 2020; 21:525-530. [PMID: 32012435 DOI: 10.1002/cphc.201901201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/28/2020] [Indexed: 11/11/2022]
Abstract
Four conformers of the non-proteinogenic α-amino acid isovaline, vaporized by laser ablation, are characterized by Fourier-transform microwave techniques in a supersonic expansion. The comparison between the experimental rotational and 14 N nuclear quadrupole coupling constants and the ab initio calculated ones provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by an N-H⋅⋅⋅O =C intramolecular hydrogen bond and a cis-COOH interaction, whereas the higher-energy conformers exhibit an N⋅⋅⋅H-O intramolecular hydrogen bond and trans-COOH, as in other aliphatic amino acids. The spectroscopic data herein reported can be used for the astrophysical purpose in a possible detection of isovaline in space.
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Affiliation(s)
- E M Neeman
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - I León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - E R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - S Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
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47
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Mechanism and kinetics of astrophysically relevant gas-phase stereoinversion in glutamic acid: A computational study. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.molap.2019.100061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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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On the possible origin of protein homochirality, structure, and biochemical function. Proc Natl Acad Sci U S A 2019; 116:26571-26579. [PMID: 31822617 DOI: 10.1073/pnas.1908241116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Living systems have chiral molecules, e.g., native proteins that almost entirely contain L-amino acids. How protein homochirality emerged from a background of equal numbers of L and D amino acids is among many questions about life's origin. The origin of homochirality and its implications are explored in computer simulations examining the stability and structural and functional properties of an artificial library of compact proteins containing 1:1 (termed demi-chiral), 3:1, and 1:3 ratios of D:L and purely L or D amino acids generated without functional selection. Demi-chiral proteins have shorter secondary structures and fewer internal hydrogen bonds and are less stable than homochiral proteins. Selection for hydrogen bonding yields a preponderance of L or D amino acids. Demi-chiral proteins have native global folds, including similarity to early ribosomal proteins, similar small molecule ligand binding pocket geometries, and many constellations of L-chiral amino acids with a 1.0-Å RMSD to native enzyme active sites. For a representative subset containing 550 active site geometries matching 457 (2) 4-digit (3-digit) enzyme classification (E.C.) numbers, native active site amino acids were generated at random for 472 of 550 cases. This increases to 548 of 550 cases when similar residues are allowed. The most frequently generated sequences correspond to ancient enzymatic functions, e.g., glycolysis, replication, and nucleotide biosynthesis. Surprisingly, even without selection, demi-chiral proteins possess the requisite marginal biochemical function and structure of modern proteins, but were thermodynamically less stable. If demi-chiral proteins were present, they could engage in early metabolism, which created the feedback loop for transcription and cell formation.
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Glavin DP, Burton AS, Elsila JE, Aponte JC, Dworkin JP. The Search for Chiral Asymmetry as a Potential Biosignature in our Solar System. Chem Rev 2019; 120:4660-4689. [DOI: 10.1021/acs.chemrev.9b00474] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Daniel P. Glavin
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
| | - Aaron S. Burton
- NASA Johnson Space Center, Houston, Texas 77058, United States
| | - Jamie E. Elsila
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
| | - José C. Aponte
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
- Catholic University of America, Washington, D.C. 20064, United States
| | - Jason P. Dworkin
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
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