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Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code. Acta Biotheor 2021; 69:745-767. [PMID: 34283307 DOI: 10.1007/s10441-021-09420-4] [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: 08/14/2020] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single -C=C bond and two nitrogen atoms in each heterocycle involved in C-N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of -C=O and/or -NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M-Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.
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Guo Z, Song Y, Wang Y, Tan T, Ji Y, Zhang G, Hu J, Zhang Y. Macrochirality of Self-Assembled and Co-assembled Supramolecular Structures of a Pair of Enantiomeric Peptides. Front Mol Biosci 2021; 8:700964. [PMID: 34250024 PMCID: PMC8260686 DOI: 10.3389/fmolb.2021.700964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022] Open
Abstract
Although macrochirality of peptides’ supramolecular structures has been found to play important roles in biological activities, how macrochirality is determined by the molecular chirality of the constituted amino acids is still unclear. Here, two chiral peptides, Ac-LKLHLHLQLKLLLVLFLFLALK-NH2 (KK-11) and Ac-DKDHDHDQDKDL DVDFDFDADK-NH2 (KKd-11), which were composed entirely of either L- or D-amino acids, were designed for studying the chiral characteristics of the supramolecular microstructures. It was found that monocomponent KK-11 or KKd-11 self-assembled into right- or left-handed helical nanofibrils, respectively. However, when they co-assembled with concentration ratios varied from 1:9 to 9:1, achiral nanowire-like structures were formed. Both circular dichroism and Fourier transform infrared spectra indicated that the secondary structures changed when the peptides co-assembled. MD simulations indicated that KK-11 or KKd-11 exhibited a strong propensity to self-assemble into right-handed or left-handed nanofibrils, respectively. However, when KK-11 and KKd-11 were both presented in a solution, they had a higher probability to co-assemble instead of self-sort. MD simulations indicated that, in their mixtures, they formed nanowires without handedness feature, a good agreement with experimental observation. Our results shed light on the molecular mechanisms of the macrochirality of peptide supramolecular microstructures.
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Affiliation(s)
- Zhen Guo
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongshun Song
- School of Science, East China University of Science and Technology, Shanghai, China
| | - Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tingyuan Tan
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuwen Ji
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangxu Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Hu
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
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Origin of Terrestrial Bioorganic Homochirality and Symmetry Breaking in the Universe. Symmetry (Basel) 2019. [DOI: 10.3390/sym11070919] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The origin of terrestrial bioorganic homochirality is one of the most important and unresolved problems in the study of chemical evolution prior to the origin of terrestrial life. One hypothesis advocated in the context of astrobiology is that polarized quantum radiation in space, such as circularly polarized photons or spin-polarized leptons, induced asymmetric chemical and physical conditions in the primitive interstellar media (the cosmic scenario). Another advocated hypothesis in the context of symmetry breaking in the universe is that the bioorganic asymmetry is intrinsically derived from the chiral asymmetric properties of elementary particles, that is, parity violation in the weak interaction (the intrinsic scenario). In this paper, the features of these two scenarios are discussed and approaches to validate them are reviewed.
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Abstract
In this brief review, possible mechanisms which could lead to complete biological homochirality are discussed from the viewpoint of fundamental physics. In particular, the role played by electroweak parity violation, including neutrino-induced homochirality, and contributions from the gravitational interaction, will be emphasized.
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Abstract
The discovery of meteoritic alpha-amino acids with significant enantiomeric excesses of the L-form has suggested that some cosmic factors could serve as the initial source for chiral imbalance of organic compounds delivered to the early Earth. The paper reviews major hypothesis considering the influence of chiral irradiation and chiral combinations of physical fields on the possible ways asymmetric synthesis and transformations of organics could take place within the solar system. They could result in a small enantiomeric imbalance of some groups of compounds. More attention is paid to the hypothesis on parity violation of weak interaction that was supposed to cause homochirality of all primary particles and a more significant homochirality of compounds directly synthesized from the latter in a plasma reactor. The first experiment with material synthesized in a plasma torch resulting from a super-high-velocity impact showed formation of alanine with the excess of L-form between 7 and 25%. The supposed conclusion is that L-amino acids could serve as a starting homochiral biomolecular pool for life to emerge all over the Universe.
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Famiano MA, Boyd RN, Kajino T, Onaka T, Mo Y. Amino Acid Chiral Selection Via Weak Interactions in Stellar Environments: Implications for the Origin of Life. Sci Rep 2018; 8:8833. [PMID: 29891867 PMCID: PMC5995967 DOI: 10.1038/s41598-018-27110-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/25/2018] [Indexed: 11/12/2022] Open
Abstract
Magnetochiral phenomena may be responsible for the selection of chiral states of biomolecules in meteoric environments. For example, the Supernova Amino Acid Processing (SNAAP) Model was proposed previously as a possible mode of magnetochiral selection of amino acids by way of the weak interaction in strong magnetic fields. In earlier work, this model was shown to produce an enantiomeric excess (ee) as high as 0.014% for alanine. In this paper we present the results of molecular quantum chemistry calculations from which ees are determined for the α-amino acids plus isovaline and norvaline, which were found to have positive ees in meteorites. Calculations are performed for both isolated and aqueous states. In some cases, the aqueous state was found to produce larger ees reaching values as high as a few percent under plausible conditions.
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Affiliation(s)
- Michael A Famiano
- Department of Physics and Joint Institute for Nuclear Astrophysics, Western Michigan Univ., 1903 W. Michigan Avenue, Kalamazoo, MI, 49008-5252, USA. .,National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.
| | - Richard N Boyd
- National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.,Department of Physics, Department of Astronomy, The Ohio State Univ., Columbus, OH, 43210, USA
| | - Toshitaka Kajino
- National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.,Department of Astronomy, Graduate School of Science, Univ. of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,School of Physics and Nuclear Energy Engineering, Beihang Univ. (Beijing Univ. of Aeronautics and Astronautics), Beijing, 100083, P.R. China
| | - Takashi Onaka
- Department of Astronomy, Graduate School of Science, Univ. of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yirong Mo
- Department of Chemistry, Western Michigan Univ., 1903 W. Michigan Avenue, Kalamazoo, MI, 49008-5252, USA
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Burton AS, Berger EL. Insights into Abiotically-Generated Amino Acid Enantiomeric Excesses Found in Meteorites. Life (Basel) 2018; 8:life8020014. [PMID: 29757224 PMCID: PMC6027462 DOI: 10.3390/life8020014] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 11/16/2022] Open
Abstract
Biology exhibits homochirality, in that only one of two possible molecular configurations (called enantiomers) is used in both proteins and nucleic acids. The origin of this phenomenon is currently unknown, as nearly all known abiotic mechanisms for generating these compounds result in equal (racemic) mixtures of both enantiomers. However, analyses of primitive meteorites have revealed that a number of amino acids of extraterrestrial origin are present in enantiomeric excess, suggesting that there was an abiotic route to synthesize amino acids in a non-racemic manner. Here we review the amino acid contents of a range of meteorites, describe mechanisms for amino acid formation and their potential to produce amino acid enantiomeric excesses, and identify processes that could have amplified enantiomeric excesses.
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Affiliation(s)
- Aaron S Burton
- Astromaterials Research and Exploration Science, NASA Johnson Space Center, Houston, TX 77058, USA.
| | - Eve L Berger
- GeoControl Systems, Jacobs JETS contract, NASA Johnson Space Center, Houston, TX 77058, USA.
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Sites that Can Produce Left-handed Amino Acids in the Supernova Neutrino Amino Acid Processing Model. ACTA ACUST UNITED AC 2018. [DOI: 10.3847/1538-4357/aaad5f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Pelloni S, Lazzeretti P. Anapolar interaction of aminoacids and sugars in nonuniform magnetic fields. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2018. [DOI: 10.1007/s12210-018-0679-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Famiano MA, Boyd RN, Kajino T, Onaka T. Selection of Amino Acid Chirality via Neutrino Interactions with 14N in Crossed Electric and Magnetic Fields. ASTROBIOLOGY 2018; 18:190-206. [PMID: 29160728 PMCID: PMC5820686 DOI: 10.1089/ast.2017.1686] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/03/2017] [Indexed: 05/09/2023]
Abstract
Previous work has suggested that the chirality of the amino acids could be established in the magnetic field of a nascent neutron star from a core-collapse supernova or massive collapsar. The magnetic field would orient the 14N nuclei, and the alignment of its nuclear spin with respect to those of the electron antineutrinos emitted from the collapsing star would determine the probability of destruction of the 14N nuclei by interactions with the antineutrinos. Subsequent work estimated the bulk polarization of the 14N nuclei in large rotating meteoroids in such an environment. The present work adds a crucial piece of this model by describing the details by which the selective 14N nuclear destruction would produce molecular chiral selectivity. The effects of the neutrino-induced interactions on the 14N nuclei bound in amino acids polarized in strong magnetic fields are studied. It is shown that electric fields in the reference frame of the nuclei modify the magnetic field at the nucleus, creating nuclear magnetizations that are asymmetric in chirality. The antineutrino cross sections depend on this magnetization, creating a selective destructive effect. The environmental conditions and sites in which such a selection mechanism could occur are discussed. Selective destruction of D-enantiomers results in enantiomeric excesses which may be sufficient to drive subsequent autocatalysis necessary to produce the few-percent enantiomeric excesses found in meteorites and subsequent homochirality. Molecular quantum chemical calculations were performed for alanine, and the chirality-dependent effects studied were included. A preference for left-handed molecules was found, and enantiomeric excesses as high as 0.02% were estimated for molecules in the electromagnetic conditions expected from a core-collapse supernova. Key Words: Amino acids-Supernovae-Antineutrinos-Enantiomeric excess-Chirality. Astrobiology 18, 190-206.
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Affiliation(s)
- Michael A. Famiano
- Department of Physics and Joint Institute for Nuclear Astrophysics, Western Michigan University, Kalamazoo, Michigan, USA
- National Astronomical Observatory of Japan, Tokyo, Japan
| | - Richard N. Boyd
- National Astronomical Observatory of Japan, Tokyo, Japan
- Department of Physics, Department of Astronomy, The Ohio State University, Columbus, Ohio, USA
| | - Toshitaka Kajino
- National Astronomical Observatory of Japan, Tokyo, Japan
- Department of Astronomy, Graduate School of Science, University of Tokyo, Tokyo, Japan
- School of Physics and Nuclear Energy Engineering, Beihang University (Beijing University of Aeronautics and Astronautics), Beijing, P.R. China
| | - Takashi Onaka
- Department of Astronomy, Graduate School of Science, University of Tokyo, Tokyo, Japan
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Determining Amino Acid Chirality in the Supernova Neutrino Processing Model. Symmetry (Basel) 2014. [DOI: 10.3390/sym6040909] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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12
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Danchin A, Sekowska A. The logic of metabolism and its fuzzy consequences. Environ Microbiol 2013; 16:19-28. [PMID: 24387040 DOI: 10.1111/1462-2920.12270] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/02/2013] [Accepted: 08/26/2013] [Indexed: 12/26/2022]
Abstract
Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L-amino acids, D-sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not the exact replicas of core metabolites. As corollary, a shadow, paralogous metabolism, is associated to standard metabolism. We focus on a logic of paralogous metabolism based on diversion of the core metabolic mimics into pathways where they are modified to minimize their input in the core pathways where they create havoc. We propose that a significant proportion of paralogues of well-characterized enzymes have evolved as the natural way to cope with paralogous metabolites. A second type of denouement uses a process where protecting/deprotecting unwanted metabolites - conceptually similar to the procedure used in the laboratory of an organic chemist - is used to enter a completely new catabolic pathway.
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Affiliation(s)
- Antoine Danchin
- Building G1, AMAbiotics SAS, 2 rue Gaston Crémieux, Evry, 91000, France
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