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Crespi S, Vadivel D, Bellisario A, Dondi D. Computational Study of the Stability of Natural Amino Acid isomers. ORIGINS LIFE EVOL B 2021; 51:287-298. [PMID: 34739664 DOI: 10.1007/s11084-021-09615-2] [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: 04/14/2021] [Accepted: 08/10/2021] [Indexed: 10/19/2022]
Abstract
The secular debate on the origin of life on our planet represents one of the open challenges for the scientific community. In this endeavour, chemistry has a pivotal role in disclosing novel scenarios that allow us to understand how the formation of simple organic molecules would be possible in the early primitive geological ages of Earth. Amino acids play a crucial role in biological processes. They are known to be formed in experiments simulating primitive conditions and were found in meteoric samples retrieved throughout the years. Understanding their formation is a key step for prebiotic chemistry. Following this reasoning, we performed a computational investigation over 100'000 structural isomers of natural amino acids. The results we have found suggest that natural amino acids are among the most thermodynamically stable structures and, therefore, one of the most probable ones to be synthesised among their possible isomers.
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Affiliation(s)
- Stefano Crespi
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dhanalakshmi Vadivel
- Dipartimento Di Chimica, Università Di Pavia, Via Taramelli 12, 27100, Pavia, Italy. .,Istituto Nazionale Di Fisica Nucleare (INFN), Via Bassi 6, 27100, Pavia, Italy.
| | - Alfredo Bellisario
- Department of Cell and Molecular Biology, Molecular Biophysics, Husargatan 3, 752 37, Uppsala, Sweden
| | - Daniele Dondi
- Dipartimento Di Chimica, Università Di Pavia, Via Taramelli 12, 27100, Pavia, Italy.,Istituto Nazionale Di Fisica Nucleare (INFN), Via Bassi 6, 27100, Pavia, Italy
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2
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Ying J, Ding R, Liu Y, Zhao Y. Prebiotic Chemistry in Aqueous Environment: A Review of Peptide Synthesis and Its Relationship with Genetic Code. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianxi Ying
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Yan Liu
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
| | - Yufen Zhao
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
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Abstract
Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.
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Son J, Baek Y, Kim S, Lee K, Lee PH. Rhodium(
III
)‐Catalyzed N−H Insertion Reaction of Phosphoryl Amides with
α‐Aryl
Diazoesters for the Synthesis of
α‐Phosphoryl
Amino Esters. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jeong‐Yu Son
- Department of ChemistryKangwon National University Chuncheon 24341 Republic of Korea
| | - Yonghyeon Baek
- Department of ChemistryKangwon National University Chuncheon 24341 Republic of Korea
| | - Sanghyuck Kim
- Department of ChemistryKangwon National University Chuncheon 24341 Republic of Korea
| | - Kyungsup Lee
- Department of ChemistryKangwon National University Chuncheon 24341 Republic of Korea
| | - Phil Ho Lee
- Department of ChemistryKangwon National University Chuncheon 24341 Republic of Korea
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Chen X, Xiao Z, Chu H, Wang B, Peng AY. Reinvestigation of the iodine-mediated phosphoramidation reaction of amines and P(OR) 3 and its synthetic applications. Org Biomol Chem 2019; 16:6783-6790. [PMID: 30198043 DOI: 10.1039/c8ob01840e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study on the iodine-mediated phosphoramidation reaction of amines and trialkyl phosphites was conducted, which not only disclosed the factors affecting the reaction but also revealed that it could proceed smoothly in CH2Cl2 at room temperature in open air. Using this method, various phosphoramidates with different aliphatic amines and aromatic amines were synthesized in good to excellent yields. Our present investigation shows that this underused method is actually a mild, practical and general way to synthesize phosphoramidates and will have wide applications.
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Affiliation(s)
- Xunwei Chen
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, 510275, China.
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How Prebiotic Chemistry and Early Life Chose Phosphate. Life (Basel) 2019; 9:life9010026. [PMID: 30832398 PMCID: PMC6462974 DOI: 10.3390/life9010026] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/18/2022] Open
Abstract
The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox about early stages: How could these species be selected in the absence of enzymes? This review is aimed at demonstrating that considering mixed anhydrides or other species more reactive than esters and anhydrides can help in solving the paradox. The consequences of this approach for chemical evolution and early stages of life are analysed.
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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Zhang S, Shi J, Shan C, Huang C, Wu Y, Ding R, Xue Y, Liu W, Zhou Q, Zhao Y, Xu P, Gao X. Stable isotope N -phosphoryl amino acids labeling for quantitative profiling of amine-containing metabolites using liquid chromatography mass spectrometry. Anal Chim Acta 2017; 978:24-34. [DOI: 10.1016/j.aca.2017.04.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/10/2017] [Accepted: 04/20/2017] [Indexed: 12/16/2022]
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Abstract
In this paper, we revisit several issues relevant to origin-of-life research and propose a Phosphate Transfer Catalyst hypothesis that furthers our understanding of some of the key events in prebiotic chemical evolution. In the Phosphate Transfer Catalyst hypothesis, we assume the existence of hypothetical metallopeptides with phosphate transfer activity that use abundant polyphosphates as both substrates and energy sources. Nonspecific catalysis by this phosphate transfer catalyst would provide a variety of different products such as phosphoryl amino acids, nucleosides, polyphosphate nucleotides, nucleic acids, and aminoacylated nucleic acids. Moreover, being an autocatalytic set and metabolic driver at the same time, it could possibly replicate itself and produce a collective system of two polymerases; a nucleic acid able to catalyze peptide bond formation and a peptide able to polymerize nucleic acids. The genetic code starts at first as a system that reduces the energy barrier by bringing substrates (2'/3' aminoacyl-nucleotides) together, an ancestral form of the catalysis performed by modern ribosomes. Key Words: Origin of life-Prebiotic chemistry-Catalysis-Nucleic acids. Astrobiology 17, 277-285.
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Yuan J, Yang L, Xiao Y, Qu L. Novel synthesis of steryl esteryl esters from β-sitosterol and N-phosphoryl amino acid under microwave irradiation. PHOSPHORUS SULFUR 2016. [DOI: 10.1080/10426507.2016.1206102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jinwei Yuan
- School of Chemistry & Chemical Engineering, Henan University of Technology, Zhengzhou, P. R. China; Academician Workstation for Natural Medical Chemistry of Henan Province, Zhengzhou, P. R. China
| | - Liangru Yang
- School of Chemistry & Chemical Engineering, Henan University of Technology, Zhengzhou, P. R. China; Academician Workstation for Natural Medical Chemistry of Henan Province, Zhengzhou, P. R. China
| | - Yongmei Xiao
- School of Chemistry & Chemical Engineering, Henan University of Technology, Zhengzhou, P. R. China; Academician Workstation for Natural Medical Chemistry of Henan Province, Zhengzhou, P. R. China
| | - Lingbo Qu
- School of Chemistry & Chemical Engineering, Henan University of Technology, Zhengzhou, P. R. China; Academician Workstation for Natural Medical Chemistry of Henan Province, Zhengzhou, P. R. China
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12
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Ni F, Fu C, Gao X, Liu Y, Xu P, Liu L, Lv Y, Fu S, Sun Y, Han D, Li Y, Zhao Y. N-phosphoryl amino acid models for P-N bonds in prebiotic chemical evolution. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5321-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Using positive-ion electrospray ionization mass spectrometry and H/D exchange study phosphoryl group transfer reactions involved in amino acid ester isopropyl phosphoramidates of Brefeldin A. Anal Chim Acta 2015; 853:391-401. [PMID: 25467484 DOI: 10.1016/j.aca.2014.09.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/22/2014] [Accepted: 09/29/2014] [Indexed: 11/21/2022]
Abstract
As mini-chemical models, amino acid ester isopropyl phosphoramidates of Brefeldin A (compounds 2a-2d) were synthesized and investigated by electrospray ionization tandem mass spectrometry in combination with H/D exchange. To further confirm the fragments's structures, off-line Fourier transform resonance tandem mass spectrometry (FT-ICR-MS/MS) was also performed. The fragmentation rules of compounds 2a-2d have been summarized and the plausible schemes for the fragmentation pathways were proposed. In this study, one dephosphorylated ion and two phosphorylated ions were observed in ESI-MS(2) spectra of [M+Na](+) ions for compounds 2a-2d. The possible mechanisms about phosphorylation and dephosphorylation were proposed and confirmed by H/D exchange. For the "dephosphorylation" rearrangement, a nitrogen atom was migrated from the phosphoryl group to the carbon atom of Brefeldin A's backbone with losing a molecule of C3H7PO3 (122 Da). For the "phosphorylation" rearrangement, an oxygen atom of one phosphoryl group attacked the sideward phosphorus atom to form a nine-member ring intermediate, then two steps of CH covalent bond cleavage with consecutive migration of hydrogen atom to lose a molecule of C16H20O2 (244 Da). The two proposed rearrangement mechanisms about phosphoryl group transfer might be valuable for the structure analysis of other analogs and provide insights into elucidating the dynamic process of the phosphorylation-dephosphorylation of proteins.
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14
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Gao X, Deng H, Tang G, Liu Y, Xu P, Zhao Y. Intermolecular Phosphoryl Transfer of N-Phosphoryl Amino Acids. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100234] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Gao X, Hu X, Zhu J, Zeng Z, Han D, Tang G, Huang X, Xu P, Zhao Y. An isotope (18O, 15N, and 2H) technique to investigate the metal ion interactions between the phosphoryl group and amino acid side chains by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:689-702. [PMID: 21472608 DOI: 10.1007/s13361-010-0069-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Revised: 12/24/2010] [Accepted: 12/28/2010] [Indexed: 05/30/2023]
Abstract
Cationic metal ion-coordinated N-diisopropyloxyphosphoryl dipeptides (DIPP-dipeptides) were analyzed by electrospray ionization multistage tandem mass spectrometry (ESI-MS(n)). Two novel rearrangement reactions with hydroxyl oxygen or carbonyl oxygen migrations were observed in ESI-MS/MS of the metallic adducts of DIPP-dipeptides, but not for the corresponding protonated DIPP-dipeptides. The possible oxygen migration mechanisms were elucidated through a combination of MS/MS experiments, isotope ((18)O, (15)N, and (2)H) labeling, accurate mass measurements, and density functional theory (DFT) calculations at the B3LYP/6-31 G(d) level. It was found that lithium and sodium cations catalyze the carbonyl oxygen migration more efficiently than does potassium and participation through a cyclic phosphoryl intermediate. In addition, dipeptides having a C-terminal hydroxyl or aromatic amino acid residue show a more favorable rearrangement through carbonyl oxygen migration, which may be due to metal cation stabilization by the donation of lone pair of the hydroxyl oxygen or aromatic π-electrons of the C-terminal amino acid residue, respectively. It was further shown that the metal ions, namely lithium, sodium, and potassium cations, could play a novel directing role for the migration of hydroxyl or carbonyl oxygen in the gas phase. This discovery suggests that interactions between phosphorylated biomolecules and proteins might involve the assistance of metal ions to coordinate the phosphoryl oxygen and protein side chains to achieve molecular recognition.
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Affiliation(s)
- Xiang Gao
- Department of Chemistry and The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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ZHAO LIJIAO, LIU TINGTING, ZHONG RUGANG. A COMPARISON OF THE STEREOISOMERIC PENTA-COORDINATED PHOSPHORUS INTERMEDIATES FORMED FROM 19 DIMETHOXYL N-PHOSPHORYL AMINO ACIDS BY DFT CALCULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633611006360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
N-phosphoryl amino acids (PAAs) are important species in the origin of life that self-catalyze and self-assemble into polypeptides and polynucleotides under mild conditions. Both experimental and theoretical studies have shown that a penta-coordinated phosphorus intermolecular mixed carboxylic-phosphoric anhydride (IMCPA) is formed as the common intermediate in these reactions. In this work, the mechanism for the formation of stereoisomeric IMCPAs from PAAs is investigated using density functional theory (DFT) calculations at the B3LYP/6-311+G(d,p) theoretical level. The molecular structures of the cis- and the trans-IMCPAs, as well as the transition states of the two stereochemical reaction pathways, were characterized in detail. The results showed that the hydroxyl groups of PAAs were situated in favorable positions for attacking the phosphorus atom from two sides of the phosphoryl group, resulting in the formation of the cis-IMCPA and the trans-IMCPA, respectively. The trans-isomers were predicted to be more likely to undergo a further reaction involving an ester exchange on the phosphorus than the cis-isomers. By comparing the relative energies of the IMCPAs and the activation energies, the trans-IMCPAs were computed to be more stable than the cis-IMCPAs, but the energy barriers for the formation of the trans- and the cis-isomers were similar. This work is expected to shed light on the stereochemical effect involved in the chemical evolution of biomolecules.
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Affiliation(s)
- LIJIAO ZHAO
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - TINGTING LIU
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - RUGANG ZHONG
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
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Gao X, Ni F, Bao J, Liu Y, Zhang Z, Xu P, Zhao Y. Formation of cyclic acylphosphoramidates in mass spectra of N-monoalkyloxyphosphoryl amino acids using electrospray ionization tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:779-787. [PMID: 20544690 DOI: 10.1002/jms.1768] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The fragmentation reactions of N-monoalkyloxyphosphoryl amino acids (N-MAP-AAs) were studied by electrospray ionization tandem mass spectrometry (ESI-MS). The sodiated cyclic acylphosphoramidates (CAPAs) were formed through a characteristic pentacoordinate phosphate participated rearrangement reaction in the positive-ion ESI-MS/MS and HR-MS/MS of N-MAP-AAs, in which the fragmentation patterns were clearly different from those observed in the corresponding ESI-MS/MS of N-dialkyloxyphosphoryl amino acids/peptides and N-phosphono amino acids. The formation of CAPAs depended on the chemical structures of N-terminal phosphoryl groups, such as alkyloxy group, negative charge and alkali metal ion. A possible integrated rearrangement mechanism for both P-N to P-O phosphoryl group migration and formation of CAPAs was proposed. The fragmentation patterns of CAPAs as novel intermediates in gas phase were also investigated. In addition, it was found that the formation of alpha-amino acid CAPAs was more favorable than beta- or gamma-CAPAs in gas phase, which was consistent with previous solution-phase experiments.
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Affiliation(s)
- Xiang Gao
- Department of Chemistry and The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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Han DX, Wang HY, Ji ZL, Hu AF, Zhao YF. Amino acid homochirality may be linked to the origin of phosphate-based life. J Mol Evol 2010; 70:572-82. [PMID: 20506019 DOI: 10.1007/s00239-010-9353-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 05/06/2010] [Indexed: 10/19/2022]
Abstract
Phosphorylation has to have been one of the key events in prebiotic evolution on earth. In this article, the emergence of phosphoryl amino acid 5'-nucleosides having a P-N bond is described as a model of the origin of amino acid homochirality and Genetic Code. It is proposed that the intramolecular interaction between the nucleotide base and the amino acid side-chain influences the stability of particular amino acid 5'-nucleotides, and the interaction also selects for the chirality of amino acids. The differences between L: - and D: -conformation energies (DeltaE (conf)) are evaluated by DFT methods at the B3LYP/6-31G(d) level. Although, as expected, these DeltaE (conf) values are not large, they do give differences in energy that can distinguish the chirality of amino acids. Based on our calculations, the chiral selection of the earliest amino acids for L: -enantiomers seems to be determined by a clear stereochemical/physicochemical relationship. As later amino acids developed from the earliest amino acids, we deduce that the chirality of these late amino acids was inherited from that of the early amino acids. This idea reaches far back into evolution, and we hope that it will guide further experiments in this area.
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Affiliation(s)
- Da Xiong Han
- Department of Pharmacy, Medical College of Xiamen University, Xiamen, 361005, China.
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19
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Ni F, Gao X, Zhao ZX, Huang C, Zhao YF. On the Electrophilicity of Cyclic Acylphosphoramidates (CAPAs) Postulated as Intermediates. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900227] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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21
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Oña Burgos P, Fernández I, Iglesias MJ, García-Granda S, López Ortiz F. Phosphinamide-Directed Benzylic Lithiation. Application to the Synthesis of Peptide Building Blocks. Org Lett 2008; 10:537-40. [DOI: 10.1021/ol7028096] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pascual Oña Burgos
- Área de Química Orgánica, Universidad de Almería, Carretera de Sacramento s/n, 04120 Almería, Spain, and Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
| | - Ignacio Fernández
- Área de Química Orgánica, Universidad de Almería, Carretera de Sacramento s/n, 04120 Almería, Spain, and Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
| | - María José Iglesias
- Área de Química Orgánica, Universidad de Almería, Carretera de Sacramento s/n, 04120 Almería, Spain, and Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
| | - Santiago García-Granda
- Área de Química Orgánica, Universidad de Almería, Carretera de Sacramento s/n, 04120 Almería, Spain, and Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
| | - Fernando López Ortiz
- Área de Química Orgánica, Universidad de Almería, Carretera de Sacramento s/n, 04120 Almería, Spain, and Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
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Fishkis M. Steps towards the formation of a protocell: the possible role of short peptides. ORIGINS LIFE EVOL B 2007; 37:537-53. [PMID: 17874202 DOI: 10.1007/s11084-007-9111-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 08/15/2007] [Indexed: 10/22/2022]
Abstract
The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.
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Affiliation(s)
- Maya Fishkis
- Evolving Systems Technology, 95 Hawkfield Crescent NW, Calgary, Alberta, Canada.
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Han D, Chen W, Han B, Zhao Y. A new theoretical model for the origin of amino acid homochirality. ACTA ACUST UNITED AC 2007; 50:580-6. [PMID: 17879054 DOI: 10.1007/s11427-007-0087-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Accepted: 07/05/2007] [Indexed: 12/21/2022]
Abstract
Amino acid homochirality, as a unique behavior of life, could have originated synchronously with the genetic code. In this paper, phosphoryl amino-acid-5'-nucleosides with P-N bond are postulated to be a chiral origin model in prebiotic molecular evolution. The enthalpy change in the intramolecular interaction between the nucleotide base and the amino-acid side-chain determines the stability of the particular complex, resulting in a preferred conformation associated with the chirality of amino acids. Based on the theoretical model, our experiments and calculations show that the chiral selection of the earliest amino acids for L-enantiomers seems to be a strict stereochemical/physicochemical determinism. As other amino acids developed biosynthetically from the earliest amino acids, we infer that the chirality of the later amino acids was inherited from the precursor amino acids. This idea probably goes far back in history, but it is hoped that it will be a guide for further experiments in this area.
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Affiliation(s)
- DaXiong Han
- Department of Pharmacy, Medical College of Xiamen University, Xiamen 361005, China.
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Qiang LM, Cao SX, Guo YC, Liao XC, Zhao YF. Interaction between N-phosphoryl-α-, β- and γ-amino acids and nucleosides. CHINESE CHEM LETT 2007. [DOI: 10.1016/j.cclet.2007.05.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
Amino acids were most likely available on the primitive Earth, produced in the primitive atmosphere or in hydrothermal vents. Import of extraterrestrial amino acids may have represented the major supply, as suggested by micrometeorite collections and simulation experiments in space and in the laboratory. Selective condensation of amino acids in water has been achieved via N-carboxy anydrides. Homochiral peptides with an alternating sequence of hydrophobic and hydrophilic amino acids adopt stereoselective and thermostable beta-pleated sheet structures. Some of the homochiral beta-sheets strongly accelerate the hydrolysis of oligoribonucleotides. The beta-sheet-forming peptides have also been shown to protect their amino acids from racemization. Even if peptides are not able to self-replicate, i.e., to replicate a complete sequence from the mixture of amino acids, the accumulation of chemically active peptides on the primitive Earth appears plausible via thermostable and stereoselective beta-sheets made of alternating sequences.
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Affiliation(s)
- André Brack
- Centre de Biophysique Moléculaire, CNRS, rue Charles Sadron, F-45071 Orléans Cedex 2.
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