101
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Grochmal A, Prout L, Makin-Taylor R, Prohens R, Tomas S. Modulation of reactivity in the cavity of liposomes promotes the formation of peptide bonds. J Am Chem Soc 2015; 137:12269-75. [PMID: 26356087 DOI: 10.1021/jacs.5b06207] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In living cells, reactions take place in membrane-bound compartments, often in response to changes in the environment. Learning how the reactions are influenced by this compartmentalization will help us gain an optimal understanding of living organisms at the molecular level and, at the same time, will offer vital clues on the behavior of simple compartmentalized systems, such as prebiotic precursors of cells and cell-inspired artificial systems. In this work we show that a reactive building block (an activated amino acid derivative) trapped in the cavity of a liposome is protected against hydrolysis and reacts nearly quantitatively with another building block, which is membrane-permeable and free in solution, to form the dipeptide. By contrast, when the activated amino acid is found outside the liposome, hydrolysis is the prevalent reaction, showing that the cavity of the liposomes promotes the formation of peptide bonds. We attribute this result to the large lipid concentration in small compartments from the point of view of a membrane-impermeable molecule. Based on this result, we show how the outcome of the reaction can be predicted as a function of the size of the compartment. The implications of these results on the behavior of biomolecules in cell compartments, abiogenesis, and the design of artificial cell-inspired systems are considered.
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Affiliation(s)
- Anna Grochmal
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Luba Prout
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Robert Makin-Taylor
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Rafel Prohens
- CIRCE Crystal Engineering , 07121 Palma de Mallorca, Spain.,Unitat de Polimorfisme i Calorimetria, CCiT, Universitat de Barcelona , 08028 Barcelona, Spain
| | - Salvador Tomas
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
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102
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Forsythe JG, Yu SS, Mamajanov I, Grover MA, Krishnamurthy R, Fernández FM, Hud NV. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503792] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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103
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Forsythe JG, Yu SS, Mamajanov I, Grover MA, Krishnamurthy R, Fernández FM, Hud NV. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth. Angew Chem Int Ed Engl 2015. [PMID: 26201989 PMCID: PMC4678426 DOI: 10.1002/anie.201503792] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors.
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Affiliation(s)
- Jay G Forsythe
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Sheng-Sheng Yu
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Irena Mamajanov
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Martha A Grover
- NSF/NASA Center for Chemical Evolution (USA).,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA (USA)
| | - Ramanarayanan Krishnamurthy
- NSF/NASA Center for Chemical Evolution (USA). .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA (USA).
| | - Facundo M Fernández
- NSF/NASA Center for Chemical Evolution (USA). .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA).
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution (USA). .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (USA).
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104
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105
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From the RNA world to the RNA/protein world: contribution of some riboswitch-binding species? J Theor Biol 2015; 370:197-201. [PMID: 25571850 DOI: 10.1016/j.jtbi.2014.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 12/16/2022]
Abstract
Some amino acids and their formal derivatives, currently riboswitch-binding species, could have interacted with polyribonucletides in prebiotic environments, leading to the peptide formation. If the resulting compounds had led to a sustainable polymerization of amino acids and the new structures had catalytic activity, such would have been an important contribution to the transition from the RNA world to the RNA/Protein world.
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106
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Feng Z, Castellarin Cudia C, Floreano L, Morgante A, Comelli G, Dri C, Cossaro A. A competitive amino-carboxylic hydrogen bond on a gold surface. Chem Commun (Camb) 2015; 51:5739-42. [DOI: 10.1039/c4cc10271a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel amino-carboxylic hetero-synthon is described, which drives the formation of a complex 2D hetero-organic architecture.
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Affiliation(s)
- Zhijing Feng
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | | | - Luca Floreano
- CNR-IOM Laboratorio Nazionale TASC
- I-34149 Trieste
- Italy
| | - Alberto Morgante
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | - Giovanni Comelli
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
| | - Carlo Dri
- Department of Physics
- University of Trieste
- Trieste
- Italy
- CNR-IOM Laboratorio Nazionale TASC
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107
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Liu Z, Beaufils D, Rossi JC, Pascal R. Evolutionary importance of the intramolecular pathways of hydrolysis of phosphate ester mixed anhydrides with amino acids and peptides. Sci Rep 2014; 4:7440. [PMID: 25501391 PMCID: PMC4262824 DOI: 10.1038/srep07440] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/21/2014] [Indexed: 01/31/2023] Open
Abstract
Aminoacyl adenylates (aa-AMPs) constitute essential intermediates of protein biosynthesis. Their polymerization in aqueous solution has often been claimed as a potential route to abiotic peptides in spite of a highly efficient CO2-promoted pathway of hydrolysis. Here we investigate the efficiency and relevance of this frequently overlooked pathway from model amino acid phosphate mixed anhydrides including aa-AMPs. Its predominance was demonstrated at CO2 concentrations matching that of physiological fluids or that of the present-day ocean, making a direct polymerization pathway unlikely. By contrast, the occurrence of the CO2-promoted pathway was observed to increase the efficiency of peptide bond formation owing to the high reactivity of the N-carboxyanhydride (NCA) intermediate. Even considering CO2 concentrations in early Earth liquid environments equivalent to present levels, mixed anhydrides would have polymerized predominantly through NCAs. The issue of a potential involvement of NCAs as biochemical metabolites could even be raised. The formation of peptide–phosphate mixed anhydrides from 5(4H)-oxazolones (transiently formed through prebiotically relevant peptide activation pathways) was also observed as well as the occurrence of the reverse cyclization process in the reactions of these mixed anhydrides. These processes constitute the core of a reaction network that could potentially have evolved towards the emergence of translation.
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Affiliation(s)
- Ziwei Liu
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
| | - Damien Beaufils
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
| | | | - Robert Pascal
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
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108
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Wang SP, Yang H, Wu JW, Gauthier N, Fukao T, Mitchell GA. Metabolism as a tool for understanding human brain evolution: lipid energy metabolism as an example. J Hum Evol 2014; 77:41-9. [PMID: 25488255 DOI: 10.1016/j.jhevol.2014.06.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 03/24/2014] [Accepted: 06/18/2014] [Indexed: 10/24/2022]
Abstract
Genes and the environment both influence the metabolic processes that determine fitness. To illustrate the importance of metabolism for human brain evolution and health, we use the example of lipid energy metabolism, i.e. the use of fat (lipid) to produce energy and the advantages that this metabolic pathway provides for the brain during environmental energy shortage. We briefly describe some features of metabolism in ancestral organisms, which provided a molecular toolkit for later development. In modern humans, lipid energy metabolism is a regulated multi-organ pathway that links triglycerides in fat tissue to the mitochondria of many tissues including the brain. Three important control points are each suppressed by insulin. (1) Lipid reserves in adipose tissue are released by lipolysis during fasting and stress, producing fatty acids (FAs) which circulate in the blood and are taken up by cells. (2) FA oxidation. Mitochondrial entry is controlled by carnitine palmitoyl transferase 1 (CPT1). Inside the mitochondria, FAs undergo beta oxidation and energy production in the Krebs cycle and respiratory chain. (3) In liver mitochondria, the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) pathway produces ketone bodies for the brain and other organs. Unlike most tissues, the brain does not capture and metabolize circulating FAs for energy production. However, the brain can use ketone bodies for energy. We discuss two examples of genetic metabolic traits that may be advantageous under most conditions but deleterious in others. (1) A CPT1A variant prevalent in Inuit people may allow increased FA oxidation under nonfasting conditions but also predispose to hypoglycemic episodes. (2) The thrifty genotype theory, which holds that energy expenditure is efficient so as to maximize energy stores, predicts that these adaptations may enhance survival in periods of famine but predispose to obesity in modern dietary environments.
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Affiliation(s)
- Shu Pei Wang
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal and CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal H3T 1C5, QC, Canada
| | - Hao Yang
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal and CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal H3T 1C5, QC, Canada; Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiang Wei Wu
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal and CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal H3T 1C5, QC, Canada
| | - Nicolas Gauthier
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal and CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal H3T 1C5, QC, Canada
| | - Toshiyuki Fukao
- Department of Pediatrics, Gifu University School of Medicine, Gifu 500, Japan
| | - Grant A Mitchell
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal and CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal H3T 1C5, QC, Canada.
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109
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Abstract
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
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110
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Beaufils D, Danger G, Boiteau L, Rossi JC, Pascal R. Diastereoselectivity in prebiotically relevant 5(4H)-oxazolone-mediated peptide couplings. Chem Commun (Camb) 2014; 50:3100-2. [PMID: 24513651 DOI: 10.1039/c3cc49580a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A stereochemical study of a potentially prebiotic peptide-forming reaction was carried out as the first part of a systems chemistry investigation of potential paths for symmetry breaking. Substantial diastereomeric excesses result from a fast epimerization of the 5(4H)-oxazolone intermediate in aqueous solution.
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Affiliation(s)
- Damien Beaufils
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS-Université Montpellier 1 & Montpellier 2, CC17006, Place E. Bataillon, 34095 Montpellier, France.
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111
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Brewer A, Davis AP. Chiral encoding may provide a simple solution to the origin of life. Nat Chem 2014; 6:569-74. [PMID: 24950314 DOI: 10.1038/nchem.1981] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 05/14/2014] [Indexed: 11/09/2022]
Abstract
The route by which the complex and specific molecules of life arose from the 'prebiotic soup' remains an unsolved problem. Evolution provides a large part of the answer, but this requires molecules that can carry information (that is, exist in many variants) and can replicate themselves. The process is commonplace in living organisms, but not so easy to achieve with simple chemical systems. It is especially difficult to contemplate in the chemical chaos of the prebiotic world. Although popular in many quarters, the notion that RNA was the first self-replicator carries many difficulties. Here, we present an alternative view, suggesting that there may be undiscovered self-replication mechanisms possible in much simpler systems. In particular, we highlight the possibility of information coding through stereochemical configurations of substituents in organic polymers. We also show that this coding system leads naturally to enantiopurity, solving the apparent problem of biological homochirality.
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Affiliation(s)
- Ashley Brewer
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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112
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Affiliation(s)
- Vanderlei G. Machado
- Departamento
de Química, Universidade Federal de Santa Catarina, UFSC, Florianópolis, SC 88040-900, Brazil
| | - Rafaela I. Stock
- Departamento
de Química, Universidade Federal de Santa Catarina, UFSC, Florianópolis, SC 88040-900, Brazil
| | - Christian Reichardt
- Fachbereich
Chemie, Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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113
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Singh P, Singh A, Kaur S, Mithu VS, Bhatti MS. Temperature, pH and H-bond synergism for peptide bond formation: synthesis of sequence specific tetra- and penta-peptides without using coupling reagent. RSC Adv 2014. [DOI: 10.1039/c4ra06187j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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114
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Van Dornshuld E, Vergenz RA, Tschumper GS. Peptide bond formation via glycine condensation in the gas phase. J Phys Chem B 2014; 118:8583-90. [PMID: 24992687 DOI: 10.1021/jp504924c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Four unique gas phase mechanisms for peptide bond formation between two glycine molecules have been mapped out with quantum mechanical electronic structure methods. Both concerted and stepwise mechanisms, each leading to a cis and trans glycylglycine product (four mechanisms total), were examined with the B3LYP and MP2 methods and Gaussian atomic orbital basis sets as large as aug-cc-pVTZ. Electronic energies of the stationary points along the reaction pathways were also computed with explicitly correlated MP2-F12 and CCSD(T)-F12 methods. The CCSD(T)-F12 computations indicate that the electronic barriers to peptide bond formation are similar for all four mechanisms (ca. 32-39 kcal mol(-1) relative to two isolated glycine fragments). The smallest barrier (32 kcal mol(-1)) is associated with the lone transition state for the concerted mechanism leading to the formation of a trans peptide bond, whereas the largest barrier (39 kcal mol(-1)) was encountered along the concerted pathway leading to the cis configuration of the glycylglycine dipeptide. Two significant barriers are encountered for the stepwise mechanisms. For both the cis and trans pathways, the early electronic barrier is 36 kcal mol(-1) and the subsequent barrier is approximately 1 kcal mol(-1) lower. A host of intermediates and transition states lie between these two barriers, but they all have very small relative electronic energies (ca. ± 4 kcal mol(-1)). The isolated cis products (glycylglycine + H2O) are virtually isoenergetic with the isolated reactants (within -1 kcal mol(-1)), whereas the trans products are about 5 kcal mol(-1) lower in energy. In both products, however, the water can hydrogen bond to the dipeptide and lower the energy by roughly 5-9 kcal mol(-1). This study indicates that the concerted process leading to a trans configuration about the peptide bond is marginally favored both thermodynamically (exothermic by ca. 5 kcal mol(-1)) and kinetically (barrier height ≈ 32 kcal mol(-1)) according to the CCSD(T)-F12/haTZ electronic energies. The other pathways have slightly larger barrier heights (by 4-8 kcal mol(-1)).
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Affiliation(s)
- Eric Van Dornshuld
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677-1848, United States
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115
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Pereira JA. Transient and sustained elementary flux mode networks on a catalytic string-based chemical evolution model. Biosystems 2014; 122:38-54. [PMID: 24971802 DOI: 10.1016/j.biosystems.2014.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 05/10/2014] [Accepted: 06/23/2014] [Indexed: 11/26/2022]
Abstract
Theoretical models designed to test the metabolism-first hypothesis for prebiotic evolution have yield strong indications about the hypothesis validity but could sometimes use a more extensive identification between model objects and real objects towards a more meaningful interpretation of results. In an attempt to go in that direction, the string-based model SSE ("steady state evolution") was developed, where abstract molecules (strings) and catalytic interaction rules are based on some of the most important features of carbon compounds in biological chemistry. The system is open with a random inflow and outflow of strings but also with a permanent string food source. Although specific catalysis is a key aspect of the model, used to define reaction rules, the focus is on energetics rather than kinetics. Standard energy change tables were constructed and used with standard formation reactions to track energy flows through the interpretation of equilibrium constant values. Detection of metabolic networks on the reaction system was done with elementary flux mode (EFM) analysis. The combination of these model design and analysis options enabled obtaining metabolic and catalytic networks showing several central features of biological metabolism, some more clearly than in previous models: metabolic networks with stepwise synthesis, energy coupling, catalysts regulation, SN2 coupling, redox coupling, intermediate cycling, coupled inverse pathways (metabolic cycling), autocatalytic cycles and catalytic cascades. The results strongly suggest that the main biological metabolism features, including the genotype-phenotype interpretation, are caused by the principles of catalytic systems and are prior to modern genetic systems principles. It also gives further theoretical support to the thesis that the basic features of biologic metabolism are a consequence of the time evolution of a random catalyst search working on an open system with a permanent food source. The importance of the food source characteristics and evolutionary possibilities are discussed.
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Affiliation(s)
- José A Pereira
- ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313 Porto, Portugal; REQUIMTE/CEQUP - Centro de Química da Universidade do Porto, R. D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal.
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116
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Parker ET, Zhou M, Burton AS, Glavin DP, Dworkin JP, Krishnamurthy R, Fernández FM, Bada JL. A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403683] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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117
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Parker ET, Zhou M, Burton AS, Glavin DP, Dworkin JP, Krishnamurthy R, Fernández FM, Bada JL. A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth. Angew Chem Int Ed Engl 2014; 53:8132-6. [DOI: 10.1002/anie.201403683] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 11/10/2022]
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118
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Wei W, Jiang N, Mei YN, Chu YL, Ge HM, Song YC, Ng SW, Tan RX. An antibacterial metabolite from Lasiodiplodia pseudotheobromae F2. PHYTOCHEMISTRY 2014; 100:103-109. [PMID: 24529576 DOI: 10.1016/j.phytochem.2014.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/17/2013] [Accepted: 01/13/2014] [Indexed: 06/03/2023]
Abstract
In searching for symbionts derived from bioactive natural products, six sulfureous diketopiperazines designated as lasiodiplines A-F (1-6) were characterized from the culture of Lasiodiplodia pseudotheobromae F2, previously residing in the apparently normal flower of Illigera rhodantha (Hernandiaceae). Identification of structures was accomplished by a combination of spectroscopic and computational approaches, in conjunction with the low-temperature (100K) single-crystal X-ray diffraction with Cu Kα radiation. Lasiodipline E (5) was demonstrated to be antibacterial against the clinical strains Streptococcus sp., Bacteroides vulgates, Peptostreptococcus sp. and Veillonella parvula, respectively, with an minimum inhibitory concentration (MIC) range of 0.12-0.25 μg/mL. In addition, compounds 4 and 6 exemplify two unusual architectures of natural cyclodipeptides, signifying the unique biochemical characteristics of the producing fungus.
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Affiliation(s)
- Wei Wei
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
| | - Nan Jiang
- School of Pharmacy, Nanjing Medical University, Nanjing 210029, PR China
| | - Ya Ning Mei
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Yan Liang Chu
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
| | - Hui Ming Ge
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
| | - Yong Chun Song
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
| | - Seik Weng Ng
- Department of Chemistry, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Ren Xiang Tan
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China.
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119
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Egel R. Origins and emergent evolution of life: the colloid microsphere hypothesis revisited. ORIGINS LIFE EVOL B 2014; 44:87-110. [PMID: 25208738 DOI: 10.1007/s11084-014-9363-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 08/14/2014] [Indexed: 11/28/2022]
Abstract
Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life's complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative 'protolife' communities, in which 'protoplasmic continuity' was maintained throughout a graded series of 'proto-biofilms', 'protoorganisms' and 'protocells' toward modern life. The proneness of organic microspheres to merge back into the bulk of sessile films by spontaneous fusion can have made large populations promiscuous from the beginning, which was important for the speed of collective evolution early on. In this protein-centered scenario, the emergent coevolution of uncoded peptides, metabolic cofactors and oligoribonucleotides was primarily optimized for system-supporting catalytic capabilities arising from nonribosomal peptide synthesis and nonreplicative ribonucleotide polymerization, which in turn incorporated other reactive micromolecular organics as vitamins and cofactors into composite macromolecular colloid films and microspheres. Template-dependent replication and gene-encoded protein synthesis emerged as secondary means for further optimization of overall efficieny later on. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms.
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Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200, Copenhagen, Denmark,
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120
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Sajewicz M, Godziek A, Maciejowska A, Kowalska T. Condensation dynamics of the L-Pro-L-Phe and L-Hyp-L-Phe binary mixtures in solution. J Chromatogr Sci 2014; 53:31-7. [PMID: 24591538 DOI: 10.1093/chromsci/bmu006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We employ the achiral liquid chromatography with diode array, evaporative light scattering and mass spectrometric detection (HPLC-DAD, HPLC-ELSD and LC-MS) to assess structural instability (understood as spontaneous oscillatory chiral conversion and spontaneous oscillatory condensation) of the two pairs of amino acids, L-proline-L-phenylalanine (L-Pro-L-Phe) and L-hydroxyproline-L-phenylalanine (L-Hyp-L-Phe), in aqueous acetonitrile. In our earlier studies, we managed to demonstrate that single amino acids in aqueous and non-aqueous solutions undergo spontaneous oscillatory chiral conversion and oscillatory condensation. We also investigated condensation in the binary L-Pro-L-Hyp mixture in aqueous solution, and proposed a theoretical model to explain the specific dynamics of this process, which involves mutual catalytic effects of the two amino acids. In this study, we demonstrate oscillatory instability with the other two amino acid pairs in the organic-aqueous solution and reflect on the dynamics of condensation in the investigated cases. The choice of L-Pro and L-Hyp is due to their important role as building blocks of collagen, which is omnipresent in the connective tissues of mammals, and largely responsible for tissue architecture and strength. L-Phe is one of the 20 exogenous amino acids and is a building block of the majority of naturally occurring proteins.
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Affiliation(s)
- Mieczysław Sajewicz
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, 40-006 Katowice, Poland
| | - Agnieszka Godziek
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, 40-006 Katowice, Poland
| | - Anna Maciejowska
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, 40-006 Katowice, Poland
| | - Teresa Kowalska
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, 40-006 Katowice, Poland
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121
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Singh P, Singh A, Kaur J, Holzer W. H-Bond activated glycosylation of nucleobases: implications for prebiotic nucleoside synthesis. RSC Adv 2014. [DOI: 10.1039/c3ra44776f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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122
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Duschmalé J, Kohrt S, Wennemers H. Peptide catalysis in aqueous emulsions. Chem Commun (Camb) 2014; 50:8109-12. [DOI: 10.1039/c4cc01759e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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123
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Danger G, Boiteau L, Rossi JC, Pascal R. Systems chemistry of α-amino acids and peptides. BIO WEB OF CONFERENCES 2014. [DOI: 10.1051/bioconf/20140204001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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124
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Goldman N, Tamblyn I. Reply to “Comment on ‘Prebiotic Chemistry Within a Simple Impacting Icy Mixture’”. J Phys Chem A 2013; 117:14295-7. [DOI: 10.1021/jp411584g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Isaac Tamblyn
- Department of Physics, University of Ontario Institute of Technology, Oshawa, Ontario L1H 7K4, Canada
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125
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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126
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Abstract
We present results of prebiotic organic synthesis in shock compressed mixtures of simple ices from quantum molecular dynamics (MD) simulations extended to close to equilibrium time scales. Given the likelihood of an inhospitable prebiotic atmosphere on early Earth, it is possible that impact processes of comets or other icy bodies were a source of prebiotic chemical compounds on the primitive planet. We observe that moderate shock pressures and temperatures within a CO2-rich icy mixture (36 GPa and 2800 K) produce a number of nitrogen containing heterocycles, which dissociate to form functionalized aromatic hydrocarbons upon expansion and cooling to ambient conditions. In contrast, higher shock conditions (48-60 GPa, 3700-4800 K) resulted in the synthesis of long carbon-chain molecules, CH4, and formaldehyde. All shock compression simulations at these conditions have produced significant quantities of simple C-N bonded compounds such as HCN, HNC, and HNCO upon expansion and cooling to ambient conditions. Our results elucidate a mechanism for impact synthesis of prebiotic molecules at realistic impact conditions that is independent of external constraints such as the presence of a catalyst, illuminating UV radiation, or pre-existing conditions on a planet.
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Affiliation(s)
- Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
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127
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Pollack JD, Gerard D, Pearl DK. Uniquely localized intra-molecular amino acid concentrations at the glycolytic enzyme catalytic/active centers of Archaea, Bacteria and Eukaryota are associated with their proposed temporal appearances on earth. ORIGINS LIFE EVOL B 2013; 43:161-87. [PMID: 23715690 DOI: 10.1007/s11084-013-9331-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 04/04/2013] [Indexed: 11/27/2022]
Abstract
The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈ 16 % of all the most-conserved sites within a volume of ≈ 7-8 Å radius from their C/ACs and decreases linearly towards the molecule's peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈ 25-30 % of all amino acids within an irregular volume bounded by ≈ 24-28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological "cost", neighbor-sequence preferences or "ordering" and some thermodynamic parameters.
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Affiliation(s)
- J Dennis Pollack
- Department of Molecular Virology, Immunology and Medical Genetics, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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128
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Danger G, Michaut A, Bucchi M, Boiteau L, Canal J, Plasson R, Pascal R. 5(4H)-Oxazolones as Intermediates in the Carbodiimide- and Cyanamide-Promoted Peptide Activations in Aqueous Solution. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207730] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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129
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Danger G, Michaut A, Bucchi M, Boiteau L, Canal J, Plasson R, Pascal R. 5(4H)-oxazolones as intermediates in the carbodiimide- and cyanamide-promoted peptide activations in aqueous solution. Angew Chem Int Ed Engl 2012; 52:611-4. [PMID: 23169705 DOI: 10.1002/anie.201207730] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/18/2012] [Indexed: 11/09/2022]
Abstract
The early days: although considered a species to be avoided in peptide chemistry, the intermediacy of 5(4H)-oxazolones is demonstrated to be essential for the formation of peptides through cyanamide and carbodiimide activation in aqueous solution.
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Affiliation(s)
- Grégoire Danger
- Spectrométries et Dynamique Moléculaire, Physique des Interactions Ioniques et Moléculaires, UMR, CNRS-Aix-Marseille Université, France.
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130
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Egel R. Life's Order, Complexity, Organization, and Its Thermodynamic-Holistic Imperatives. Life (Basel) 2012; 2:323-63. [PMID: 25371269 PMCID: PMC4187152 DOI: 10.3390/life2040323] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/30/2012] [Accepted: 11/05/2012] [Indexed: 12/17/2022] Open
Abstract
In memoriam Jeffrey S. Wicken (1942-2002)-the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken's legacy. (i) Connecting life's origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic 'charging' of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called 'microspheres' is more realistic as a kinetic transition model of primal biogenesis than 'hypercycle replication' theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic 'microspheres'. On the 'continuist vs. miraculist' schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic 'continuist' views and agenda.
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Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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