1
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Zhang L, Zhang M, Guo X, Gan D, Ye Y, Zhao Y, Ying J. A model for N-to-C direction in prebiotic peptide synthesis. Chem Commun (Camb) 2024; 60:2748-2751. [PMID: 38362617 DOI: 10.1039/d3cc06101a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Drawing inspiration from the initiating amino acid modification in biosynthetic peptides, we have successfully demonstrated a biomimetic mechanism for N-to-C terminal extension in prebiotic peptide synthesis. This achievement was accomplished by using acetylated amino acid amides as the N-terminal substrate for peptide synthesis and amino acid amides as the C-terminal extension, with the reaction carried out in a dry-wet cycle at 80 °C without requiring any activators. This provides a plausible pathway for the formation of prebiotic peptides.
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Affiliation(s)
- Li Zhang
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, China.
| | - Min Zhang
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, China.
| | - Xiaofan Guo
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, China.
| | - Dingwei Gan
- School of Electrical Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, China
| | - Yong Ye
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, China.
- College of Chemistry and Chemical Engineering, Xiamen University, No. 422, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, China.
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2
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Sheng Q, Intoy BF, Halley JW. Effects of Activation Barriers on Quenching to Stabilize Prebiotic Chemical Systems. Life (Basel) 2024; 14:116. [PMID: 38255731 PMCID: PMC11232558 DOI: 10.3390/life14010116] [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: 12/04/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
We have previously shown in model studies that rapid quenches of systems of monomers interacting to form polymer chains can fix nonequilibrium chemistries with some lifelike properties. We suggested that such quenching processes might have occurred at very high rates on early Earth, giving an efficient mechanism for natural sorting through enormous numbers of nonequilibrium chemistries from which the most lifelike ones could be naturally selected. However, the model used for these studies did not take account of activation barriers to polymer scission (peptide bond hydrolysis in the case of proteins). Such barriers are known to exist and are expected to enhance the quenching effect. Here, we introduce a modified model which takes activation barriers into account and we compare the results to data from experiments on quenched systems of amino acids. We find that the model results turn out to be sensitive to the width of the distribution of barrier heights but quite insensitive to its average value. The results of the new model are in significantly better agreement with the experiments than those found using our previous model. The new parametrization of the model only requires one new parameter and the parametrization is more physical than the previous one, providing a chemical interpretation of the parameter p in our previous models. Within the model, a characteristic temperature Tc emerges such that if the temperature of the hot stage is above Tc and the temperature of the cold stage is below it, then the 'freezing out', in a quench, of a disequilibrium ensemble of long polymers is expected. We discuss the possible relevance of this to models of the origin of life in emissions from deep ocean rifts.
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Affiliation(s)
| | | | - J. W. Halley
- School of Physics and Astronomy, University of Minnesota-Twin
Cities, Minneapolis, MN 55455, USA (B.F.I.)
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3
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Boigenzahn H, Gagrani P, Yin J. Enhancement of Prebiotic Peptide Formation in Cyclic Environments. ORIGINS LIFE EVOL B 2023; 53:157-173. [PMID: 37897620 DOI: 10.1007/s11084-023-09641-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 10/30/2023]
Abstract
The dynamic behaviors of prebiotic reaction networks may be critically important to understanding how larger biopolymers could emerge, despite being unfavorable to form in water. We focus on understanding the dynamics of simple systems, prior to the emergence of replication mechanisms, and what role they may have played in biopolymer formation. We specifically consider the dynamics in cyclic environments using both model and experimental data. Cyclic environmental conditions prevent a system from reaching thermodynamic equilibrium, improving the chance of observing interesting kinetic behaviors. We used an approximate kinetic model to simulate the dynamics of trimetaphosphate (TP)-activated peptide formation from glycine in cyclic wet-dry conditions. The model predicts that environmental cycling allows trimer and tetramer peptides to sustain concentrations above the predicted fixed points of the model due to overshoot, a dynamic phenomenon. Our experiments demonstrate that oscillatory environments can shift product distributions in favor of longer peptides. However, experimental validation of certain behaviors in the kinetic model is challenging, considering that open systems with cyclic environmental conditions break many of the common assumptions in classical chemical kinetics. Overall, our results suggest that the dynamics of simple peptide reaction networks in cyclic environments may have been important for the formation of longer polymers on the early Earth. Similar phenomena may have also contributed to the emergence of reaction networks with product distributions determined not by thermodynamics, but rather by kinetics.
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Affiliation(s)
- Hayley Boigenzahn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA
| | - Praful Gagrani
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA.
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4
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Boigenzahn H, González LD, Thompson JC, Zavala VM, Yin J. Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network. J Mol Evol 2023; 91:730-744. [PMID: 37796316 DOI: 10.1007/s00239-023-10132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
Abstract
Although our understanding of how life emerged on Earth from simple organic precursors is speculative, early precursors likely included amino acids. The polymerization of amino acids into peptides and interactions between peptides are of interest because peptides and proteins participate in complex interaction networks in extant biology. However, peptide reaction networks can be challenging to study because of the potential for multiple species and systems-level interactions between species. We developed and employed a computational network model to describe reactions between amino acids to form di-, tri-, and tetra-peptides. Our experiments were initiated with two of the simplest amino acids, glycine and alanine, mediated by trimetaphosphate-activation and drying to promote peptide bond formation. The parameter estimates for bond formation and hydrolysis reactions in the system were found to be poorly constrained due to a network property known as sloppiness. In a sloppy model, the behavior mostly depends on only a subset of parameter combinations, but there is no straightforward way to determine which parameters should be included or excluded. Despite our inability to determine the exact values of specific kinetic parameters, we could make reasonably accurate predictions of model behavior. In short, our modeling has highlighted challenges and opportunities toward understanding the behaviors of complex prebiotic chemical experiments.
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Affiliation(s)
- Hayley Boigenzahn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - Leonardo D González
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Jaron C Thompson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Victor M Zavala
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA.
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5
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Boigenzahn H, Yin J. Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments. ORIGINS LIFE EVOL B 2022; 52:249-261. [DOI: 10.1007/s11084-022-09634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022]
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6
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Some Factors from Theory, Simulation, Experiment and Proteomes in the Current Biosphere Supporting Deep Oceans as the Location of the Origin of Terrestrial Life. Life (Basel) 2022; 12:life12091330. [PMID: 36143367 PMCID: PMC9503746 DOI: 10.3390/life12091330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/01/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Some standard arguments are reviewed supporting deep ocean trenches as a likely location for the origin of terrestrial life. An analysis of proteomes of contemporary prokaryotes carried out by this group is cited as supporting evidence, indicating that the original proteins were formed by quenching from temperatures close to the boiling point of water. Coarse-grained simulations of the network formation process which agree quite well with experiments of such quenches both in drying and rapid fluid emission from a hot to a cold fluid are also described and cited as support for such a scenario. We suggest further experiments, observations and theoretical and simulation work to explore this hypothesis.
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7
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Gan D, Ying J, Zhao Y. Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution. Front Chem 2022; 10:941228. [PMID: 35910738 PMCID: PMC9326000 DOI: 10.3389/fchem.2022.941228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 11/22/2022] Open
Abstract
Life’s origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth’s biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the “mystery of life".
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Affiliation(s)
- Dingwei Gan
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- *Correspondence: Jianxi Ying,
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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8
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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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9
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Guo Y, Ying J, Sun D, Zhang Y, Zheng M, Ding R, Liu Y, Zhao Y. Cyclic Dipeptides Formation From Linear Dipeptides Under Potentially Prebiotic Earth Conditions. Front Chem 2021; 9:675821. [PMID: 34262893 PMCID: PMC8273163 DOI: 10.3389/fchem.2021.675821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/14/2021] [Indexed: 11/30/2022] Open
Abstract
Cyclic dipeptides (DKPs) are peptide precursors and chiral catalysts in the prebiotic process. This study reports proline-containing DKPs that were spontaneously obtained from linear dipeptides under an aqueous solution. Significantly, the yields of DKPs were affected by the sequence of linear dipeptides and whether the reaction contains trimetaphosphate. These findings provide the possibility that DKPs might play a key role in the origin of life.
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Affiliation(s)
- Yeting Guo
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Yumeng Zhang
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Minyang Zheng
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Yan Liu
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China.,Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.,Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
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10
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Chizzolini F, Kent AD, Passalacqua LFM, Lupták A. Enzymatic RNA Production from NTPs Synthesized from Nucleosides and Trimetaphosphate*. Chembiochem 2021; 22:2098-2101. [PMID: 33798271 DOI: 10.1002/cbic.202100085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Indexed: 01/22/2023]
Abstract
A mechanism of nucleoside triphosphorylation would have been critical in an evolving "RNA world" to provide high-energy substrates for reactions such as RNA polymerization. However, synthetic approaches to produce ribonucleoside triphosphates (rNTPs) have suffered from conditions such as high temperatures or high pH that lead to increased RNA degradation, as well as substrate production that cannot sustain replication. Previous reports have demonstrated that cyclic trimetaphosphate (cTmp) can react with nucleosides to form rNTPs under prebiotically-relevant conditions, but their reaction rates were unknown and the influence of reaction conditions not well-characterized. Here we established a sensitive assay that allowed for the determination of second-order rate constants for all four rNTPs, ranging from 1.7×10-6 to 6.5×10-6 M-1 s-1 . The ATP reaction shows a linear dependence on pH and Mg2+ , and an enthalpy of activation of 88±4 kJ/mol. At millimolar nucleoside and cTmp concentrations, the rNTP production rate is sufficient to facilitate RNA synthesis by both T7 RNA polymerase and a polymerase ribozyme. We suggest that the optimized reaction of cTmp with nucleosides may provide a viable connection between prebiotic nucleotide synthesis and RNA replication.
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Affiliation(s)
- Fabio Chizzolini
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA
| | - Alexandra D Kent
- Department of Chemistry, University of California at Irvine, Irvine, CA, 92617, USA
| | - Luiz F M Passalacqua
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA.,Department of Chemistry, University of California at Irvine, Irvine, CA, 92617, USA.,Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, 92617, USA
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11
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Ashaolu TJ, Ashaolu JO. Prebiotic peptides, their formation, fermentation in the gut, and health implications. Biotechnol Prog 2021; 37:e3142. [PMID: 33666376 DOI: 10.1002/btpr.3142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 12/19/2022]
Abstract
Prebiotics can be synthesized from sources other than dietary fibers, such as proteins. The proteins, when processed into peptides have healthful or deleterious effects on the host. Outside living systems, prebiotic peptides (PP) are formed via preformation of amino acids or related monomeric building blocks, resulting in nonenzymatic polymerization/ligation to produce peptides. Whereas, inside living systems like the human gut, many metabolic pathways are involved in PP production, and mostly involve host-microbiota interactions. The interplay is responsible for PP activities and their implications on host amino acid balance and metabolism. Similar to carbohydrates fermentation, PP will yield short chain fatty acids (SCFA), but also branched chain fatty acids (BCFAs), phenols, indole, hydrogen sulfide, amines, and ammonia, capable of biologically mediating molecular signals. This holistic review considers a brief description of prebiotics, and tracks down prebiotic peptides formation processes, interactions with gut microbes, and health outcomes.
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Affiliation(s)
- Tolulope Joshua Ashaolu
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam.,Faculty of Environmental and Chemical Engineering, Duy Tan University, Da Nang, Vietnam
| | - Joseph O Ashaolu
- International Health Programme, School of Medicine, National Yang-Ming University, Taipei, Taiwan
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12
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Sibilska-Kaminski IK, Yin J. Toward Molecular Cooperation by De Novo Peptides. ORIGINS LIFE EVOL B 2021; 51:71-82. [PMID: 33566281 PMCID: PMC8212187 DOI: 10.1007/s11084-021-09603-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
Theoretical models of the chemical origins of life depend on self-replication or autocatalysis, processes that arise from molecular interactions, recruitment, and cooperation. Such models often lack details about the molecules and reactions involved, giving little guidance to those seeking to detect signs of interaction, recruitment, or cooperation in the laboratory. Here, we develop minimal mathematical models of reactions involving specific chemical entities: amino acids and their condensation reactions to form de novo peptides. Reactions between two amino acids form a dipeptide product, which enriches linearly in time; subsequent recruitment of such products to form longer peptides exhibit super-linear growth. Such recruitment can be reciprocated: a peptide contributes to and benefits from the formation of one or more other peptides; in this manner, peptides can cooperate and thereby exhibit autocatalytic or exponential growth. We have started to test these predictions by quantitative analysis of de novo peptide synthesis conducted by wet-dry cycling of a five-amino acid mixture over 21 days. Using high-performance liquid chromatography, we tracked abundance changes for >60 unique peptide species. Some species were highly transient, with the emergence of up to 17 new species and the extinction of nine species between samplings, while other species persisted across many cycles. Of the persisting species, most exhibited super-linear growth, a sign of recruitment anticipated by our models. This work shows how mathematical modeling and quantitative analysis of kinetic data can guide the search for prebiotic chemistries that have the potential to cooperate and replicate.
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Affiliation(s)
- Izabela K Sibilska-Kaminski
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery , University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery , University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA.
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13
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Sheng Q, Intoy B, Halley JW. Quenching to fix metastable states in models of prebiotic chemistry. Phys Rev E 2021; 102:062412. [PMID: 33465996 DOI: 10.1103/physreve.102.062412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/13/2020] [Indexed: 11/07/2022]
Abstract
For prebiotic chemistry to succeed in producing a starting metastable, autocatalytic and reproducing system subject to evolutionary selection it must satisfy at least two apparently contradictory requirements: Because such systems are rare, a search among vast numbers of molecular combinations must take place naturally, requiring rapid rearrangement and breaking of covalent bonds. But once a relevant system is found, such rapid disruption and rearrangement would be very likely to destroy the system before much evolution could take place. In this paper we explore the possibility, using a model developed previously, that the search process could occur under different environmental conditions than the subsequent fixation and growth of a lifelike chemical system. We use the example of a rapid change in temperature to illustrate the effect and refer to the rapid change as a "quench"borrowing terminology from study of the physics and chemistry of glass formation. The model study shows that interrupting a high-temperature nonequilibrium state with a rapid quench to lower temperatures can substantially increase the probability of producing a chemical state with lifelike characteristics of nonequilibrium metastability, internal dynamics and exponential population growth in time. Previously published data on the length distributions of proteomes of prokaryotes may be consistent with such an idea and suggest a prebiotic high-temperature "search" phase near the boiling point of water. A rapid change in pH could have a similar effect. We discuss possible scenarios on early Earth which might have allowed frequent quenches of the sort considered here to have occurred. The models show a strong dependence of the effect on the number of chemical monomers available for bond formation.
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Affiliation(s)
- Qianyi Sheng
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ben Intoy
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J W Halley
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
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14
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Kovalenko SP. Physicochemical Processes That Probably Originated Life. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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A Polymeric Composite Material (rGO/PANI) for Acid Blue 129 Adsorption. Polymers (Basel) 2020; 12:polym12051051. [PMID: 32375280 PMCID: PMC7285098 DOI: 10.3390/polym12051051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Over the years, polyaniline (PANI) has received enormous attention due to its unique properties. Herein, it was chosen to develop a new polymeric composite material: reduced graphene oxide/polyaniline (rGO/PANI). The composite was prepared by a simple and cost-effective fabrication method of formation by mixing and sonication in various conditions. The obtained materials were characterized and identified using various techniques such as scanning electron microscopy (SEM), Raman and ATR–FTIR spectroscopy, and X-ray diffraction (XRD). The objective of the paper was to confirm its applicability for the removal of contaminants from water. Water could be contaminated by various types of pollutants, e.g., inorganics, heavy metals, and many other industrial compounds, including dyes. We confirmed that the Acid Blue 129 dyes can be substantially removed through adsorption on prepared rGO/PANI. The adsorption kinetic data were modeled using the pseudo-first-order and pseudo-second-order models and the adsorption isotherm model was identified.
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16
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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