1
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Samrout OE, Berlier G, Lambert JF. Amino Acid Polymerization on Silica Surfaces. Chempluschem 2024; 89:e202300642. [PMID: 38226922 DOI: 10.1002/cplu.202300642] [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: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.
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Affiliation(s)
- Ola El Samrout
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Gloria Berlier
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, LRS, Sorbonne Université Place Jussieu, 75005, Paris, France
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2
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Zhang B, Jiang R, Dong K, Li J, Zhang Y, Ghorani B, Emadzadeh B, Nishinari K, Yang N. Controlling Solvent Polarity to Regulate Protein Self-Assembly Morphology and Its Universal Insight for Fibrillation Mechanism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7733-7746. [PMID: 38538620 DOI: 10.1021/acs.langmuir.4c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The mechanism of ethanol-induced fibrillation of β-lactoglobulin (β-lg) in the acidic aqueous solution upon heating was investigated using various techniques, mainly thioflavin T fluorescence, atomic force microscopy, nonreducing electrophoresis, mass spectrometry, Fourier transform infrared spectroscopy, and circular dichroism spectroscopy. The results showed that fibrillation occurred with a heating time increase, but high ethanol content slowed down the process. At a low ethanol volume fraction, peptides existed after heating for 2 h, with long and straight fibrils formed after 4-6 h, while at a high ethanol volume fraction, the proteins aggregated with very few peptides appeared at the early stage of heating, and short and curved fibrils formed after heating for 8 h. Ethanol weakened the hydrophobic interactions between proteins in the aqueous solution; therefore the latter could not completely balance the electrostatic repulsion, and thus suppressing the fibrillation process. It is believed that the fibrillation of β-lg in the acidic solution upon heating is mainly dominated by the polypeptide model; however, ethanol inhibited the hydrolysis of proteins, and the self-assembly mechanism changed to the monomer model.
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Affiliation(s)
- Bao Zhang
- Glyn O. Phillips Hydrocolloid Research Centre, National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering of Ministry of Education, Key Laboratory of Industrial Microbiology in Hubei Province, Department of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Ruisheng Jiang
- Glyn O. Phillips Hydrocolloid Research Centre, National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering of Ministry of Education, Key Laboratory of Industrial Microbiology in Hubei Province, Department of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Kexin Dong
- Glyn O. Phillips Hydrocolloid Research Centre, National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering of Ministry of Education, Key Laboratory of Industrial Microbiology in Hubei Province, Department of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Jing Li
- Glyn O. Phillips Hydrocolloid Research Centre, National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering of Ministry of Education, Key Laboratory of Industrial Microbiology in Hubei Province, Department of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Yan Zhang
- Glyn O. Phillips Hydrocolloid Research Centre, National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering of Ministry of Education, Key Laboratory of Industrial Microbiology in Hubei Province, Department of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
- Food Hydrocolloid International Science and Technology Cooperation Base of Hubei Province, Hubei University of Technology, Wuhan 430068, China
| | - Behrouz Ghorani
- Department of Food Nanotechnology, Research Institute of Food Science & Technology (RIFST), Mashhad 91895-157-356, Iran
| | - Bahareh Emadzadeh
- Department of Food Nanotechnology, Research Institute of Food Science & Technology (RIFST), Mashhad 91895-157-356, Iran
| | - Katsuyoshi Nishinari
- Glyn O. Phillips Hydrocolloid Research Centre, National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering of Ministry of Education, Key Laboratory of Industrial Microbiology in Hubei Province, Department of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
- Food Hydrocolloid International Science and Technology Cooperation Base of Hubei Province, Hubei University of Technology, Wuhan 430068, China
| | - Nan Yang
- Glyn O. Phillips Hydrocolloid Research Centre, National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering of Ministry of Education, Key Laboratory of Industrial Microbiology in Hubei Province, Department of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
- Food Hydrocolloid International Science and Technology Cooperation Base of Hubei Province, Hubei University of Technology, Wuhan 430068, China
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3
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Verma A, Mateo T, Quintero Botero J, Mohankumar N, Fraccia TP. Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions. Life (Basel) 2024; 14:472. [PMID: 38672743 PMCID: PMC11050796 DOI: 10.3390/life14040472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.
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Affiliation(s)
- Ajay Verma
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tiphaine Mateo
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | | | - Nishanth Mohankumar
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tommaso P. Fraccia
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
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4
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Šponer JE, Šponer J, Výravský J, Matyášek R, Kovařík A, Dudziak W, Ślepokura K. Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context. iScience 2023; 26:107600. [PMID: 37664611 PMCID: PMC10470394 DOI: 10.1016/j.isci.2023.107600] [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: 03/29/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o, Libušina třída 1, 62300 Brno, Czech Republic
- Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Wojciech Dudziak
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Katarzyna Ślepokura
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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5
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Kristoffersen KA, Måge I, Wubshet SG, Böcker U, Riiser Dankel K, Lislelid A, Rønningen MA, Afseth NK. FTIR-based prediction of collagen content in hydrolyzed protein samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 301:122919. [PMID: 37295376 DOI: 10.1016/j.saa.2023.122919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Fourier transform infrared spectroscopy (FTIR) is a powerful analytical tool that has been used for protein and peptide characterization for decades. In the present study, the objective was to investigate if FTIR can be used to predict collagen content in hydrolyzed protein samples. All samples were obtained from enzymatic protein hydrolysis (EPH) of poultry by-products providing a span in collagen content from 0.3% to 37.9% (dry weight), and the FTIR analysis was performed using dry film FTIR. Since nonlinear effects were revealed by calibration using standard partial least squares (PLS) regression, Hierarchical Cluster-based PLS (HC-PLS) calibration models were constructed. The HC-PLS model provided a low prediction error when validated using an independent test set (RMSE = 3.3% collagen), while validation using real industrial samples also showed satisfying results (RMSE = 3.2%). The results corresponded well with previously published FTIR-based studies of collagen, and characteristic spectral features for collagen were well identified in the regression models. Covariance between collagen content and other EPH related processing parameters could also be ruled out in the regression models. To the authors' knowledge, this is the first time that collagen content has been systematically studied in solutions of hydrolysed proteins using FTIR. This is also one of few examples where FTIR is successfully used to quantify protein composition. The dry-film FTIR approach presented in the study is expected to be an important tool in the growing industrial segment that is based on sustainable utilization of collagen-rich biomass.
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Affiliation(s)
- Kenneth Aase Kristoffersen
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway; Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Ingrid Måge
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Sileshi Gizachew Wubshet
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Ulrike Böcker
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Katinka Riiser Dankel
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Andreas Lislelid
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway; Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet - Oslo Metropolitan University, P.O. Box 4, St. Olavs plass, NO-0130 Oslo, Norway
| | - Mats Aksnes Rønningen
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway; Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet - Oslo Metropolitan University, P.O. Box 4, St. Olavs plass, NO-0130 Oslo, Norway
| | - Nils Kristian Afseth
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway.
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El Samrout O, Berlier G, Lambert JF, Martra G. Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces. J Phys Chem B 2023; 127:673-684. [PMID: 36637235 PMCID: PMC9884078 DOI: 10.1021/acs.jpcb.2c07382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peptide formation by amino acids condensation represents a crucial reaction in the quest of the origins of life as well as in synthetic chemistry. However, it is still poorly understood in terms of efficiency and reaction mechanism. In the present work, peptide formation has been investigated through thermal condensation of gas-phase glycine in fluctuating silica environments as a model of prebiotic environments. In-situ IR spectroscopy measurements under a controlled atmosphere reveal that a humidity fluctuating system subjected to both temperature and water activity variations results in the formation of more abundant peptides compared to a dehydrated system subjected only to temperature fluctuations cycles. A model is proposed in which hydration steps result in the hydrolysis and redistribution of the oligomers formed during previous deposition in dry conditions. This results in the formation of self-assembled aggregates with well-defined secondary structures (especially β-sheets). Upon further monomers feeding, structural elements are conserved in newly growing chains, with indications of templated polymerization. The structural dynamics of peptides were also evaluated. Rigid self-assembled structures with a high resistance to further wetting/drying cycles and inaccessibility to isotopic exchange were present in the humidity fluctuating system compared to more flexible structures in the dehydrated system. The resistance and growth of self-assembled structures were also investigated for an extended duration of Gly deposition using isotope labeling.
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Affiliation(s)
- Ola El Samrout
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy,Laboratoire
de Réactivité de Surface, LRS (UMR 7197 CNRS), Sorbonne Université, Place Jussieu, 75005Paris, France
| | - Gloria Berlier
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy,
| | - Jean-François Lambert
- Laboratoire
de Réactivité de Surface, LRS (UMR 7197 CNRS), Sorbonne Université, Place Jussieu, 75005Paris, France,
| | - Gianmario Martra
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy
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7
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El Samrout O, Fabbiani M, Berlier G, Lambert JF, Martra G. Emergence of Order in Origin-of-Life Scenarios on Mineral Surfaces: Polyglycine Chains on Silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15516-15525. [PMID: 36469018 PMCID: PMC9776562 DOI: 10.1021/acs.langmuir.2c02106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/21/2022] [Indexed: 06/17/2023]
Abstract
The polymerization of amino acids (AAs) to peptides on oxide surfaces has attracted interest owing to its high importance in biotechnology, prebiotic chemistry, and origin of life theories. However, its mechanism is still poorly understood. We tried to elucidate the reactivity of glycine (Gly) from the vapor phase on the surface of amorphous silica under controlled atmosphere at 160 °C. Infrared (IR) spectroscopy reveals that Gly functionalizes the silica surface through the formation of ester species, which represent, together with the weakly interacting silanols, crucial elements for monomers activation and polymerization. Once activated, β-turns start to form as initiators for the growth of long linear polypeptides (poly-Gly) chains, which elongate into ordered structures containing both β-sheet and helical conformations. The work also points to the role of water vapor in the formation of further self-assembled β-sheet structures that are highly resistant to hydrolysis.
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Affiliation(s)
- Ola El Samrout
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
- Laboratoire
de Réactivité de Surface, LRS, Sorbonne Université, Place Jussieu, 75005 Paris, France
| | - Marco Fabbiani
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Gloria Berlier
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Jean-François Lambert
- Laboratoire
de Réactivité de Surface, LRS, Sorbonne Université, Place Jussieu, 75005 Paris, France
| | - Gianmario Martra
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
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8
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Pantaleone S, Sodupe M, Ugliengo P, Rimola A. On the stability of peptide secondary structures on the TiO 2 (101) anatase surface: a computational insight. Phys Chem Chem Phys 2022; 25:392-401. [PMID: 36477070 DOI: 10.1039/d2cp04395e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The biological activity of proteins is partly due to their secondary structures and conformational states. Peptide chains are rather flexible so that finding ways inducing protein folding in a well-defined state is of great importance. Among the different constraint techniques, the interaction of proteins with inorganic surfaces is a fruitful strategy to stabilize selected folded states. Surface-induced peptide folding can have potential applications in different biomedicine areas, but it can also be of fundamental interest in prebiotic chemistry since the biological activity of a peptide can turn-on when folded in a given state. In this work, periodic quantum mechanical simulations (including implicit solvation effects) at the PBE-D2* level have been carried out to study the adsorption and the stability of the secondary structures (α-helix and β-sheet) of polypeptides with different chemical composition (i.e., polyglycine, polyalanine, polyglutamic acid, polylysine, and polyarginine) on the TiO2 (101) anatase surface. The computational cost is reduced by applying periodic boundary conditions to both the surface and the peptides, thus obtaining full periodic polypeptide/TiO2 surface systems. At variance with polyglycine, the interaction of the other polypeptides with the surface takes place with the lateral chain functionalities, leaving the secondary structures almost undistorted. Results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet, with the exception of the polyglutamic acid. According to the calculated adsorption energies, the affinity trend of the polypeptides with the (101) anatase surface is: polyarginine ≈ polylysine > polyglutamic acid > polyglycine ≈ polyalanine, both when adsorbed in gas phase and in presence of the implicit water solvent, which is very similar to the trend for the single amino acids. A set of implications related to the areas of surface-induced peptide folding, biomedicine and prebiotic chemistry are finally discussed.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain. .,Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
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9
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Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:ijms23084252. [PMID: 35457069 PMCID: PMC9030215 DOI: 10.3390/ijms23084252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/28/2022] Open
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
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11
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Pantaleone S, Rimola A, Ugliengo P, Sodupe M. First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO 2 (101) Anatase Surface Adopting a Full Periodic Approach. J Chem Inf Model 2021; 61:5484-5498. [PMID: 34752107 DOI: 10.1021/acs.jcim.1c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain.,Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, Perugia I-06123, Italy
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
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12
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Polisi M, Fabbiani M, Vezzalini G, Di Renzo F, Pastero L, Quartieri S, Arletti R. Amino acid encapsulation in zeolite MOR: Effect of spatial confinement. Phys Chem Chem Phys 2021; 23:20541-20552. [PMID: 34505580 DOI: 10.1039/d1cp02676c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study the absorption of glycine, α-alanine and β-alanine amino acids into the pores of the synthetic zeolite Na-mordenite was investigated with the aim of: (i) evaluating the effectiveness of the MOR framework type in amino acid adsorption (via vapor and aqueous loading); (ii) understanding the host-guest and guest-guest interactions to possibly design a tailor made material and a loading procedure able to maximize the amino acid adsorption; (iii) studying the effect of pressure on the adsorbed amino acids such as, for instance, possible amino acid condensation. The structural characterization, carried out with the combination of diffractometric and infrared spectroscopy analyses, shows that MOR can adsorb amino acids, which are found both in protonated/deprotonated (possibly also generating zwitterions) form. Vapor loading is ineffective for α-alanine, while it is effective in β-alanine and glycine adsorption, even if using different loading degrees. The shape and size of MOR channels make this zeolite suitable to accommodate a peptide. In a glycine loaded sample some molecules condensate to form cyclic dimers, while linear oligomers are detected only in a β-alanine MOR hybrid. The sample loaded with α-L-alanine from aqueous solution does not show the presence of amide bond signals, indicating that the molecules are mostly hosted in zwitterionic form in Na-MOR channels. The application of external baric stimuli does not induce substantial modifications in the structure of the glycine loaded zeolite; this result may be explained by the low number of molecules hosted in the channels. The amino acid amount within the zeolite pores is the most important reactivity parameter and an increased loading could induce chemical modifications.
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Affiliation(s)
- Michelangelo Polisi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.
| | - Marco Fabbiani
- Department of Chemistry, University of Torino, 10125 Torino, Italy.,Interdepartmental Centre "Nanostructured Surfaces and Interfaces" - NIS, University of Torino, 10125 Torino, Italy.,ICGM, UMR 5253 Univ Montpellier-CNRS-ENSCM, Montpellier, France
| | - Giovanna Vezzalini
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.
| | | | - Linda Pastero
- Department of Earth Sciences, University of Torino, 10125 Torino, Italy
| | - Simona Quartieri
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.
| | - Rossella Arletti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.
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13
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Šponer JE, Šponer J, Výravský J, Šedo O, Zdráhal Z, Costanzo G, Di Mauro E, Wunnava S, Braun D, Matyášek R, Kovařík A. Nonenzymatic, Template‐Free Polymerization of 3’,5’ Cyclic Guanosine Monophosphate on Mineral Surfaces. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o. Libušina třída 1 62300 Brno Czech Republic
- Department of Geological Sciences Faculty of Science Masaryk University Kotlářská 2 61137 Brno Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Sreekar Wunnava
- Physics Department Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Dieter Braun
- Physics Department Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
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14
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de Azambuja F, Loosen A, Conic D, van den Besselaar M, Harvey JN, Parac-Vogt TN. En Route to a Heterogeneous Catalytic Direct Peptide Bond Formation by Zr-Based Metal–Organic Framework Catalysts. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Alexandra Loosen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Dragan Conic
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | | | - Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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15
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation*. Angew Chem Int Ed Engl 2021; 60:12727-12731. [PMID: 33769680 DOI: 10.1002/anie.202100806] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. Prebiotically plausible pathways to peptides from inactivated amino acids are still unclear as most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Now, a combination of prebiotically plausible minerals and mechanochemical activation enables the oligomerization of glycine at ambient temperature in the absence of water. Raising the reaction temperature increases the degree of oligomerization concomitantly with the formation of a commonly unwanted cyclic glycine dimer (DKP). However, DKP is a productive intermediate in the mechanochemical oligomerization of glycine. The findings of this research show that mechanochemical peptide bond formation is a dynamic process that provides alternative routes towards oligopeptides and establishes new synthetic approaches for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Nikola Cindro
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - José G Hernández
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
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16
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Nikola Cindro
- Department of Organic Chemistry Faculty of Science University of Zagreb Horvatovac 102a 10000 Zagreb Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - José G. Hernández
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
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17
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Navrotsky A, Hervig R, Lyons J, Seo DK, Shock E, Voskanyan A. Cooperative formation of porous silica and peptides on the prebiotic Earth. Proc Natl Acad Sci U S A 2021; 118:e2021117118. [PMID: 33376204 PMCID: PMC7812765 DOI: 10.1073/pnas.2021117118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modern technology has perfected the synthesis of catalysts such as zeolites and mesoporous silicas using organic structure directing agents (SDA) and their industrial use to catalyze a large variety of organic reactions within their pores. We suggest that early in prebiotic evolution, synergistic interplay arose between organic species in aqueous solution and silica formed from rocks by dynamic dissolution-recrystallization. The natural organics, for example, amino acids, small peptides, and fatty acids, acted as SDA for assembly of functional porous silica structures that induced further polymerization of amino acids and peptides, as well as other organic reactions. Positive feedback between synthesis and catalysis in the silica-organic system may have accelerated the early stages of abiotic evolution by increasing the formation of polymerized species.
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Affiliation(s)
- Alexandra Navrotsky
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287;
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287
| | - Richard Hervig
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287
| | - James Lyons
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287
| | - Dong-Kyun Seo
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Everett Shock
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287
| | - Albert Voskanyan
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
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18
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Chien CY, Yu SS. Ester-mediated peptide formation promoted by deep eutectic solvents: a facile pathway to proto-peptides. Chem Commun (Camb) 2020; 56:11949-11952. [PMID: 32929424 DOI: 10.1039/d0cc03319g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ester-amide exchange reaction enables spontaneous formation of prebiotic proto-peptides under mild conditions. However, this reaction also leads to oligomers with a vast sequence diversity of ester and amide linkages. Here, we demonstrate using deep eutectic solvents as a universal strategy to regulate the reaction pathways and promote the formation of amino acid-enriched oligomers with peptide backbones.
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Affiliation(s)
- Chen-Yu Chien
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City, 70101, Taiwan, Republic of China.
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19
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Pantaleone S, Rimola A, Sodupe M. Canonical, deprotonated, or zwitterionic? II. A computational study on amino acid interaction with the TiO 2(110) rutile surface: comparison with the anatase (101) surface. Phys Chem Chem Phys 2020; 22:16862-16876. [PMID: 32666992 DOI: 10.1039/d0cp01429j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adsorption of 11 amino acids (Gly, Leu, Met, Phe, Ser, Cys, Glu, Gln, Arg, Lys, and His) on the TiO2(110) rutile surface is investigated adopting a theoretical approach, using the PBE-D2* functional as implemented in the periodic VASP code. The adsorption of the amino acids is considered in their canonical, deprotonated and zwitterionic forms. For all cases, the most stable adsorption mode adopts a bidentate (O,O) binding with surface undercoordinated Ti atoms, in agreement with previous experimental and computational studies using glycine as a test case. Such a binding mode is possible due to the surface morphology, because the Ti-Ti distances match very well with the carboxylic O-O distance. The most stable adsorption states are the deprotonated and the zwitterionic ones, the canonical one lying significantly above in energy. The relative stability between the deprotonated and the zwitterionic states results in a delicate trade-off among dative interactions (O, N, and S atoms of the amino acids with Ti atoms of the surface), H-bond interactions, dispersive forces and, to a lesser extent, steric hindrance of the amino acidic lateral chains. Finally, the difference in the amino acid adsorption between the (110) rutile and the (101) anatase surfaces is discussed both from the energetic and surface morphological standpoints, highlighting the larger reactivity of the rutile polymorph in adsorbing and deprotonating the amino acids compared with the anatase one.
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Affiliation(s)
- S Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain.
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20
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Fourier-transform infrared spectroscopy for monitoring proteolytic reactions using dry-films treated with trifluoroacetic acid. Sci Rep 2020; 10:7844. [PMID: 32398689 PMCID: PMC7217958 DOI: 10.1038/s41598-020-64583-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/16/2020] [Indexed: 12/15/2022] Open
Abstract
In this study we explore the potential of using Fourier-transform infrared (FTIR) spectra of trifluoroacetate-protein and peptide complexes for monitoring proteolytic reactions. The idea of treating dry-films of protein hydrolysates with trifluoroacetic acid (TFA) prior to FTIR analysis is based on the unique properties of TFA. By adding a large excess of TFA to protein hydrolysate samples, the possible protonation sites of the proteins and peptides will be saturated. In addition, TFA has a low boiling point when protonated as well as complex-forming abilities. When forming TFA-treated dry-films of protein hydrolysates, the excess TFA will evaporate and the deprotonated acid (CF3COO−) will interact as a counter ion with the positive charges on the sample materials. In the study, spectral changes in TFA-treated dry-films of protein hydrolysates from a pure protein and poultry by-products, were compared to the FTIR fingerprints of untreated dry-films. The results show that time-dependent information related to proteolytic reactions and, consequently, on the characteristics of the protein hydrolysates can be obtained. With additional developments, FTIR on dry-films treated with TFA may be regarded as a potential future tool for the analysis of all types of proteolytic reactions in the laboratory as well as in industry.
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21
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Pantaleone S, Salvini C, Zamirri L, Signorile M, Bonino F, Ugliengo P. A quantum mechanical study of dehydration vs. decarbonylation of formamide catalysed by amorphous silica surfaces. Phys Chem Chem Phys 2020; 22:8353-8363. [PMID: 32266913 DOI: 10.1039/d0cp00572j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formamide is abundant in the interstellar medium and was also present during the formation of the Solar system through the accretion process of interstellar dust. Under the physicochemical conditions of primordial Earth, formamide could have undergone decomposition, either via dehydration (HCN + H2O) or via decarbonylation (CO + NH3). The first reactive channel provides HCN, which is an essential molecular building block for the formation of RNA/DNA bases, crucial for the emergence of life on Earth. In this work, we studied, at the CCSD(T)/cc-pVTZ level, the two competitive routes of formamide decomposition, i.e. dehydration and decarbonylation, either in liquid formamide (by using the polarization continuum model technique) or at the interface between liquid formamide and amorphous silica. Amorphous silica was adopted as a convenient model of the crystalline silica phases ubiquitously present in the primordial (and actual) Earth's crust, and also due to its relevance in catalysis, adsorption and chromatography. Results show that: (i) silica surface sites catalyse both decomposition channels by reducing the activation barriers by about 100 kJ mol-1 with respect to the reactions in homogeneous medium, and (ii) the dehydration channel, giving rise to HCN, is strongly favoured from a kinetic standpoint over decarbonylation, the latter being, instead, slightly favoured from a thermodynamic point of view.
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Affiliation(s)
- Stefano Pantaleone
- Univ. Grenoble Alpes, CNRS, Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), 38000 Grenoble, France.
| | - Clara Salvini
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Lorenzo Zamirri
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Matteo Signorile
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Francesca Bonino
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
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22
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Sun Y, Frenkel-Pinter M, Liotta CL, Grover MA. The pH dependent mechanisms of non-enzymatic peptide bond cleavage reactions. Phys Chem Chem Phys 2020; 22:107-113. [DOI: 10.1039/c9cp05240b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide cleavage can occur through scission and backbiting, depending on the pH.
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Affiliation(s)
- Yi Sun
- School of Chemical & Biomolecular Engineering
- Georgia Institute of Technology
- Atlanta
- USA
- NSF/NASA Center for Chemical Evolution
| | - Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry & Biochemistry
- Georgia Institute of Technology
- Atlanta
| | - Charles L. Liotta
- School of Chemical & Biomolecular Engineering
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry & Biochemistry
| | - Martha A. Grover
- School of Chemical & Biomolecular Engineering
- Georgia Institute of Technology
- Atlanta
- USA
- NSF/NASA Center for Chemical Evolution
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23
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Kristoffersen KA, Liland KH, Böcker U, Wubshet SG, Lindberg D, Horn SJ, Afseth NK. FTIR-based hierarchical modeling for prediction of average molecular weights of protein hydrolysates. Talanta 2019; 205:120084. [DOI: 10.1016/j.talanta.2019.06.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 02/04/2023]
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24
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Martínez-Bachs B, Rimola A. Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations. Life (Basel) 2019; 9:life9030075. [PMID: 31527465 PMCID: PMC6789625 DOI: 10.3390/life9030075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022] Open
Abstract
Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies.
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Affiliation(s)
- Berta Martínez-Bachs
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Albert Rimola
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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25
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Barcaro G, Sementa L, Carravetta V, Yano TA, Hara M, Monti S. Experimental and theoretical elucidation of catalytic pathways in TiO 2-initiated prebiotic polymerization. Phys Chem Chem Phys 2019; 21:5435-5447. [PMID: 30793143 DOI: 10.1039/c9cp00167k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.
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Affiliation(s)
- Giovanni Barcaro
- CNR-IPCF, Institute of Chemical and Physical Processes, via G. Moruzzi 1, I-56124 Pisa, Italy.
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26
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Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO 2 (101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019; 58:12431-12434. [PMID: 31310450 DOI: 10.1002/anie.201906709] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 01/20/2023]
Abstract
Carboxylic-acid adsorption on anatase TiO2 is a relevant process in many technological applications. Yet, despite several decades of investigations, the acid-proton localization-either on the molecule or on the surface-is still an open issue. By modeling the adsorption of formic acid on top of anatase(101) surfaces, we highlight the formation of a short strong hydrogen bond. In the 0 K limit, the acid-proton behavior is ruled by quantum delocalization effects in a single potential well, while at ambient conditions, the proton undergoes a rapid classical shuttling in a shallow two-well free-energy profile. This picture, supported by agreement with available experiments, shows that the anatase surface acts like a protecting group for the carboxylic acid functionality. Such a new conceptual insight might help rationalize chemical processes involving carboxylic acids on oxide surfaces.
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Affiliation(s)
- Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Ettore Fois
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
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27
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Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO
2
(101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gloria Tabacchi
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Ettore Fois
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
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28
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Sakhno Y, Battistella A, Mezzetti A, Jaber M, Georgelin T, Michot L, Lambert JF. One Step up the Ladder of Prebiotic Complexity: Formation of Nonrandom Linear Polypeptides from Binary Systems of Amino Acids on Silica. Chemistry 2019; 25:1275-1285. [PMID: 30284764 DOI: 10.1002/chem.201803845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 12/17/2022]
Abstract
Evidence for the formation of linear oligopeptides with nonrandom sequences from mixtures of amino acids coadsorbed on silica and submitted to a simple thermal activation is presented. The amino acid couples (glutamic acid+leucine) and (aspartic acid+valine) were deposited on a fumed silica and submitted to a single heating step at moderate temperature. The evolution of the systems was characterized by X-ray diffraction, infrared spectroscopy, thermosgravimetric analysis, HPLC, and electrospray ionization mass spectrometry (ESI-MS). Evidence for the formation of amide bonds was found in all systems studied. While the products of single amino acids activation on silica could be considered as evolutionary dead ends, (glutamic acid+leucine) and, at to some extent, (aspartic acid+valine) gave rise to the high yield formation of linear peptides up to the hexamers. Oligopeptides of such length have not been observed before in surface polymerization scenarios (unless the amino acids had been deposited by chemical vapor deposition, which is not realistic in a prebiotic environment). Furthermore, not all possible amino acid sequences were present in the activation products, which is indicative of polymerization selectivity. These results are promising for origins of life studies because they suggest the emergence of nonrandom biopolymers in a simple prebiotic scenario.
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Affiliation(s)
- Yuriy Sakhno
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Alice Battistella
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Alberto Mezzetti
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Maguy Jaber
- Laboratoire d'Archéologie Moléculaire et Structurale, UMR 8220, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Thomas Georgelin
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France.,Temporary address: Centre de Biophysique Moléculaire, UPR 4301, CNRS, Rue Charles Sadron CS 80054, 45071, Orléans CEDEX 2, France
| | - Laurent Michot
- Laboratoire de Physicochimie des Electrolytes et Nanosystèmes Interfaciaux, UMR 8234, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
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Rimola A, Sodupe M, Ugliengo P. Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies. Life (Basel) 2019; 9:E10. [PMID: 30658501 PMCID: PMC6463156 DOI: 10.3390/life9010010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 01/07/2023] Open
Abstract
There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy.
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Pantaleone S, Ugliengo P, Sodupe M, Rimola A. When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO 2 (101) Anatase Surface through Periodic DFT-D2 Simulations. Chemistry 2018; 24:16292-16301. [PMID: 30212609 DOI: 10.1002/chem.201803263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
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Signorile M, Salvini C, Zamirri L, Bonino F, Martra G, Sodupe M, Ugliengo P. Formamide Adsorption at the Amorphous Silica Surface: A Combined Experimental and Computational Approach. Life (Basel) 2018; 8:life8040042. [PMID: 30249032 PMCID: PMC6316577 DOI: 10.3390/life8040042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 11/16/2022] Open
Abstract
Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. Formamide has been shown to be a pluripotent molecule, generating a wide distribution of relevant prebiotic products. In particular, the outcomes of its reactivity are strongly related to the presence of mineral phases acting as catalysts toward specific reaction pathways. While the mineral–products relationship has been deeply studied for a large pool of materials, the fundamental description of formamide reactivity over mineral surfaces at a microscopic level is missing in the literature. In particular, a key step of formamide chemistry at surfaces is adsorption on available interaction sites. This report aims to investigate the adsorption of formamide over a well-defined amorphous silica, chosen as a model mineral surface. An experimental IR investigation of formamide adsorption was carried out and its outcomes were interpreted on the basis of first principles simulation of the process, adopting a realistic model of amorphous silica.
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Affiliation(s)
- Matteo Signorile
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Clara Salvini
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Lorenzo Zamirri
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Francesca Bonino
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Gianmario Martra
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalogna, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
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English SL, Forsythe JG. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of model prebiotic peptides: Optimization of sample preparation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1507-1513. [PMID: 29885215 DOI: 10.1002/rcm.8201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Depsipeptides, or peptides with a mixture of amide and ester linkages, may have evolved into peptides on primordial Earth. Previous studies on depsipeptides utilized electrospray ionization ion mobility quadrupole time-of-flight (ESI-IM-QTOF) tandem mass spectrometry; such analysis was thorough yet time-consuming. Here, a complementary matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) approach was optimized for rapid characterization of depsipeptide length and monomer composition. METHODS Depsipeptide mixtures of varying hydrophobicity were formed by subjecting aqueous mixtures of α-hydroxy acids and α-amino acids to evaporative cycles. Ester and amide content of depsipeptides was orthogonally confirmed using infrared spectroscopy. MALDI-TOF MS analysis was performed on a Voyager DE-STR in reflection geometry and positive ion mode. Optimization parameters included choice of matrix, sample solvent, matrix-to-analyte ratio, and ionization additives. RESULTS It was determined that evaporated depsipeptide samples should be mixed with 2,5-dihydroxybenzoic acid (DHB) matrix in order to detect the highest number of unique signals. Low matrix-to-analyte ratios were found to generate higher quality spectra, likely due to a combination of matrix suppression and improved co-crystallization. Using this optimized protocol, a new depsipeptide mixture was characterized. CONCLUSIONS Understanding the diversity and chemical evolution of proto-peptides is of interest to origins-of-life research. Here, we have demonstrated MALDI-TOF MS can be used to rapidly screen the length and monomer composition of model prebiotic peptides containing a mixture of ester and amide backbone linkages.
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Affiliation(s)
- Sloane L English
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424
- NSF/NASA Center for Chemical Evolution
| | - Jay G Forsythe
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424
- NSF/NASA Center for Chemical Evolution
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McKee AD, Solano M, Saydjari A, Bennett CJ, Hud NV, Orlando TM. A Possible Path to Prebiotic Peptides Involving Silica and Hydroxy Acid‐Mediated Amide Bond Formation. Chembiochem 2018; 19:1913-1917. [DOI: 10.1002/cbic.201800217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron D. McKee
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Martin Solano
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Andrew Saydjari
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
| | - Christopher J. Bennett
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- Department of Physics University of Central Florida Physical Sciences Bldg. 430 4111 Libra Drive Orlando FL 32816 USA
| | - Nicholas V. Hud
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Thomas M. Orlando
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
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Malar EJP, Divya P. Structural Stability in Dimer and Tetramer Clusters of l-Alanine in the Gas Phase and the Feasibility of Peptide Bond Formation. J Phys Chem B 2018; 122:6462-6470. [DOI: 10.1021/acs.jpcb.8b01629] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. J. Padma Malar
- National Centre for Ultrafast Processes, University of Madras, Taramani Campus, Chennai 600113, India
| | - P. Divya
- National Centre for Ultrafast Processes, University of Madras, Taramani Campus, Chennai 600113, India
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Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research. Life (Basel) 2018; 8:life8020010. [PMID: 29738443 PMCID: PMC6027067 DOI: 10.3390/life8020010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 01/20/2023] Open
Abstract
An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.
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Rimola A, Fabbiani M, Sodupe M, Ugliengo P, Martra G. How Does Silica Catalyze the Amide Bond Formation under Dry Conditions? Role of Specific Surface Silanol Pairs. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03961] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marco Fabbiani
- Dipartimento de Scienza e Alta Tecnologia, Università degli Studi dell’insubria, Via Valleggio 11, 22100 Como, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Gianmario Martra
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy
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37
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Dalai P, Pleyer HL, Strasdeit H, Fox S. The Influence of Mineral Matrices on the Thermal Behavior of Glycine. ORIGINS LIFE EVOL B 2017; 47:427-452. [PMID: 27757771 DOI: 10.1007/s11084-016-9523-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 08/27/2016] [Indexed: 10/20/2022]
Abstract
On the Hadean-Early Archean Earth, the first islands must have provided hot and dry environments for abiotically formed organic molecules. The heat sources, mainly volcanism and meteorite impacts, were also available on Mars during the Noachian period. In recent work simulating this scenario, we have shown that neat glycine forms a black, sparingly water-soluble polymer ("thermomelanoid") when dry-heated at 200 °C under pure nitrogen. The present study explores whether relevant minerals and mineral mixtures can change this thermal behavior. Most experiments were conducted at 200 or 250 °C for 2 or 7 days. The mineral matrices used were phyllosilicates (Ca-montmorillonites SAz-1 and STx-1, Na-montmorillonite SAz-1-Na, nontronite NAu-1, kaolinite KGa-1), salts (NaCl, NaCl-KCl, CaCl2, artificial sea salt, gypsum, magnesite), picritic basalt, and three Martian regolith simulants (P-MRS, S-MRS, JSC Mars-1A). The main analytical method employed was high-performance liquid chromatography (HPLC). Glycine intercalated in SAz-1 and SAz-1-Na was well protected against thermomelanoid formation and sublimation at 200 °C: after 2 days, 95 and 79 %, respectively, had either survived unaltered or been transformed into the cyclic dipeptide (DKP) and linear peptides up to Gly6. The glycine survival rate followed the order SAz-1 > SAz-1-Na > STx-1 ≈ NAu-1 > KGa-1. Very good protection was also provided by artificial sea salt (84 % unaltered glycine after 200 °C for 7 days). P-MRS promoted the condensation up to Gly6, consistent with its high phyllosilicate content. The remaining matrices were less effective in preserving glycine as such or as peptides.
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Affiliation(s)
- Punam Dalai
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Hannes Lukas Pleyer
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Henry Strasdeit
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
| | - Stefan Fox
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
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Fabbiani M, Rebba E, Pazzi M, Vincenti M, Fois E, Martra G. Solvent-free synthesis of Ser–His dipeptide from non-activated amino acids and its potential function as organocatalyst. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-3198-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kitadai N, Oonishi H, Umemoto K, Usui T, Fukushi K, Nakashima S. Glycine Polymerization on Oxide Minerals. ORIGINS LIFE EVOL B 2017; 47:123-143. [PMID: 27473494 DOI: 10.1007/s11084-016-9516-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 11/24/2022]
Abstract
It has long been suggested that mineral surfaces played an important role in peptide bond formation on the primitive Earth. However, it remains unclear which mineral species was key to the prebiotic processes. This is because great discrepancies exist among the reported catalytic efficiencies of minerals for amino acid polymerizations, owing to mutually different experimental conditions. This study examined polymerization of glycine (Gly) on nine oxide minerals (amorphous silica, quartz, α-alumina and γ-alumina, anatase, rutile, hematite, magnetite, and forsterite) using identical preparation, heating, and analytical procedures. Results showed that a rutile surface is the most effective site for Gly polymerization in terms of both amounts and lengths of Gly polymers synthesized. The catalytic efficiency decreased as rutile > anatase > γ-alumina > forsterite > α- alumina > magnetite > hematite > quartz > amorphous silica. Based on reported molecular-level information for adsorption of Gly on these minerals, polymerization activation was inferred to have arisen from deprotonation of the NH3+ group of adsorbed Gly to the nucleophilic NH2 group, and from withdrawal of electron density from the carboxyl carbon to the surface metal ions. The orientation of adsorbed Gly on minerals is also a factor influencing the Gly reactivity. The examination of Gly-mineral interactions under identical experimental conditions has enabled the direct comparison of various minerals' catalytic efficiencies and has made discussion of polymerization mechanisms and their relative influences possible Further systematic investigations using the approach reported herein (which are expected to be fruitful) combined with future microscopic surface analyses will elucidate the role of minerals in the process of abiotic peptide bond formation.
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Affiliation(s)
- Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Hiroyuki Oonishi
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Koichiro Umemoto
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tomohiro Usui
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Keisuke Fukushi
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Satoru Nakashima
- Department of Earth and Space Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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40
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Guo C, Jordan JS, Yarger JL, Holland GP. Highly Efficient Fumed Silica Nanoparticles for Peptide Bond Formation: Converting Alanine to Alanine Anhydride. ACS APPLIED MATERIALS & INTERFACES 2017; 9:17653-17661. [PMID: 28452465 DOI: 10.1021/acsami.7b04887] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, thermal condensation of alanine adsorbed on fumed silica nanoparticles is investigated using thermal analysis and multiple spectroscopic techniques, including infrared (IR), Raman, and nuclear magnetic resonance (NMR) spectroscopies. Thermal analysis shows that adsorbed alanine can undergo thermal condensation, forming peptide bonds within a short time period and at a lower temperature (∼170 °C) on fumed silica nanoparticle surfaces than that in bulk (∼210 °C). Spectroscopic results further show that alanine is converted to alanine anhydride with a yield of 98.8% during thermal condensation. After comparing peptide formation on solution-derived colloidal silica nanoparticles, it is found that fumed silica nanoparticles show much better efficiency and selectivity than solution-derived colloidal silica nanoparticles for synthesizing alanine anhydride. Furthermore, Raman spectroscopy provides evidence that the high efficiency for fumed silica nanoparticles is likely related to their unique surface features: the intrinsic high population of strained ring structures present at the surface. This work indicates the great potential of fumed silica nanoparticles in synthesizing peptides with high efficiency and selectivity.
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Affiliation(s)
- Chengchen Guo
- School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Jacob S Jordan
- School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Jeffery L Yarger
- School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Gregory P Holland
- Department of Chemistry and Biochemistry, San Diego State University , 5500 Campanile Drive, San Diego, California 92182-1030, United States
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41
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Iron(III) Oxide Nanoparticles as Catalysts for the Formation of Linear Glycine Peptides. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601296] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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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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43
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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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Fox S, Dalai P, Lambert JF, Strasdeit H. Hypercondensation of an amino acid: synthesis and characterization of a black glycine polymer. Chemistry 2015; 21:8897-904. [PMID: 25933438 DOI: 10.1002/chem.201500820] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Indexed: 12/24/2022]
Abstract
A granular material was obtained by thermal polymerization of glycine at 200 °C. It has been named "thermomelanoid" because of its strikingly deep-black color. The polymerization process is mainly a dehydration condensation leading to conventional amide bonds, and also CC double bonds that are formed from CO and CH2 groups ("hypercondensation"). Spectroscopic data, in particular from (13) C and (15) N solid-state cross-polarization magic angle spinning (CP-MAS) NMR spectra, suggest that the black color is due to (cross-)conjugated CC, CO, and NH groups. Small glycine peptides, especially triglycine, appear to be key intermediates in the formation of the thermomelanoid. This has been concluded by comparing the thermal behavior of glyn homopeptides (n=2-6) and glycine. The glycine polymerization was accompanied by the formation of small amounts of byproducts. Notably, a few percent of alanine and aspartic acid could be detected in the polymer. By using (13) C-labeled glycine, it was shown that these two amino acids formed through a common pathway, namely CαCα bond formation between glycine molecules. The thermomelanoid is hydrolyzed by strong acids and bases at room temperature, forming brown solutions.
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Affiliation(s)
- Stefan Fox
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Punam Dalai
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75252 Paris Cedex 05 (France)
| | - Henry Strasdeit
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany).
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