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Castanedo LA, Matta CF. On the prebiotic selection of nucleotide anomers: A computational study. Heliyon 2022; 8:e09657. [PMID: 35785221 PMCID: PMC9243047 DOI: 10.1016/j.heliyon.2022.e09657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/14/2022] [Accepted: 05/31/2022] [Indexed: 11/19/2022] Open
Abstract
Present-day known predominance of the β- over the α-anomers in nucleosides and nucleotides emerges from a thermodynamic analysis of their assembly from their components, i.e. bases, sugars, and a phosphate group. Furthermore, the incorporation of uracil into RNA and thymine into DNA rather than the other way around is also predicted from the calculations. An interplay of kinetics and thermodynamics must have driven evolutionary selection of life's building blocks. In this work, based on quantum chemical calculations, we focus on the latter control as a tool for “natural selection”.
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Affiliation(s)
- Lázaro A.M. Castanedo
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada
| | - Chérif F. Matta
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada
- Dép. de chimie, Université Laval, Québec, Québec, G1V 0A6, Canada
- Corresponding author at: Department of Chemistry, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada.
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2
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Petera L, Mrazikova K, Nejdl L, Zemankova K, Vaculovicova M, Pastorek A, Civis S, Kubelik P, Heays A, Cassone G, Sponer J, Ferus M, Sponer J. Prebiotic Route to Thymine from Formamide-A Combined Experimental-Theoretical Study. Molecules 2021; 26:molecules26082248. [PMID: 33924594 PMCID: PMC8069957 DOI: 10.3390/molecules26082248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.
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Affiliation(s)
- Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ 61200 Brno, Czech Republic
- Correspondence: (L.N.); (M.F.); (J.S.)
| | - Kristyna Zemankova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ 61200 Brno, Czech Republic
| | - Adam Pastorek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Svatopluk Civis
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Petr Kubelik
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Alan Heays
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, Italian National Research Council (IPCF-CNR), Viale Ferdinando Stagno d’Alcontres 37, 98158 Messina, Italy;
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
- Correspondence: (L.N.); (M.F.); (J.S.)
| | - Judit Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
- Correspondence: (L.N.); (M.F.); (J.S.)
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3
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Bizzarri BM, Fanelli A, Kapralov M, Krasavin E, Saladino R. Meteorite-catalyzed intermolecular trans-glycosylation produces nucleosides under proton beam irradiation. RSC Adv 2021; 11:19258-19264. [PMID: 35478633 PMCID: PMC9033569 DOI: 10.1039/d1ra02379a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/14/2021] [Indexed: 11/23/2022] Open
Abstract
Di-glycosylated adenines act as glycosyl donors in the intermolecular trans-glycosylation of pyrimidine nucleobases under proton beam irradiation conditions. Formamide and chondrite meteorite NWA 1465 increased the yield and the selectivity of the reaction. The glycosyl transfer process was highly regioselective in yielding canonical N1-pyrimidine nucleosides, the natural β-anomers prevailing in the presence of formamide and NWA 1465. These data highlight the possible role of intermolecular trans-glycosylation in the prebiotic formation of purine and pyrimidine nucleosides, avoiding the occurrence of independent synthetic pathways. Di-glycosylated adenines act as glycosyl donors in the intermolecular trans-glycosylation of pyrimidine nucleobases under proton beam irradiation conditions.![]()
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Affiliation(s)
| | - Angelica Fanelli
- Ecological and Biological Sciences Department (DEB)
- University of Tuscia
- Viterbo
- Italy
| | - Michail Kapralov
- Joint Institute for Nuclear Research
- JINR's Laboratory of Radiation Biology
- Russia
- Dubna State University
- Ulitsa Universitetskaya
| | - Eugene Krasavin
- Joint Institute for Nuclear Research
- JINR's Laboratory of Radiation Biology
- Russia
- Dubna State University
- Ulitsa Universitetskaya
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB)
- University of Tuscia
- Viterbo
- Italy
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4
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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5
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Šponer JE, Šponer J, Di Mauro E. Structural and Energetic Compatibility: The Driving Principles of Molecular Evolution. ASTROBIOLOGY 2019; 19:1117-1122. [PMID: 31045430 DOI: 10.1089/ast.2018.1978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, we provide an answer to the question formulated by Albert Eschenmoser: "How would you envisage the bridge between potentially primordial geochemistry that had been disordered and one that gradually became self-organizing?" Analysis of the free-energy profiles of some of the key reactions leading to formation of nucleotides and their oligomers shows that, whereas the first part of the pathway, up to nucleotides, is energy-driven, in the second low-energy part entropic control in the form of structural compatibility becomes more important. We suggest that the birth of modern metabolism requires structural compatibility, which is enabled by the commensurability of the thermodynamics of the synthetic steps with the stabilizing effect of those intermolecular interactions that play a key role in dictating entropic control of these reactions.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ernesto Di Mauro
- Institute for Molecular Biology and Pathology, CNR, c/o Università Sapienza, Roma, Italy
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6
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Rodrigues F, Georgelin T, Gabant G, Rigaud B, Gaslain F, Zhuang G, Gardênnia da Fonseca M, Valtchev V, Touboul D, Jaber M. Confinement and Time Immemorial: Prebiotic Synthesis of Nucleotides on a Porous Mineral Nanoreactor. J Phys Chem Lett 2019; 10:4192-4196. [PMID: 31305079 DOI: 10.1021/acs.jpclett.9b01448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the successful one-pot synthesis of adenosine mono-, di-, and triphosphate in the confined space of a mordenite zeolite. This is also the first report of ATP synthesized onto a porous mineral surface. The results revealed a plausible prebiotic route to ribonucleotides and highlighted the contribution of microporous minerals in the origins of life.
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Affiliation(s)
- Francisco Rodrigues
- Sorbonne University , CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale , 4 Place Jussieu , F-75005 Paris , France
- Department of Chemistry , State University of Paraíba , UEPB, Campina Grande , Paraíba 58429-500, Brazil
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire , CNRS, Rue Charles Sadron, 45000 Orléans , France
| | - Guillaume Gabant
- Centre de Biophysique Moléculaire , CNRS, Rue Charles Sadron, 45000 Orléans , France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482) , 4 Place Jussieu , 75005 Paris , France
| | - Fabrice Gaslain
- MINES ParisTech , PSL - Research University , MAT - Centre des Matériaux, CNRS UMR 7633, BP 87, F-91003 Evry , France
| | - Guanzheng Zhuang
- Sorbonne University , CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale , 4 Place Jussieu , F-75005 Paris , France
| | - Maria Gardênnia da Fonseca
- Department of Chemistry , Federal University of Paraíba , UFPB, João Pessoa , Paraíba 58059-900 , Brazil
| | - Valentin Valtchev
- Normandy University , Laboratoire Catalyse & Spectrochimie, ENSICAEN , 6 bl Maréchal Juin , 14050 Caen , France
| | - David Touboul
- CNRS-Institut de Chimie des Substances Naturelles, UPR2301 , Université Paris-Saclay , 91198 Gif-sur-Yvette cedex, France
| | - Maguy Jaber
- Sorbonne University , CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale , 4 Place Jussieu , F-75005 Paris , France
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7
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Kaur S, Sharma P, Wetmore SD. Can Cyanuric Acid and 2,4,6-Triaminopyrimidine Containing Ribonucleosides be Components of Prebiotic RNA? Insights from QM Calculations and MD Simulations. Chemphyschem 2019; 20:1425-1436. [PMID: 30997731 DOI: 10.1002/cphc.201900237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/09/2019] [Indexed: 01/05/2023]
Abstract
As a step toward assessing their fitness as pre-RNA nucleobases, we employ DFT and MD simulations to analyze the noncovalent interactions of cyanuric acid (CA) and 2,4,6-triaminopyrimidine (TAP), and the structural properties of the associated ribonucleosides (rNs) and oligonucleotides. Our calculations reveal that the TAP : CA pair has a comparable hydrogen-bond strength to the canonical A : U pair. This strengthens the candidature of CA and TAP as prebiotic nucleobases. Further, the stacking between two canonical nucleobases is stronger than those between TAP or CA and a canonical base, as well as those between two TAP and/or CA, which indicates that enhanced stacking may have served as a driving force for the evolution from prebiotic to canonical nucleobases. Similarities in the DFT-derived anti/syn rotational barriers and MD-derived (anti) glycosidic conformation of the CA and TAP rNs and canonical rNs further substantiate their candidature as pre-RNA components. Greater deglycosylation barriers (as obtained by DFT calculations) for TAP rNs compared to canonical rNs suggest TAP rNs indicate higher resistance to environmental factors, while lower barriers indicate that CA rNs were likely more suitable for less-challenging locations. Finally, the tight packing in narrow CA:TAP-containing helices suggests that the prebiotic polymers were shielded from water, which would aid their evolution into self-replicating systems. Our calculations thus support proposals that CA and TAP can act as nucleobases of pre-RNA.
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Affiliation(s)
- Sarabjeet Kaur
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Alberta, T1K 3M4, Canada
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8
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Catalytic abiotic synthesis of uracil from cysteine and urea: Theoretical studies. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.08.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Pérez-Villa A, Saitta AM, Georgelin T, Lambert JF, Guyot F, Maurel MC, Pietrucci F. Synthesis of RNA Nucleotides in Plausible Prebiotic Conditions from ab Initio Computer Simulations. J Phys Chem Lett 2018; 9:4981-4987. [PMID: 30107125 DOI: 10.1021/acs.jpclett.8b02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-d-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds. Combining ab initio molecular dynamics simulations with recently developed reaction exploration and enhanced sampling methods, we show that nucleobases and α-PRPP should spontaneously combine, under mild hydrothermal conditions, with an exothermic reaction and a facile mechanism, forming both purine and pyrimidine ribonucleotides. Surprisingly, this mechanism is very similar to the biological one and yields ribonucleotides with the same anomeric carbon chirality as in biological systems. Mass spectrometry experiments performed on solutions of adenine and PRPP in similar conditions support the formation of AMP. These results suggest that natural selection might have optimized, through enzymes, a pre-existing ribonucleotide formation mechanism, carrying it forward to modern life forms.
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Affiliation(s)
- Andrea Pérez-Villa
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - A Marco Saitta
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - Thomas Georgelin
- Sorbonne Université, CNRS UMR 7197, Laboratoire de Réactivité de Surface, LRS, F-75005 Paris , France
- Centre de Biophysique Moléculaire, CNRS UPR 4301, F-45071 Orléans , France
| | - Jean-François Lambert
- Sorbonne Université, CNRS UMR 7197, Laboratoire de Réactivité de Surface, LRS, F-75005 Paris , France
| | - François Guyot
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - Marie-Christine Maurel
- Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS MNHN UMR 7205, Institut de Systématique, Evolution, Biodiversité, ISyEB, F-75005 Paris , France
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
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10
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Šponer JE, Szabla R, Góra RW, Saitta AM, Pietrucci F, Saija F, Di Mauro E, Saladino R, Ferus M, Civiš S, Šponer J. Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments. Phys Chem Chem Phys 2018; 18:20047-66. [PMID: 27136968 DOI: 10.1039/c6cp00670a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | - Robert W Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - A Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Fabio Pietrucci
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Ernesto Di Mauro
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Raffaele Saladino
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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11
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Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study. Catalysts 2017. [DOI: 10.3390/catal7120363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Spontaneous, nonenzymatic reactions in proteins are known to have relevance to aging and age-related diseases, such as cataract and Alzheimer’s disease. Among such reactions is the racemization of Ser residues, but its mechanism in vivo remains to be clarified. The most likely intermediate is an enol. Although being nonenzymatic, the enolization would need to be catalyzed to occur at a biologically relevant rate. In the present study, we computationally found plausible reaction pathways for the enolization of a Ser residue where a dihydrogen phosphate ion, H2PO4−, acts as a catalyst. The H2PO4− ion mediates the proton transfer required for the enolization by acting simultaneously as both a general base and a general acid. Using the B3LYP density functional theory method, reaction pathways were located in the gas phase and hydration effects were evaluated by single-point calculations using the SM8 continuum model. The activation barriers calculated for the reaction pathways found were around 100 kJ mol−1, which is consistent with spontaneous reactions occurring at physiological temperature. Our results are also consistent with experimental observations that Ser residue racemization occurs more readily in flexible regions in proteins.
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12
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Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702633] [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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13
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Akouche M, Jaber M, Maurel MC, Lambert JF, Georgelin T. Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017; 56:7920-7923. [PMID: 28558156 DOI: 10.1002/anie.201702633] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/15/2017] [Indexed: 11/07/2022]
Abstract
In this contribution, we report the formation under prebiotic conditions of phosphoribosyl pyrophosphate (PRPP) as a molecular precursor in the one-pot synthesis of a canonical nucleotide, namely adenosine monophosphate (AMP) from its building blocks (KH2 PO4 or Pi , adenine, and d-ribose), on a fumed silica surface. The on-the-rocks approach has been successfully applied to the simultaneous phosphorylation and glycosylation of ribose. The one-pot formation mechanism of AMP involves a two-step pathway via an activated intermediate, namely PRPP, obtained by multiple ribose phosphorylations upon mild thermal activation.
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Affiliation(s)
- Mariame Akouche
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Maguy Jaber
- Sorbonne Universités, UPMC Paris06, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, 75005, Paris, France
| | | | - Jean-Francois Lambert
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Thomas Georgelin
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
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14
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Ai Y, Xia S, Liao RZ. Theoretical Studies on the Photochemistry of Pentose Aminooxazoline, a Hypothetical Intermediate Product in the Prebiotic Synthetic Scenario of RNA Nucleotides. J Phys Chem B 2016; 120:9329-37. [PMID: 27525736 DOI: 10.1021/acs.jpcb.6b06061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Aminooxazole is generally considered a prebiotic precursor of ribonucleotides on the early earth. Its pentose compound, pentose aminooxazoline, has been suggested to be a key intermediate in the prebiotic synthetic scenario. In this article, detailed mechanism of the photochemistry of pentose aminooxazoline has been studied by performing density functional theory and multireference complete active space self-consistent field calculations. Parallel to the "ring-puckering" process, which leads to ultrafast nonradiative deactivation, several other photodissociation channels are explored in detail. In addition, the influences of the pentose structure and solvation effects with both implicit and explicit water models have been uncovered for both neutral and protonated forms. The current theoretical results provide very important information not only for the photostability of RNA nucleotides but also for an in-depth understanding of the synthesis of other prebiotic nucleotides.
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Affiliation(s)
- Yuejie Ai
- School of Environmental and Chemical Engineering, North China Electric Power University , Beijing 102206, China
| | - Shuhua Xia
- College of Life and Environmental Science, Minzu University of China , Beijing 100081, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
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15
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Šponer JE, Šponer J, Nováková O, Brabec V, Šedo O, Zdráhal Z, Costanzo G, Pino S, Saladino R, Di Mauro E. Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. Chemistry 2016; 22:3572-86. [PMID: 26807661 DOI: 10.1002/chem.201503906] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 02/02/2023]
Abstract
50 years after the historical Miller-Urey experiment, the formamide-based scenario is perhaps the most powerful concurrent hypothesis for the origin of life on our planet besides the traditional HCN-based concept. The information accumulated during the last 15 years in this topic is astonishingly growing and nowadays the formamide-based model represents one of the most complete and coherent pathways leading from simple prebiotic precursors up to the first catalytically active RNA molecules. In this work, we overview the major events of this long pathway that have emerged from recent experimental and theoretical studies, mainly concentrating on the mechanistic, methodological, and structural aspects of this research.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. .,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic.
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Olga Nováková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Ondrej Šedo
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Zbyněk Zdráhal
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome, 00185, Italy
| | - Samanta Pino
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro, 5, Rome, 00185, Italy
| | - Raffaele Saladino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Via San Camillo De Lellis, 01100, Viterbo, Italy
| | - Ernesto Di Mauro
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro, 5, Rome, 00185, Italy
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16
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Sutherland JD. The Origin of Life--Out of the Blue. Angew Chem Int Ed Engl 2015; 55:104-21. [PMID: 26510485 DOI: 10.1002/anie.201506585] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 01/28/2023]
Abstract
Either to sustain autotrophy, or as a prelude to heterotrophy, organic synthesis from an environmentally available C1 feedstock molecule is crucial to the origin of life. Recent findings augment key literature results and suggest that hydrogen cyanide--"Blausäure"--was that feedstock.
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Affiliation(s)
- John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (UK).
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17
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18
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Anizelli PR, Baú JPT, Nabeshima HS, da Costa MF, de Santana H, Zaia DAM. An experimental and theoretical vibrational study of interaction of adenine and thymine with artificial seawaters: A prebiotic chemistry experiment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 126:184-196. [PMID: 24607468 DOI: 10.1016/j.saa.2014.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/29/2014] [Accepted: 02/07/2014] [Indexed: 06/03/2023]
Abstract
Nucleic acid bases play important roles in living beings. Thus, their interaction with salts the prebiotic Earth could be an important issue for the understanding of origin of life. In this study, the effect of pH and artificial seawaters on the structure of adenine and thymine was studied via parallel determinations using FT-IR, Raman spectroscopy and theoretical calculations. Thymine and adenine lyophilized in solutions at basic and acidic conditions showed characteristic bands of the enol-imino tautomer due to the deprotonation and the hydrochloride form due to protonation, respectively. The interaction of thymine and adenine with different seawaters representative of different geological periods on Earth was also studied. In the case of thymine a strong interaction with Sr(2+) promoted changes in the Raman and infrared spectra. For adenine changes in infrared and Raman spectra were observed in the presence of salts from all seawaters tested. The experimental results were compared to theoretical calculations, which showed structural changes due to the presence of ions Na(+), Mg(2+), Ca(2+) and Sr(2+) of artificial seawaters. For thymine the bands arising from C4=C5 and C6=O stretching were shifted to lower values, and for adenine, a new band at 1310cm(-1) was observed. The reactivity of adenine and thymine was studied by comparing changes in nucleophilicity and energy of the HOMO orbital.
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Affiliation(s)
- Pedro R Anizelli
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - João P T Baú
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Henrique S Nabeshima
- Departamento de Física-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Marcello F da Costa
- Departamento de Física-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Henrique de Santana
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Dimas A M Zaia
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil.
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19
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Gong W, Huang F, Sun C, Zhao X, Chen D. Mechanism and diastereoselectivity of the prebiotic synthesis of deoxyribonucleotide precursors C5-thiazoline: A DFT study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Sponer JE, Mládek A, Sponer J. Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions. Phys Chem Chem Phys 2013; 15:6235-42. [PMID: 23515462 DOI: 10.1039/c3cp44156c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recently, it has been reported that the montmorillonite-catalyzed oligomerization of activated nucleotides exhibits remarkable enantioselectivity. In the current paper we investigate the structures and intrinsic energies of homochiral and heterochiral cyclic dinucleotides by means of accurate quantum chemical calculations in gas-phase and in bulk water. The steric effect of the clay is represented with geometrical constraints. Our computations reveal that the heterochiral dimer geometries are systematically less stable than their homochiral counterparts due to steric clashes inside the sugar-phosphate ring geometry. Thus we suggest that the homochiral selectivity observed in the cyclic dinucleotide formation in confined spaces may arise from the energetic destabilization of the heterochiral ring geometries as compared to their homochiral analogues. In the present paper we provide the first model of the 3D structure of d,l cyclic dinucleotides, which until now has eluded experimental observation.
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Affiliation(s)
- Judit E Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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21
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Szabla R, Šponer JE, Šponer J, Góra RW. Theoretical studies of the mechanism of 2-aminooxazole formation under prebiotically plausible conditions. Phys Chem Chem Phys 2013; 15:7812-8. [DOI: 10.1039/c3cp50320h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Ferus M, Civiš S, Mládek A, Šponer J, Juha L, Šponer JE. On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event. J Am Chem Soc 2012. [DOI: 10.1021/ja310421z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Libor Juha
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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23
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Is formamide natureʼs choice to create life? Phys Life Rev 2012; 9:109-10; discussion 121-3. [DOI: 10.1016/j.plrev.2011.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 11/21/2022]
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24
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Wu R, Gong W, Liu T, Zhang Y, Cao Z. QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase. J Phys Chem B 2012; 116:1984-91. [DOI: 10.1021/jp211403j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ruibo Wu
- School of
Pharmaceutical Sciences,
East Campus, Sun Yat-sen University, Guangzhou
510006, China
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Wengjin Gong
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Ting, Liu
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Zexing Cao
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
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25
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Šponer JE, Mládek A, Šponer J, Fuentes-Cabrera M. Formamide-Based Prebiotic Synthesis of Nucleobases: A Kinetically Accessible Reaction Route. J Phys Chem A 2011; 116:720-6. [DOI: 10.1021/jp209886b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences and Computer Sciences and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, P.O. Box 2008, Oak Ridge, Tennessee 37831-6494, United States
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