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Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
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2
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Horváth AK. Law of Mass Action Type Chemical Mechanisms for Modeling Autocatalysis and Hypercycles: Their Role in the Evolutionary Race. Chemphyschem 2020; 21:1703-1710. [PMID: 32367607 PMCID: PMC7496691 DOI: 10.1002/cphc.202000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 01/21/2023]
Abstract
One of our most appealing challenge is to unravel the role of a presumably autocatalytic system in controlling the origin and spreading of Life on our entire planet. Here we show that in the simplest autocatalytic loop involving reactions capable of self-replication and obeying law of mass action kinetics, concentration growth of the autocatalyst may be characterized by parametrization of direct and autocatalytic pathways rather than by kinetic orders of the autocatalyst. Extending this model by feasible elementary steps allows us to outline super-exponential growth where kinetic order of the autocatalyst is higher than unity. Furthermore, it is shown in case of the simplest hypercycle that such a situation might appear where the otherwise more sluggish autocatalytic route receives a decisive support from the crosscatalytic pathway to become an apparently stronger autocatalytic loop even if the other route contains a more efficient autocatalysis. If the hypercycle is performed under flow conditions selection of autocatalyst depends on kinetic and flow parameters influenced by external factors mimicking that the most adaptive loop of hypercycle eventually finds its wining way in the evolutionary race.
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Affiliation(s)
- Attila K. Horváth
- Department of Inorganic ChemistryFaculty of SciencesUniversity of PécsIfjúság u. 6.H-7624PécsHungary
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3
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Rink WM, Thomas F. De Novo Designed α-Helical Coiled-Coil Peptides as Scaffolds for Chemical Reactions. Chemistry 2018; 25:1665-1677. [DOI: 10.1002/chem.201802849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 01/31/2023]
Affiliation(s)
- W. Mathis Rink
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Straße 3a 37075 Göttingen Germany
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4
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Orrillo AG, Escalante AM, Martinez-Amezaga M, Cabezudo I, Furlan RLE. Molecular Networks in Dynamic Multilevel Systems. Chemistry 2018; 25:1118-1127. [DOI: 10.1002/chem.201804143] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/17/2018] [Indexed: 11/07/2022]
Affiliation(s)
- A. Gastón Orrillo
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario-CONICET; S2002LRK Rosario Argentina
| | - Andrea M. Escalante
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario-CONICET; S2002LRK Rosario Argentina
| | - Maitena Martinez-Amezaga
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario-CONICET; S2002LRK Rosario Argentina
| | - Ignacio Cabezudo
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario-CONICET; S2002LRK Rosario Argentina
| | - Ricardo L. E. Furlan
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario-CONICET; S2002LRK Rosario Argentina
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5
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Altay Y, Altay M, Otto S. Existing Self-Replicators Can Direct the Emergence of New Ones. Chemistry 2018; 24:11911-11915. [PMID: 29901838 DOI: 10.1002/chem.201803027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Indexed: 12/24/2022]
Abstract
The study of the interplay between different self-replicating molecules constitutes an important new phase in the synthesis of life and in unravelling the origin of life. Here we show how existing replicators can direct the nature of a newly formed replicator. Starting from the same building block, 6-ring replicators formed when the mixture was exposed to pre-existing 6-membered replicators, while pre-formed 8-membered replicators funneled the building block into 8-ring replicators. Not only ring size, but also the mode of assembly of the rings into stacks was inherited from the pre-existing replicators. These results show that the nature of self-replicating molecules can be strongly influenced by the interplay between different self-replicators, overriding preferences innate to the structure of the building block.
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Affiliation(s)
- Yigit Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Meniz Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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6
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Hordijk W, Shichor S, Ashkenasy G. The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics. Chemphyschem 2018; 19:2437-2444. [PMID: 29813174 DOI: 10.1002/cphc.201800101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Indexed: 11/09/2022]
Abstract
Chemical networks often exhibit emergent, systems-level properties that cannot be simply derived from the linear sum of the individual components. The design and analysis of increasingly complex chemical networks thus constitute a major area of research in Systems Chemistry. In particular, much research is focused on the emergence of functional properties in prebiotic chemical networks relevant to the origin and early evolution of life. Here, we apply a formal framework known as RAF theory to study the dynamics of a complex network of mutually catalytic peptides. We investigate in detail the influence of network modularity, initial template seeding, and product inhibition on the network dynamics. We show that these results can be useful for designing new experiments, and further argue how they are relevant to origin of life studies.
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Affiliation(s)
- Wim Hordijk
- Institute for Advanced Study, University of Amsterdam, The Netherlands
| | - Shira Shichor
- Ben-Gurion University of the Negev, Be'er Sheva, Israel
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7
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Bader A, Cockroft SL. Simultaneous G-Quadruplex DNA Logic. Chemistry 2018; 24:4820-4824. [DOI: 10.1002/chem.201800756] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Antoine Bader
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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8
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Orrillo AG, La-Venia A, Escalante AM, Furlan RLE. Rewiring Chemical Networks Based on Dynamic Dithioacetal and Disulfide Bonds. Chemistry 2018; 24:3141-3146. [DOI: 10.1002/chem.201705654] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 01/09/2023]
Affiliation(s)
- A. Gastón Orrillo
- Instituto de Investigaciones para el Descubrimiento de, Fármacos de Rosario (UNR-CONICET); Ocampo y Esmeralda; 2000 Rosario Argentina
| | - Agustina La-Venia
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Suipacha 531 S2002LRK Rosario Argentina
| | - Andrea M. Escalante
- Instituto de Investigaciones para el Descubrimiento de, Fármacos de Rosario (UNR-CONICET); Ocampo y Esmeralda; 2000 Rosario Argentina
| | - Ricardo L. E. Furlan
- Instituto de Investigaciones para el Descubrimiento de, Fármacos de Rosario (UNR-CONICET); Ocampo y Esmeralda; 2000 Rosario Argentina
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; S2002LRK Rosario Argentina
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9
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Li Y, Sun S, Fan L, Hu S, Huang Y, Zhang K, Nie Z, Yao S. Peptide Logic Circuits Based on Chemoenzymatic Ligation for Programmable Cell Apoptosis. Angew Chem Int Ed Engl 2017; 56:14888-14892. [DOI: 10.1002/anie.201708327] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Yong Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Sujuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Lin Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shanfang Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology; Northeastern University; Boston MA 02115 USA
- Institute of Chemical Biology and Nanomedicine; Hunan University; Changsha 410081 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shouzhou Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
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10
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Li Y, Sun S, Fan L, Hu S, Huang Y, Zhang K, Nie Z, Yao S. Peptide Logic Circuits Based on Chemoenzymatic Ligation for Programmable Cell Apoptosis. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yong Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Sujuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Lin Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shanfang Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology; Northeastern University; Boston MA 02115 USA
- Institute of Chemical Biology and Nanomedicine; Hunan University; Changsha 410081 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shouzhou Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
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11
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Singh N, Escuder B. Competition versus Cooperation in Catalytic Hydrogelators for anti-Selective Mannich Reaction. Chemistry 2017; 23:9946-9951. [PMID: 28513914 DOI: 10.1002/chem.201701724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 01/08/2023]
Abstract
Chemical systems find similarities in different sociological and biological processes, in which the entities compete or cooperate for a favorable outcome. The structural and functional adaptations leading to emergent properties, especially in catalysis, are based on factors such as abundance of substrates, stability of the transition state, and structural/functional attributes of catalysts. Proline and acid groups appended to catalytic fibers of two self-sorting hydrogelators compete for the Mannich reaction between aniline, benzaldehyde, and cyclohexanone to give low overall selectivity (anti/syn 77:23). In a sol-gel system of the same molecules, on the other hand, the soluble acid appended molecules tend to cooperate with the fibers of proline-appended catalyst to give improved selectivity (anti/syn 95:5). The available options for the catalytic molecules are to carry out the reaction independently or in cooperation. However, these options are chosen based on the efficiency, selectivity, and mobility of catalysts as a result of their abilities to self-assemble.
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Affiliation(s)
- Nishant Singh
- Department de Química Inorgànica i Orgànica, Universitat Jaume I, Av Sos Baynat, Castellón, 12071, Spain
| | - Beatriu Escuder
- Department de Química Inorgànica i Orgànica, Universitat Jaume I, Av Sos Baynat, Castellón, 12071, Spain
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12
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Wagner N, Mukherjee R, Maity I, Peacock-Lopez E, Ashkenasy G. Bistability and Bifurcation in Minimal Self-Replication and Nonenzymatic Catalytic Networks. Chemphyschem 2017; 18:1842-1850. [PMID: 28112462 DOI: 10.1002/cphc.201601293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/23/2017] [Indexed: 11/08/2022]
Abstract
Bistability and bifurcation, found in a wide range of biochemical networks, are central to the proper function of living systems. We investigate herein recent model systems that show bistable behavior based on nonenzymatic self-replication reactions. Such models were used before to investigate catalytic growth, chemical logic operations, and additional processes of self-organization leading to complexification. By solving for their steady-state solutions by using various analytical and numerical methods, we analyze how and when these systems yield bistability and bifurcation and discover specific cases and conditions producing bistability. We demonstrate that the onset of bistability requires at least second-order catalysis and results from a mismatch between the various forward and reverse processes. Our findings may have far-reaching implications in understanding early evolutionary processes of complexification, emergence, and potentially the origin of life.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Rakesh Mukherjee
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | | | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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13
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Kushida Y, Sawato T, Saito N, Shigeno M, Satozono H, Yamaguchi M. Spatially Heterogeneous Nature of Self-Catalytic Reaction in Hetero-Double Helix Formation of Helicene Oligomers. Chemphyschem 2016; 17:3283-3288. [DOI: 10.1002/cphc.201600627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Yo Kushida
- Department of Organic Chemistry; Graduate School of Pharmaceutical Sciences; Tohoku University, Aoba; Sendai 980-8578 Japan
| | - Tsukasa Sawato
- Department of Organic Chemistry; Graduate School of Pharmaceutical Sciences; Tohoku University, Aoba; Sendai 980-8578 Japan
| | - Nozomi Saito
- Department of Organic Chemistry; Graduate School of Pharmaceutical Sciences; Tohoku University, Aoba; Sendai 980-8578 Japan
| | - Masanori Shigeno
- Department of Organic Chemistry; Graduate School of Pharmaceutical Sciences; Tohoku University, Aoba; Sendai 980-8578 Japan
| | - Hiroshi Satozono
- Central Research Laboratory; Hamamatsu Photonics K. K. Hamakita, Hamamatsu; Shizuoka 434-8601 Japan
| | - Masahiko Yamaguchi
- Department of Organic Chemistry; Graduate School of Pharmaceutical Sciences; Tohoku University, Aoba; Sendai 980-8578 Japan
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14
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Mukherjee R, Cohen-Luria R, Wagner N, Ashkenasy G. A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template-Directed Ligation. Angew Chem Int Ed Engl 2015; 54:12452-6. [DOI: 10.1002/anie.201503898] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/21/2015] [Indexed: 11/08/2022]
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15
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Mukherjee R, Cohen-Luria R, Wagner N, Ashkenasy G. A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template-Directed Ligation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503898] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Atcher J, Moure A, Bujons J, Alfonso I. Salt-Induced Adaptation of a Dynamic Combinatorial Library of Pseudopeptidic Macrocycles: Unraveling the Electrostatic Effects in Mixed Aqueous Media. Chemistry 2015; 21:6869-78. [DOI: 10.1002/chem.201406155] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Joan Atcher
- Department of Biological Chemistry and Molecular Modeling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona (Spain)
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17
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Dadon Z, Wagner N, Alasibi S, Samiappan M, Mukherjee R, Ashkenasy G. Competition and Cooperation in Dynamic Replication Networks. Chemistry 2014; 21:648-54. [DOI: 10.1002/chem.201405195] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Indexed: 11/09/2022]
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19
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Bissette AJ, Fletcher SP. Mechanisms of Autocatalysis. Angew Chem Int Ed Engl 2013; 52:12800-26. [DOI: 10.1002/anie.201303822] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Indexed: 12/17/2022]
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Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A High-Resolution Structure that Provides Insight into Coiled-Coil Thiodepsipeptide Dynamic Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303900] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A high-resolution structure that provides insight into coiled-coil thiodepsipeptide dynamic chemistry. Angew Chem Int Ed Engl 2013; 52:9944-7. [PMID: 23929823 DOI: 10.1002/anie.201303900] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/16/2013] [Indexed: 01/29/2023]
Abstract
Stable and reactive: A crystal structure at 1.35 Å of a thioester coiled-coil protein reveals high similarity to all-peptide-bond proteins. In these assemblies, the thioester bonds are kept reactive towards thiol molecules in the mixture. This enables efficient domain exchange between proteins in response to changes in folding conditions or introduction of external templates.
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Affiliation(s)
- Zehavit Dadon
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 84105 (Israel)
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22
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Ashkenasy G, Dadon Z, Alesebi S, Wagner N, Ashkenasy N. Building Logic into Peptide Networks: Bottom-Up and Top-Down. Isr J Chem 2011. [DOI: 10.1002/ijch.201000071] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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del Amo V, Philp D. Integrating Replication-Based Selection Strategies in Dynamic Covalent Systems. Chemistry 2010; 16:13304-18. [DOI: 10.1002/chem.201000423] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Dadon Z, Samiappan M, Safranchik EY, Ashkenasy G. Light-Induced Peptide Replication Controls Logic Operations in Small Networks. Chemistry 2010; 16:12096-9. [DOI: 10.1002/chem.201001488] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski BA. Reaction-diffusion systems in intracellular molecular transport and control. Angew Chem Int Ed Engl 2010; 49:4170-98. [PMID: 20518023 PMCID: PMC3697936 DOI: 10.1002/anie.200905513] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.
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Affiliation(s)
- Siowling Soh
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Marta Byrska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Kristiana Kandere-Grzybowska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Bartosz A. Grzybowski
- Department of Chemistry, Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, Homepage: http://www.dysa.northwestern.edu
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski B. Reaktions-Diffusions-Systeme für intrazellulären Transport und Kontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905513] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Rubinov B, Wagner N, Rapaport H, Ashkenasy G. Self-replicating amphiphilic beta-sheet peptides. Angew Chem Int Ed Engl 2009; 48:6683-6. [PMID: 19644990 DOI: 10.1002/anie.200902790] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Boris Rubinov
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
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Busch M, Schlageter M, Weingand D, Gehring T. Systematic studies using 2-(1-adamantylethynyl)pyrimidine-5-carbaldehyde as a starting material in Soai's asymmetric autocatalysis. Chemistry 2009; 15:8251-8. [PMID: 19585641 DOI: 10.1002/chem.200900634] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Herein, we present a new substrate for the Soai reaction, which has an adamantylethynyl residue (1 g) and exhibits asymmetric autocatalysis, yielding products with enantiomeric excesses above 99%. For the first time, all reactions were performed on a parallel synthesizer system to ensure identical reaction conditions. A detailed systematic study of reaction parameters was performed and we report the highest enhancements of enantiomeric excess reported so far in the Soai reaction in one reaction cycle (7.2-->94.1% ee or 3.1-->92.1% ee). Our results led to a set of reaction parameters that yield reproducible results. Therefore, our new starting material 1 g is suitable for systematic and mechanistic studies on this remarkable reaction. A series of experiments designed to quantify the amplification of enantiomeric excess demonstrated that the reaction can be used in principle as a tool for the detection of low enantiomeric excesses: under definite conditions, an unknown low enantiomeric excess (0.1-7%) was amplified to a detectable one. A back calculation to the original value offers a new method for the determination of small enantiomeric excesses.
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Affiliation(s)
- Mark Busch
- Institut für Organische Chemie, Universität Karlsruhe (TH), Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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29
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Rubinov B, Wagner N, Rapaport H, Ashkenasy G. Self-Replicating Amphiphilic β-Sheet Peptides. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902790] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Pross A. Seeking the Chemical Roots of Darwinism: Bridging between Chemistry and Biology. Chemistry 2009; 15:8374-8381. [DOI: 10.1002/chem.200900805] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Wagner N, Ashkenasy G. Systems chemistry: logic gates, arithmetic units, and network motifs in small networks. Chemistry 2009; 15:1765-75. [PMID: 19107891 DOI: 10.1002/chem.200801850] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mixture of molecules can be regarded as a network if all the molecular components participate in some kind of interaction with other molecules--either physical or functional interactions. Template-assisted ligation reactions that direct replication processes can serve as the functional elements that connect two members of a chemical network. In such a process, the template does not necessarily catalyze its own formation, but rather the formation of another molecule, which in turn can operate as a template for reactions within the network medium. It was postulated that even networks made up of small numbers of molecules possess a wealth of molecular information sufficient to perform rather complex behavior. To probe this assumption, we have constructed virtual arrays consisting of three replicating molecules, in which dimer templates are capable of catalyzing reactants to form additional templates. By using realistic parameters from peptides or DNA replication experiments, we simulate the construction of various functional motifs within the networks. Specifically, we have designed and implemented each of the three-element Boolean logic gates, and show how these networks are assembled from four basic "building blocks". We also show how the catalytic pathways can be wired together to perform more complex arithmetic units and network motifs, such as the half adder and half subtractor computational modules, and the coherent feed-forward loop network motifs under different sets of parameters. As in previous studies of chemical networks, some of the systems described display behavior that would be difficult to predict without the numerical simulations. Furthermore, the simulations reveal trends and characteristics that should be useful as "recipes" for future design of experimental functional motifs and for potential integration into modular circuits and molecular computation devices.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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Nguyen R, Allouche L, Buhler E, Giuseppone N. Dynamic Combinatorial Evolution within Self-Replicating Supramolecular Assemblies. Angew Chem Int Ed Engl 2009; 48:1093-6. [DOI: 10.1002/anie.200804602] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Nguyen R, Allouche L, Buhler E, Giuseppone N. Dynamic Combinatorial Evolution within Self-Replicating Supramolecular Assemblies. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804602] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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34
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Sadownik J, Philp D. A Simple Synthetic Replicator Amplifies Itself from a Dynamic Reagent Pool. Angew Chem Int Ed Engl 2008; 47:9965-70. [DOI: 10.1002/anie.200804223] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Sadownik J, Philp D. A Simple Synthetic Replicator Amplifies Itself from a Dynamic Reagent Pool. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200804223] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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