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Reja A, Pal S, Mahato K, Saha B, Delle Piane M, Pavan GM, Das D. Emergence of Photomodulated Protometabolism by Short Peptide-Based Assemblies. J Am Chem Soc 2023; 145:21114-21121. [PMID: 37708200 DOI: 10.1021/jacs.3c08158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
In the early Earth, rudimentary enzymes must have utilized the available light energy source to modulate protometabolic processes. Herein, we report the light-responsive C-C bond manipulation via short peptide-based assemblies bound to the photosensitive molecular cofactor (azo-based photoswitch) where the energy of the light source regulated the binding sites which subsequently modulated the retro-aldolase activity. In the presence of a continual source of high-energy photons, temporal realization of a catalytically more proficient state could be achieved under nonequilibrium conditions. Further, the hydrophobic surface of peptide assemblies facilitated the binding of an orthogonal molecular catalyst that showed augmented activity (promiscuous hydrolytic activity) upon binding. This latent activity was utilized for the in situ generation of light-sensitive cofactor that subsequently modulated the retro-aldolase activity, thus creating a reaction network.
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Affiliation(s)
- Antara Reja
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Sumit Pal
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Kishalay Mahato
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Baishakhi Saha
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Massimo Delle Piane
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy
| | - Giovanni M Pavan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Dibyendu Das
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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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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Wagner N, Hochberg D, Peacock-Lopez E, Maity I, Ashkenasy G. Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior. Life (Basel) 2019; 9:life9020045. [PMID: 31163645 PMCID: PMC6617095 DOI: 10.3390/life9020045] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 12/05/2022] Open
Abstract
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of these simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra Ajalvir Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain.
| | | | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
- Present address: Institute for Macromolecular Chemistry, Albert Ludwigs University of Freiburg, D-79104 Freiburg, Germany.
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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Skorb EV, Semenov SN. Mathematical Analysis of a Prototypical Autocatalytic Reaction Network. Life (Basel) 2019; 9:E42. [PMID: 31137534 PMCID: PMC6616502 DOI: 10.3390/life9020042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/15/2019] [Accepted: 05/18/2019] [Indexed: 12/19/2022] Open
Abstract
Network autocatalysis, which is autocatalysis whereby a catalyst is not directly produced in a catalytic cycle, is likely to be more common in chemistry than direct autocatalysis is. Nevertheless, the kinetics of autocatalytic networks often does not exactly follow simple quadratic or cubic rate laws and largely depends on the structure of the network. In this article, we analyzed one of the simplest and most chemically plausible autocatalytic networks where a catalytic cycle is coupled to an ancillary reaction that produces the catalyst. We analytically analyzed deviations in the kinetics of this network from its exponential growth and numerically studied the competition between two networks for common substrates. Our results showed that when quasi-steady-state approximation is applicable for at least one of the components, the deviation from the exponential growth is small. Numerical simulations showed that competition between networks results in the mutual exclusion of autocatalysts; however, the presence of a substantial noncatalytic conversion of substrates will create broad regions where autocatalysts can coexist. Thus, we should avoid the accumulation of intermediates and the noncatalytic conversion of the substrate when designing experimental systems that need autocatalysis as a source of positive feedback or as a source of evolutionary pressure.
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Affiliation(s)
- Ekaterina V Skorb
- ChemBio Cluster, ITMO University, Lomonosova St. 9, Saint Petersburg 191002, Russia.
| | - Sergey N Semenov
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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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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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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Baroncini M, Semeraro M, Credi A. Unconventional Nonlinear Input-Output Response in a Luminescent Molecular Switch by Inner Filtering Effects. Chemphyschem 2017; 18:1755-1759. [DOI: 10.1002/cphc.201700046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Massimo Baroncini
- Dipartimento di Scienze e Tecnologie Agro-alimentari; Alma Mater Studiorum; Università di Bologna; Viale Fanin 50 40127 Bologna Italy
| | - Monica Semeraro
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Alberto Credi
- Dipartimento di Scienze e Tecnologie Agro-alimentari; Alma Mater Studiorum; Università di Bologna; Viale Fanin 50 40127 Bologna Italy
- Istituto ISOF-CNR; Via Gobetti 101 40129 Bologna Italy
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