1
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Kriukov DV, Huskens J, Wong ASY. Exploring the programmability of autocatalytic chemical reaction networks. Nat Commun 2024; 15:8289. [PMID: 39333532 DOI: 10.1038/s41467-024-52649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Networks of chemical reactions exhibit emergent properties under out-of-equilibrium conditions. Recent advances in systems chemistry demonstrate that networks with sufficient chemical complexity can be harnessed to emulate properties important for neuromorphic computing. In all examples, autocatalysis appears an essential element for facilitating the nonlinear integration of the input and self-regulatory abilities in the output. How this chemical analogue of a positive feedback mechanism can be controlled in a programmable manner is, however, unexplored. Here, we develop a strategy that uses metal ions (Ca2+, La3+, and Nd3+) to control the rate of a trypsin-catalysed autocatalytic reaction network. We demonstrate that this type of control allows for tuning the kinetics in the network, thereby changing the nature of the positive feedback. The simulations and experiments reveal that an input with one or more metal ions allow for temporal and history-dependent outputs that can be mapped onto a variety of mathematical functions.
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Affiliation(s)
- Dmitrii V Kriukov
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Enschede, the Netherlands
- MESA+ Institute, University of Twente, Enschede, the Netherlands
- BRAINS (Center for Brain-inspired Nano Systems), University of Twente, Enschede, the Netherlands
| | - Jurriaan Huskens
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Enschede, the Netherlands
- MESA+ Institute, University of Twente, Enschede, the Netherlands
| | - Albert S Y Wong
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Enschede, the Netherlands.
- MESA+ Institute, University of Twente, Enschede, the Netherlands.
- BRAINS (Center for Brain-inspired Nano Systems), University of Twente, Enschede, the Netherlands.
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2
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Singh A, Parvin P, Saha B, Das D. Non-equilibrium self-assembly for living matter-like properties. Nat Rev Chem 2024:10.1038/s41570-024-00640-z. [PMID: 39179623 DOI: 10.1038/s41570-024-00640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
The soft and wet machines of life emerged as the spatially enclosed ensemble of biomolecules with replicating capabilities integrated with metabolic reaction cycles that operate at far-from-equilibrium. A thorough step-by-step synthetic integration of these elements, namely metabolic and replicative properties all confined and operating far-from-equilibrium, can set the stage from which we can ask questions related to the construction of chemical-based evolving systems with living matter-like properties - a monumental endeavour of systems chemistry. The overarching concept of this Review maps the discoveries on this possible integration of reaction networks, self-reproduction and compartmentalization under non-equilibrium conditions. We deconvolute the events of reaction networks and transient compartmentalization and extend the discussion towards self-reproducing systems that can be sustained under non-equilibrium conditions. Although enormous challenges lie ahead in terms of molecular diversity, information transfer, adaptation and selection that are required for open-ended evolution, emerging strategies to generate minimal metabolic cycles can extend our growing understanding of the chemical emergence of the biosphere of Earth.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Payel Parvin
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Bapan Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
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3
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Komáromy D, Monzón DM, Marić I, Monreal Santiago G, Ottelé J, Altay M, Schaeffer G, Otto S. Generalist versus Specialist Self-Replicators. Chemistry 2024; 30:e202303837. [PMID: 38294075 DOI: 10.1002/chem.202303837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide-based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide-containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide-based replicator and hexameric ethyleneoxide-based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators.
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Affiliation(s)
- Dávid Komáromy
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Diego M Monzón
- Instituto de Bio-Orgánica "Antonio González" (IUBO-AG), Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, 38206, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Ivana Marić
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Guillermo Monreal Santiago
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jim Ottelé
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Meniz Altay
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gaël Schaeffer
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Sijbren Otto
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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4
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Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
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Affiliation(s)
- Vinay Ambekar Ranganath
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| | - Indrajit Maity
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
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5
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Ribó JM, Hochberg D. Physical Chemistry Models for Chemical Research in the XXth and XXIst Centuries. ACS PHYSICAL CHEMISTRY AU 2024; 4:122-134. [PMID: 38560750 PMCID: PMC10979499 DOI: 10.1021/acsphyschemau.3c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 04/04/2024]
Abstract
Thermodynamic hypotheses and models are the touchstone for chemical results, but the actual models based on time-invariance, which have performed efficiently in the development of chemistry, are nowadays invalid for the interpretation of the behavior of complex systems exhibiting nonlinear kinetics and with matter and energy exchange flows with the surroundings. Such fields of research will necessarily foment and drive the use of thermodynamic models based on the description of irreversibility at the macroscopic level, instead of the current models which are strongly anchored in microreversibility.
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Affiliation(s)
- Josep M. Ribó
- Department
of Inorganic and Organic Chemistry, University
of Barcelona, c. Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
- Institute
of Cosmos Science (IEEC-UB), c. Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - David Hochberg
- Department
of Molecular Evolution, Centro de Astrobiología
(CSIC-INTA), E-28850 Torrejón de Ardóz, Madrid, Spain
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6
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Singh AY, Jain S. Multistable Protocells Can Aid the Evolution of Prebiotic Autocatalytic Sets. Life (Basel) 2023; 13:2327. [PMID: 38137928 PMCID: PMC10744544 DOI: 10.3390/life13122327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 12/24/2023] Open
Abstract
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model, the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division dynamics of the compartment. Bistability in the dynamics of the autocatalytic set results in a protocell that can exist with two distinct growth rates. Stochasticity in chemical reactions plays the role of mutations and causes transitions from one growth regime to another. We show that the system exhibits 'natural selection', where a 'mutant' protocell in which the autocatalytic set is active arises by chance in a population of inactive protocells, and then takes over the population because of its higher growth rate or 'fitness'. The work integrates three levels of dynamics: intracellular chemical, single protocell, and population (or ecosystem) of protocells.
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Affiliation(s)
- Angad Yuvraj Singh
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India;
| | - Sanjay Jain
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India;
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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7
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Dev D, Wagner N, Pramanik B, Sharma B, Maity I, Cohen-Luria R, Peacock-Lopez E, Ashkenasy G. A Peptide-Based Oscillator. J Am Chem Soc 2023; 145:26279-26286. [PMID: 37984498 DOI: 10.1021/jacs.3c09377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.
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Affiliation(s)
- Dharm Dev
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bhawna Sharma
- 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
- Centre for Nano and Material Sciences, Jain Global Campus, Bangalore, Karnataka 560070, India
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Enrique Peacock-Lopez
- Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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8
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Sangchai T, Al Shehimy S, Penocchio E, Ragazzon G. Artificial Molecular Ratchets: Tools Enabling Endergonic Processes. Angew Chem Int Ed Engl 2023; 62:e202309501. [PMID: 37545196 DOI: 10.1002/anie.202309501] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type-rather than the application domain or energy source-we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.
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Affiliation(s)
- Thitiporn Sangchai
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Shaymaa Al Shehimy
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Emanuele Penocchio
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Giulio Ragazzon
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
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9
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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10
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Lantos E, Tóth Á, Horváth D. Oscillatory dynamics in a reaction network based on imine hydrolysis. CHAOS (WOODBURY, N.Y.) 2023; 33:103104. [PMID: 37782830 DOI: 10.1063/5.0169860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
We have built an autocatalytic reaction network, based on the hydrolysis of certain imines, which exhibits bistability in an open system. The positive feedback originates from the interplay of fast acid-base equilibria, leading to hydroxide ion production, and pH-dependent hydrolysis rates. The addition of a first-order removal of the autocatalyst can result in sustained pH oscillations close to physiological conditions. The unit-amplitude pH oscillations are accompanied by the stoichiometric conversion of imine into amine back and forth. A systematic parameter search is carried out to characterize the rich observable dynamics and identify the evolving bifurcations.
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Affiliation(s)
- Emese Lantos
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1., Szeged H-6720, Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1., Szeged H-6720, Hungary
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1., Szeged H-6720, Hungary
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11
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Lantos E, Mótyán G, Frank É, Eelkema R, van Esch J, Horváth D, Tóth Á. Dynamics of hydroxide-ion-driven reversible autocatalytic networks. RSC Adv 2023; 13:20243-20247. [PMID: 37416909 PMCID: PMC10321365 DOI: 10.1039/d3ra04215d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023] Open
Abstract
In living systems adaptive regulation requires the presence of nonlinear responses in the underlying chemical networks. Positive feedbacks, for example, can lead to autocatalytic bursts that provide switches between two stable states or to oscillatory dynamics. The stereostructure stabilized by hydrogen bonds provides an enzyme its selectivity, rendering pH regulation essential for its functioning. For effective control, triggers by small concentration changes play roles where the strength of feedback is important. Here we show that the interaction of acid-base equilibria with simple reactions with pH-dependent rate can lead to the emergence of a positive feedback in hydroxide ion concentration during the hydrolysis of some Schiff bases in the physiological pH range. The underlying reaction network can also support bistability in an open system.
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Affiliation(s)
- Emese Lantos
- Department of Physical Chemistry and Materials Science, University of Szeged Rerrich Béla tér 1 Szeged H-6720 Hungary
| | - Gergő Mótyán
- Department of Organic Chemistry, University of Szeged Dóm tér 8. Szeged H-6720 Hungary
| | - Éva Frank
- Department of Organic Chemistry, University of Szeged Dóm tér 8. Szeged H-6720 Hungary
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft Netherlands
| | - Jan van Esch
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft Netherlands
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged Rerrich Béla tér 1 Szeged H-6720 Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged Rerrich Béla tér 1 Szeged H-6720 Hungary
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12
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Bartus É, Tököli A, Mag B, Bajcsi Á, Kecskeméti G, Wéber E, Kele Z, Fenteany G, Martinek TA. Light-Fueled Primitive Replication and Selection in Biomimetic Chemical Systems. J Am Chem Soc 2023. [PMID: 37285516 DOI: 10.1021/jacs.3c03597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The concept of chemically evolvable replicators is central to abiogenesis. Chemical evolvability requires three essential components: energy-harvesting mechanisms for nonequilibrium dissipation, kinetically asymmetric replication and decomposition pathways, and structure-dependent selective templating in the autocatalytic cycles. We observed a UVA light-fueled chemical system displaying sequence-dependent replication and replicator decomposition. The system was constructed with primitive peptidic foldamer components. The photocatalytic formation-recombination cycle of thiyl radicals was coupled with the molecular recognition steps in the replication cycles. Thiyl radical-mediated chain reaction was responsible for the replicator death mechanism. The competing and kinetically asymmetric replication and decomposition processes led to light intensity-dependent selection far from equilibrium. Here, we show that this system can dynamically adapt to energy influx and seeding. The results highlight that mimicking chemical evolution is feasible with primitive building blocks and simple chemical reactions.
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Affiliation(s)
- Éva Bartus
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Attila Tököli
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Beáta Mag
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Áron Bajcsi
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Gábor Kecskeméti
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Zoltán Kele
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Gabriel Fenteany
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- Institute of Genetics, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
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13
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Sharma C, Maity I, Walther A. pH-feedback systems to program autonomous self-assembly and material lifecycles. Chem Commun (Camb) 2023; 59:1125-1144. [PMID: 36629372 DOI: 10.1039/d2cc06402b] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
pH-responsive systems have gained importance for the development of smart materials and for biomedical applications because they can switch between different states by simple acid/base triggers. However, such equilibrium systems lack the autonomous behaviour that is so ubiquitous in living systems that self-regulate out of equilibrium. As a contribution to the emerging field of autonomous chemical systems, we have developed pH-feedback systems (pH-FS) based on the coupling of acid- and base-producing steps in chemical reaction networks. The resulting autonomous nonlinear pH curves can be coupled with a variety of pH-sensitive building blocks to program the lifecycles of the associated transient state at the level of self-assemblies and material systems. In this article, we discuss the different generations of such pH-feedback systems, the principles of their coupling to self-assemblies with lifecycles and highlight emerging concepts for the design of autonomous functional materials. The specificity, robustness, and flexible operation of such pH-FS can also be used to realize chemo-structural and chemo-mechanical feedbacks that extend the behaviour of such materials systems toward complex and functional life-like systems.
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Affiliation(s)
- Charu Sharma
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
| | - Indrajit Maity
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
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14
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Gagnon LG, Czaikowski ME, Peacock-López E. Dynamic properties of a self-replicating peptide network with inhibition. J Chem Phys 2022; 157:225101. [PMID: 36546800 DOI: 10.1063/5.0119945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In this paper, we report an open system consisting of three self-replicating peptides, in which peptide 1 inhibits the duplex template of peptide 2, peptide 2 inhibits duplex 3, and peptide 3 inhibits duplex 1 to complete the negative feedback loop. This interacting chemical network yields oscillations in the concentrations of all species over time and establishes a possible mechanism for pre-biotic chemical systems organization. The first focus of our analysis is the effect of altering rates of duplex formation and inhibition on oscillations. We then examine the autocatalytic rate constant in the symmetric and asymmetric cases.
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Affiliation(s)
- Lucille G Gagnon
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
| | - Maia E Czaikowski
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
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15
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Reardon TJ, Na B, Parquette JR. Dissipative self-assembly of a proline catalyst for temporal regulation of the aldol reaction. NANOSCALE 2022; 14:14711-14716. [PMID: 36169284 DOI: 10.1039/d2nr03991e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The spatiotemporal regulation of chemical reactivity in biological systems permits a network of metabolic reactions to take place within the same cellular environment. The exquisite control of reactivity is often mediated by out-of-equilibrium structures that remain functional only as long as fuel is present to maintain the higher energy, active state. An important goal in supramolecular chemistry aims to develop functional, energy dissipating systems that approach the sophistication of biological machinery. The challenge is to create strategies that couple the energy consumption needed to promote a molecule to a higher energy, assembled state to a functional property such as catalytic activity. In this work, we demonstrated that the assembly of a spiropyran (SP) dipeptide (1) transiently promoted the proline-catalyzed aldol reaction in water when visible light was present as fuel. The transient catalytic activity emerged from 1 under light illumination due to the photoisomerization of the monomeric, O-protonated (1-MCH+) merocyanine form to the spiropyran (1-SP) state, which rapidly assembled into nanosheets capable of catalyzing the aldol reaction in water. When the light source was removed, thermal isomerization to the more stable MCH+ form caused the nanosheets to dissociate into a catalytically inactive, monomeric state. Under these conditions, the aldol reaction could be repeatedly activated and deactivated by switching the light source on and off.
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Affiliation(s)
- Thomas J Reardon
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Ave. Columbus, Ohio 43210, USA.
| | - Baichuan Na
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Ave. Columbus, Ohio 43210, USA.
| | - Jon R Parquette
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Ave. Columbus, Ohio 43210, USA.
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16
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Vela-Gallego S, Pardo-Botero Z, Moya C, de la Escosura A. Collective adaptability in a replication network of minimal nucleobase sequences. Chem Sci 2022; 13:10715-10724. [PMID: 36320689 PMCID: PMC9491195 DOI: 10.1039/d2sc02419e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/05/2022] [Indexed: 12/05/2022] Open
Abstract
A major challenge for understanding the origins of life is to explore how replication networks can engage in an evolutionary process. Herein, we shed light on this problem by implementing a network constituted by two different types of extremely simple biological components: the amino acid cysteine and the canonical nucleobases adenine and thymine, connected through amide bonds to the cysteine amino group and oxidation of its thiol into three possible disulfides. Supramolecular and kinetic analyses revealed that both self- and mutual interactions between such dinucleobase compounds drive their assembly and replication pathways. Those pathways involving sequence complementarity led to enhanced replication rates, suggesting a potential bias for selection. The interplay of synergistic dynamics and competition between replicators was then simulated, under conditions that are not easily accessible with experiments, in an open reactor parametrized and constrained with the unprecedentedly complete experimental kinetic data obtained for our replicative network. Interestingly, the simulations show bistability, as a selective amplification of different species depending on the initial mixture composition. Overall, this network configuration can favor a collective adaptability to changes in the availability of feedstock molecules, with disulfide exchange reactions serving as 'wires' that connect the different individual auto- and cross-catalytic pathways.
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Affiliation(s)
- Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
| | | | - Cristian Moya
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
- Institute for Advanced Research in Chemistry (IAdChem) Cantoblanco 28049 Madrid Spain
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17
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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18
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Sharko A, Livitz D, De Piccoli S, Bishop KJM, Hermans TM. Insights into Chemically Fueled Supramolecular Polymers. Chem Rev 2022; 122:11759-11777. [PMID: 35674495 DOI: 10.1021/acs.chemrev.1c00958] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Supramolecular polymerization can be controlled in space and time by chemical fuels. A nonassembled monomer is activated by the fuel and subsequently self-assembles into a polymer. Deactivation of the molecule either in solution or inside the polymer leads to disassembly. Whereas biology has already mastered this approach, fully artificial examples have only appeared in the past decade. Here, we map the available literature examples into four distinct regimes depending on their activation/deactivation rates and the equivalents of deactivating fuel. We present increasingly complex mathematical models, first considering only the chemical activation/deactivation rates (i.e., transient activation) and later including the full details of the isodesmic or cooperative supramolecular processes (i.e., transient self-assembly). We finish by showing that sustained oscillations are possible in chemically fueled cooperative supramolecular polymerization and provide mechanistic insights. We hope our models encourage the quantification of activation, deactivation, assembly, and disassembly kinetics in future studies.
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Affiliation(s)
| | - Dimitri Livitz
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | | | - Kyle J M Bishop
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Thomas M Hermans
- University of Strasbourg & CNRS, UMR7140, Strasbourg 67000, France
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19
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Orrillo AG, Furlan RLE. Sulfur in Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2022; 61:e202201168. [PMID: 35447003 DOI: 10.1002/anie.202201168] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Indexed: 12/21/2022]
Abstract
Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur-based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.
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Affiliation(s)
- A Gastón Orrillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, Rosario, S2002LRK, Argentina
| | - Ricardo L E Furlan
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, Rosario, S2002LRK, Argentina
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20
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Schnitter F, Rieß B, Jandl C, Boekhoven J. Memory, switches, and an OR-port through bistability in chemically fueled crystals. Nat Commun 2022; 13:2816. [PMID: 35595758 PMCID: PMC9122941 DOI: 10.1038/s41467-022-30424-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/29/2022] [Indexed: 11/12/2022] Open
Abstract
The ability to store information in chemical reaction networks is essential for the complex behavior we associate with life. In biology, cellular memory is regulated through transcriptional states that are bistable, i.e., a state that can either be on or off and can be flipped from one to another through a transient signal. Such memory circuits have been realized synthetically through the rewiring of genetic systems in vivo or through the rational design of reaction networks based on DNA and highly evolved enzymes in vitro. Completely bottom-up analogs based on small molecules are rare and hard to design and thus represent a challenge for systems chemistry. In this work, we show that bistability can be designed from a simple non-equilibrium reaction cycle that is coupled to crystallization. The crystals exert the necessary feedback on the reaction cycle required for the bistability resulting in an on-state with assemblies and an off-state without. Each state represents volatile memory that can be stored in continuously stirred tank reactors indefinitely even though molecules are turned over on a minute-timescale. We showcase the system’s abilities by creating a matrix display that can store images and by creating an OR-gate by coupling several switches together. In biology, information is stored and processed using highly evolved molecules in bistable states. Here, the authors demonstrate bistability in a synthetic system without the need for evolved biomolecules or autocatalytic networks.
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Affiliation(s)
- Fabian Schnitter
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Benedikt Rieß
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Christian Jandl
- Catalysis Research Centre, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany. .,Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2a, 85748, Garching, Germany.
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21
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out-of-Equilibrium Self-Replication Allows Selection for Dynamic Kinetic Stability in a System of Competing Replicators. Angew Chem Int Ed Engl 2022; 61:e202117605. [PMID: 35179808 PMCID: PMC9314957 DOI: 10.1002/anie.202117605] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 12/16/2022]
Abstract
Among the key characteristics of living systems are their ability to self-replicate and the fact that they exist in an open system away from equilibrium. Herein, we show how the outcome of the competition between two self-replicators, differing in size and building block composition, is different depending on whether the experiments are conducted in a closed vial or in an open and out-of-equilibrium replication-destruction regime. In the closed system, the slower replicator eventually prevails over the faster competitor. In a replication-destruction regime, implemented through a flow system, the outcome of the competition is reversed and the faster replicator dominates. The interpretation of the experimental observations is supported by a mass-action-kinetics model. These results represent one of the few experimental manifestations of selection among competing self-replicators based on dynamic kinetic stability and pave the way towards Darwinian evolution of abiotic systems.
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Affiliation(s)
- Bin Liu
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Juntian Wu
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Marc Geerts
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Omer Markovitch
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
- Origins CenterUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Groningen Institute for Evolutionary Life SciencesUniversity of Groningen9747 AGGroningenThe Netherlands
| | - Charalampos G. Pappas
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Kai Liu
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Sijbren Otto
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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22
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Orrillo AG, Furlan RLE. Sulfur in Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alfredo Gastón Orrillo
- Universidad Nacional de Rosario Facultad de Ciencias Bioquimicas y Farmaceuticas Organic Chemistry Suipacha 530 2000 Rosario ARGENTINA
| | - Ricardo L. E. Furlan
- Universidad Nacional de Rosario Facultad de Ciencias Bioquimicas y Farmaceuticas Organic Chemistry Suipacha 530 2000 Rosario ARGENTINA
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23
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Wu S, Zhou T, Tian T. A robust method for designing multistable systems by embedding bistable subsystems. NPJ Syst Biol Appl 2022; 8:10. [PMID: 35338169 PMCID: PMC8956579 DOI: 10.1038/s41540-022-00220-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/15/2022] [Indexed: 12/21/2022] Open
Abstract
Although multistability is an important dynamic property of a wide range of complex systems, it is still a challenge to develop mathematical models for realising high order multistability using realistic regulatory mechanisms. To address this issue, we propose a robust method to develop multistable mathematical models by embedding bistable models together. Using the GATA1-GATA2-PU.1 module in hematopoiesis as the test system, we first develop a tristable model based on two bistable models without any high cooperative coefficients, and then modify the tristable model based on experimentally determined mechanisms. The modified model successfully realises four stable steady states and accurately reflects a recent experimental observation showing four transcriptional states. In addition, we develop a stochastic model, and stochastic simulations successfully realise the experimental observations in single cells. These results suggest that the proposed method is a general approach to develop mathematical models for realising multistability and heterogeneity in complex systems.
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Affiliation(s)
- Siyuan Wu
- School of Mathematics, Monash University, Melbourne, VIC, Australia
| | - Tianshou Zhou
- School of Mathematics and Statistics, Sun Yet-Sen University, Guangzhou, China
| | - Tianhai Tian
- School of Mathematics, Monash University, Melbourne, VIC, Australia.
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24
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out‐of‐equilibrium self‐replication allows selection for dynamic kinetic stability in a system of competing replicators. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bin Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Juntian Wu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Marc Geerts
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Omer Markovitch
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Charalampos G. Pappas
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Kai Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Sijbren Otto
- Stratingh Institute University of Groningen Centre for Systems Chemistry Nijenborgh 4 9747AG Groningen NETHERLANDS
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25
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Afrose SP, Mahato C, Sharma P, Roy L, Das D. Nonequilibrium Catalytic Supramolecular Assemblies of Melamine- and Imidazole-Based Dynamic Building Blocks. J Am Chem Soc 2022; 144:673-678. [PMID: 34990140 DOI: 10.1021/jacs.1c11457] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The development of synthetic nonequilibrium systems has gathered increasing attention due to their potential to illustrate the dynamic, complex, and emergent traits of biological systems. Simple building blocks capable of interacting via dynamic covalent chemistry and physical assembly in a reaction network under nonequilibrium conditions can contribute to our understanding of complex systems of life and its origin. Herein, we have demonstrated the nonequilibrium generation of catalytic supramolecular assemblies from simple heterocycle melamine driven by a thermodynamically activated ester. Utilizing a reversible covalent linkage, an imidazole moiety was recruited by the assemblies to access a catalytic transient state that dissipated energy via accelerated hydrolysis of the activated ester. The nonequilibrium assemblies were further capable of temporally binding to a hydrophobic guest to modulate its photophysical properties. Notably, the presence of an exogenous aromatic base augmented the lifetime of the catalytic microphases, reflecting their higher kinetic stability.
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Affiliation(s)
- Syed Pavel Afrose
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Chiranjit Mahato
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Pooja Sharma
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Lisa Roy
- Institute of Chemical Technology Mumbai-IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension Centre, Bhubaneswar 751013, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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26
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Abstract
As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials.
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Affiliation(s)
- Sijbren Otto
- Centre for Systems Chemistry, Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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27
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Schwarz PS, Tena-Solsona M, Dai K, Boekhoven J. Carbodiimide-fueled catalytic reaction cycles to regulate supramolecular processes. Chem Commun (Camb) 2022; 58:1284-1297. [PMID: 35014639 DOI: 10.1039/d1cc06428b] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Using molecular self-assembly, supramolecular chemists can create Gigadalton-structures with angstrom precision held together by non-covalent interactions. However, despite relying on the same molecular toolbox for self-assembly, these synthetic structures lack the complexity and sophistication of biological assemblies. Those assemblies are non-equilibrium structures that rely on the constant consumption of energy transduced from the hydrolysis of chemical fuels like ATP and GTP, which endows them with dynamic properties, e.g., temporal and spatial control and self-healing ability. Thus, to synthesize life-like materials, we have to find a reaction cycle that converts chemical energy to regulate self-assembly. We and others recently found that this can be done by a reaction cycle that hydrates carbodiimides. This feature article aims to provide an overview of how the energy transduced from carbodiimide hydration can alter the function of molecules and regulate molecular assemblies. The goal is to offer the reader design considerations for carbodiimide-driven reaction cycles to create a desired morphology or function of the assembly and ultimately to push chemically fueled self-assembly further towards the bottom-up synthesis of life.
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Affiliation(s)
- Patrick S Schwarz
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Marta Tena-Solsona
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Kun Dai
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany. .,Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, 85748, Garching, Germany
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28
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Liu M, Creemer CN, Reardon TJ, Parquette JR. Light-driven dissipative self-assembly of a peptide hydrogel. Chem Commun (Camb) 2021; 57:13776-13779. [PMID: 34860221 DOI: 10.1039/d1cc04971b] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Light energy provides an attractive fuel source for energy dissipating systems because of the lack of waste production, wavelength tunability and the potential for spatial and temporal resolution. In this work, we describe a peptide-spiropyran conjugate that assembled into a transient nanofiber hydrogel in the presence of visible light, and dissociated when the light source was removed.
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Affiliation(s)
- Mengmeng Liu
- Department of Chemistry and Biochemistry, The Ohio State University 100 W, 18th Ave. Columbus, Ohio 43210, USA.
| | - Cassidy N Creemer
- Department of Chemistry and Biochemistry, The Ohio State University 100 W, 18th Ave. Columbus, Ohio 43210, USA.
| | - Thomas J Reardon
- Department of Chemistry and Biochemistry, The Ohio State University 100 W, 18th Ave. Columbus, Ohio 43210, USA.
| | - Jon R Parquette
- Department of Chemistry and Biochemistry, The Ohio State University 100 W, 18th Ave. Columbus, Ohio 43210, USA.
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29
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Maćešić S, Tóth Á, Horváth D. Origins of oscillatory dynamics in the model of reactive oxygen species in the rhizosphere. J Chem Phys 2021; 155:175102. [PMID: 34742207 DOI: 10.1063/5.0062139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oscillatory processes are essential for normal functioning and survival of biological systems, and reactive oxygen species have a prominent role in many of them. A mechanism representing the dynamics of these species in the rhizosphere is analyzed using stoichiometric network analysis with the aim to determine its capabilities to simulate various dynamical states, including oscillations. A detailed analysis has shown that unstable steady states result from four destabilizing feedback cycles, among which the cycle involving hydroquinone, an electron acceptor, and its semi-reduced form is the dominant one responsible for the existence of saddle-node and Andronov-Hopf bifurcations. This requires a higher steady-state concentration for the reduced electron acceptor compared to that of the remaining species, where the level of oxygen steady-state concentration determines whether the Andronov-Hopf or saddle-node bifurcation will occur.
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Affiliation(s)
- Stevan Maćešić
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
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30
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Maity I, Sharma C, Lossada F, Walther A. Feedback and Communication in Active Hydrogel Spheres with pH Fronts: Facile Approaches to Grow Soft Hydrogel Structures. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Indrajit Maity
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
- Freiburg Institute for Advanced Studies University of Freiburg Freiburg Germany
| | - Charu Sharma
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Francisco Lossada
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Andreas Walther
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
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31
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Maity I, Sharma C, Lossada F, Walther A. Feedback and Communication in Active Hydrogel Spheres with pH Fronts: Facile Approaches to Grow Soft Hydrogel Structures. Angew Chem Int Ed Engl 2021; 60:22537-22546. [PMID: 34347941 PMCID: PMC8518392 DOI: 10.1002/anie.202109735] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 12/12/2022]
Abstract
Compartmentalized reaction networks regulating signal processing, communication and pattern formation are central to living systems. Towards achieving life-like materials, we compartmentalized urea-urease and more complex urea-urease/ester-esterase pH-feedback reaction networks into hydrogel spheres and investigate how fuel-driven pH fronts can be sent out from these spheres and regulated by internal reaction networks. Membrane characteristics are installed by covering urease spheres with responsive hydrogel shells. We then encapsulate the two networks (urea-urease and ester-esterase) separately into different hydrogel spheres to devise communication, pattern formation and attraction. Moreover, these pH fronts and patterns can be used for self-growing hydrogels, and for developing complex geometries from non-injectable hydrogels without 3D printing tools. This study opens possibilities for compartmentalized feedback reactions and their use in next generation materials fabrication.
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Affiliation(s)
- Indrajit Maity
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
- Freiburg Institute for Advanced StudiesUniversity of FreiburgFreiburgGermany
| | - Charu Sharma
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Francisco Lossada
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Andreas Walther
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
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32
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Miao X, Paikar A, Lerner B, Diskin‐Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out‐of‐Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Yael Diskin‐Posner
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Guy Shmul
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Sergey N. Semenov
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
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33
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Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks. Proc Natl Acad Sci U S A 2021; 118:2015285118. [PMID: 33622789 DOI: 10.1073/pnas.2015285118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.
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34
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Miao X, Paikar A, Lerner B, Diskin-Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out-of-Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021; 60:20366-20375. [PMID: 34144635 DOI: 10.1002/anie.202105790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Indexed: 02/05/2023]
Abstract
Autocatalytic reaction networks are instrumental for validating scenarios for the emergence of life on Earth and for synthesizing life de novo. Here, we demonstrate that dimeric thioesters of tripeptides with the general structure (Cys-Xxx-Gly-SEt)2 form strongly interconnected autocatalytic reaction networks that predominantly generate macrocyclic peptides up to 69 amino acids long. Some macrocycles of 6-12 amino acids were isolated from the product pool and were characterized by NMR spectroscopy and single-crystal X-ray analysis. We studied the autocatalytic formation of macrocycles in a flow reactor in the presence of acrylamide, whose conjugate addition to thiols served as a model "removal" reaction. These results indicate that even not template-assisted autocatalytic production combined with competing removal of molecular species in an open compartment could be a feasible route for selecting functional molecules during the pre-Darwinian stages of molecular evolution.
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Affiliation(s)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yael Diskin-Posner
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Guy Shmul
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sergey N Semenov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
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35
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Kriebisch CME, Bergmann AM, Boekhoven J. Fuel-Driven Dynamic Combinatorial Libraries. J Am Chem Soc 2021; 143:7719-7725. [PMID: 33978418 DOI: 10.1021/jacs.1c01616] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In dynamic combinatorial libraries, molecules react with each other reversibly to form intricate networks under thermodynamic control. In biological systems, chemical reaction networks operate under kinetic control by the transduction of chemical energy. We thus introduced the notion of energy transduction, via chemical reaction cycles, to a dynamic combinatorial library. In the library, monomers can be oligomerized, oligomers can be deoligomerized, and oligomers can recombine. Interestingly, we found that the dynamics of the library's components were dominated by transacylation, which is an equilibrium reaction. In contrast, the library's dynamics were dictated by fuel-driven activation, which is a nonequilibrium reaction. Finally, we found that self-assembly can play a large role in affecting the reaction's kinetics via feedback mechanisms. The interplay of the simultaneously operating reactions and feedback mechanisms can result in hysteresis effects in which the outcome of the competition for fuel depends on events that occurred in the past. In future work, we envision diversifying the library by modifying building blocks with catalytically active motifs and information-containing monomers.
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Affiliation(s)
- Christine M E Kriebisch
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Alexander M Bergmann
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2a, 85748 Garching, Germany
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36
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Yang S, Schaeffer G, Mattia E, Markovitch O, Liu K, Hussain AS, Ottelé J, Sood A, Otto S. Chemical Fueling Enables Molecular Complexification of Self-Replicators*. Angew Chem Int Ed Engl 2021; 60:11344-11349. [PMID: 33689197 PMCID: PMC8251556 DOI: 10.1002/anie.202016196] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/09/2021] [Indexed: 12/21/2022]
Abstract
Unravelling how the complexity of living systems can (have) emerge(d) from simple chemical reactions is one of the grand challenges in contemporary science. Evolving systems of self-replicating molecules may hold the key to this question. Here we show that, when a system of replicators is subjected to a regime where replication competes with replicator destruction, simple and fast replicators can give way to more complex and slower ones. The structurally more complex replicator was found to be functionally more proficient in the catalysis of a model reaction. These results show that chemical fueling can maintain systems of replicators out of equilibrium, populating more complex replicators that are otherwise not readily accessible. Such complexification represents an important requirement for achieving open-ended evolution as it should allow improved and ultimately also new functions to emerge.
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Affiliation(s)
- Shuo Yang
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Gael Schaeffer
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Elio Mattia
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Omer Markovitch
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
- Origins CenterUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Kai Liu
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Andreas S. Hussain
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Jim Ottelé
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Ankush Sood
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Sijbren Otto
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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37
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Yang S, Schaeffer G, Mattia E, Markovitch O, Liu K, Hussain AS, Ottelé J, Sood A, Otto S. Chemical Fueling Enables Molecular Complexification of Self‐Replicators**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shuo Yang
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gael Schaeffer
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Elio Mattia
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- Origins Center University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Kai Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Andreas S. Hussain
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ankush Sood
- 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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38
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Ameta S, Matsubara YJ, Chakraborty N, Krishna S, Thutupalli S. Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems. Life (Basel) 2021; 11:308. [PMID: 33916135 PMCID: PMC8066523 DOI: 10.3390/life11040308] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.
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Affiliation(s)
- Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Yoshiya J. Matsubara
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Nayan Chakraborty
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bangalore 560089, India
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39
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Indrajit Maity
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for Macromolecular Chemistry Freiburg Institute for Advanced Studies Albert Ludwigs University of Freiburg 79104 Freiburg Germany
| | - Dharm Dev
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Kingshuk Basu
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Nathaniel Wagner
- 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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40
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021; 60:4512-4517. [PMID: 33006406 PMCID: PMC7984337 DOI: 10.1002/anie.202012837] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 12/23/2022]
Abstract
Living cells exploit bistable and oscillatory behaviors as memory mechanisms, facilitating the integration of transient stimuli into sustained molecular responses that control downstream functions. Synthetic bistable networks have also been studied as memory entities, but have rarely been utilized to control orthogonal functions in coupled dynamic systems. We herein present a new cascade pathway, for which we have exploited a well-characterized switchable peptide-based replicating network, operating far from equilibrium, that yields two alternative steady-state outputs, which in turn serve as the input signals for consecutive processes that regulate various features of Au nanoparticle shape and assembly. This study further sheds light on how bridging together the fields of systems chemistry and nanotechnology may open up new opportunities for the dynamically controlled design of functional materials.
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Affiliation(s)
- Indrajit Maity
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
- Institute for Macromolecular ChemistryFreiburg Institute for Advanced StudiesAlbert Ludwigs University of Freiburg79104FreiburgGermany
| | - Dharm Dev
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Kingshuk Basu
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Nathaniel Wagner
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Gonen Ashkenasy
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
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41
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Kariyawasam LS, Hossain MM, Hartley CS. The Transient Covalent Bond in Abiotic Nonequilibrium Systems. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014678] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - C. Scott Hartley
- Department of Chemistry & Biochemistry Miami University Oxford OH 45056 USA
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42
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Kariyawasam LS, Hossain MM, Hartley CS. The Transient Covalent Bond in Abiotic Nonequilibrium Systems. Angew Chem Int Ed Engl 2021; 60:12648-12658. [PMID: 33264456 DOI: 10.1002/anie.202014678] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 12/20/2022]
Abstract
Biochemical systems accomplish many critical functions with by operating out-of-equilibrium using the energy of chemical fuels. The formation of a transient covalent bond is a simple but very effective tool in designing analogous reaction networks. This Minireview focuses on the fuel chemistries that have been used to generate transient bonds in recent demonstrations of abiotic nonequilibrium systems (i.e., systems that do not make use of biological components). Fuel reactions are divided into two fundamental classifications depending on whether the fuel contributes structural elements to the activated state, a distinction that dictates how they can be used. Reported systems are further categorized by overall fuel reaction (e.g., hydrolysis of alkylating agents, carbodiimide hydration) and illustrate how similar chemistry can be used to effect a wide range of nonequilibrium behavior, ranging from self-assembly to the operation of molecular machines.
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Affiliation(s)
- Lasith S Kariyawasam
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH, 45056, USA
| | | | - C Scott Hartley
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH, 45056, USA
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43
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Hochberg D, Ribó JM. Entropic analysis of bistability and the general evolution criterion. Phys Chem Chem Phys 2021; 23:14051-14063. [DOI: 10.1039/d1cp01236c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An open flow bistable Schlögl model in a well-stirred isothermal reaction volume V showing the balance of the entropy production and the exchange entropy on the non-equilibrium stationary states.
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Affiliation(s)
- David Hochberg
- Department of Molecular Evolution
- Centro de Astrobiología (CSIC-INTA)
- 28850 Torrejón de Ardoz
- Spain
| | - Josep M. Ribó
- Department of Organic and Inorganic Chemistry
- Institute of Cosmos Science (IEEC-UB)
- University of Barcelona
- Barcelona
- Spain
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44
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Kobernik V, Berkovich I, Levy A, Lemcoff NG, Diesendruck CE. Chemical Communication between Organometallic Single‐Chain Polymer Nanoparticles. Chemistry 2020; 26:15835-15838. [DOI: 10.1002/chem.202003330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/22/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Victoria Kobernik
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Inbal Berkovich
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Avishai Levy
- Schulich Faculty of Chemistry and Russell-Berrie Nanotechnology Center Technion-Israel Institute of Technology Haifa 32000 Israel
| | - N. Gabriel Lemcoff
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Charles E. Diesendruck
- Schulich Faculty of Chemistry and Russell-Berrie Nanotechnology Center Technion-Israel Institute of Technology Haifa 32000 Israel
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45
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Pogodaev AA, Lap TT, Huck WTS. The Dynamics of an Oscillating Enzymatic Reaction Network is Crucially Determined by Side Reactions. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Aleksandr A. Pogodaev
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Tijs T. Lap
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
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46
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47
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Kumar M, Sementa D, Narang V, Riedo E, Ulijn RV. Self-Assembly Propensity Dictates Lifetimes in Transient Naphthalimide-Dipeptide Nanofibers. Chemistry 2020; 26:8372-8376. [PMID: 32428282 DOI: 10.1002/chem.202001008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/05/2020] [Indexed: 01/07/2023]
Abstract
Transient self-assembly of dipeptide nanofibers with lifetimes that are predictably variable through dipeptide sequence design are presented. This was achieved using 1,8-naphthalimide (NI) amino acid methyl-esters (Phe, Tyr, Leu) that are biocatalytically coupled to amino acid-amides (Phe, Tyr, Leu, Val, Ala, Ser) to form self-assembling NI-dipeptides. However, competing hydrolysis of the dipeptides results in disassembly. It was demonstrated that the kinetic parameters like lifetimes of these nanofibers can be predictably regulated by the thermodynamic parameter, namely the self-assembly propensity of the constituent dipeptide sequence. These lifetimes could vary from minutes, to hours, to permanent gels that do not degrade. Moreover, the in-built NI fluorophore was utilized to image the transient nanostructures in solution with stimulated emission depletion (STED) based super-resolution fluorescence microscopy.
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Affiliation(s)
- Mohit Kumar
- Nanoscience Initiative at Advanced Science Research Center (ASRC), The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA
| | - Deborah Sementa
- Nanoscience Initiative at Advanced Science Research Center (ASRC), The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA
| | - Vishal Narang
- Nanoscience Initiative at Advanced Science Research Center (ASRC), The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA
| | - Elisa Riedo
- Tandon School of Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center (ASRC), The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA.,Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY, 10065, USA
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48
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49
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Wagner N, Mukherjee R, Maity I, Kraun S, Ashkenasy G. Programming Multistationarity in Chemical Replication Networks. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.201900048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nathaniel Wagner
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
| | - Rakesh Mukherjee
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for chemical sciences and engineeringEcole Polytechnique Federale de Lausanne 1015 Lausanne Switzerland
| | - Indrajit Maity
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for Macromolecular ChemistryAlbert Ludwigs University of Freiburg 79104 Freiburg Germany
| | - Sagi Kraun
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
| | - Gonen Ashkenasy
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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