1
|
Ams MR, McAuliffe JR, Semenick RS, Zeller M. Self-Replication Without Hydrogen-Bonds: An Exobiotic Design. Chemistry 2024; 30:e202401446. [PMID: 38958604 DOI: 10.1002/chem.202401446] [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: 06/17/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
Life on Earth uses DNA as the central template for self-replication, genetic encoding, and information transfer. However, there are no physical laws precluding life's existence elsewhere in space, and alternative life forms may not need DNA. In the search for exobiology, knowing what to look for as a biosignature remains a challenge - especially if it is not from the obvious list of biologic building blocks. Clues from chemicals recently discovered on Mars and in the Taurus Molecular Cloud 1 (TMC-1), show that intriguing organic compounds exist beyond Earth, which could provide a starting point for unconventional exobiotic designs. Here we present a new potential self-replicating system with structural similarities to recently discovered compounds on Mars and TMC-1. Rather than using DNA's hydrogen-bonding motif for reliable base-paring, our design employs sulfur-nitrogen interactions to selectively template unique benzothiadiazole units in sequence. We synthesized and studied two versions of this system, one reversible and the other irreversible, and found experimental evidence of self-replication in d-chloroform solvent. These results are part of a larger pursuit in our lab for developing a basis for a potential exobiological system using starting blocks closely related to these cosmic compounds.
Collapse
Affiliation(s)
- Mark R Ams
- Department of Chemistry, New Mexico Institute of Mining and Technology, 801 Leroy Place, Socorro, NM, 87801, USA
| | - Joseph R McAuliffe
- Department of Chemistry, Allegheny College, 520 North Main Street, Meadville, PA, 16335, USA
| | - Raina S Semenick
- Department of Chemistry, Allegheny College, 520 North Main Street, Meadville, PA, 16335, USA
| | - Matt Zeller
- X-ray Crystallography, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| |
Collapse
|
2
|
Rieu T, Osypenko A, Lehn JM. Triple Adaptation of Constitutional Dynamic Networks of Imines in Response to Micellar Agents: Internal Uptake-Interfacial Localization-Shape Transition. J Am Chem Soc 2024; 146:9096-9111. [PMID: 38526415 DOI: 10.1021/jacs.3c14200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Understanding the behavior of complex chemical reaction networks and how environmental conditions can modulate their organization as well as the associated outcomes may take advantage of the design of related artificial systems. Microenvironments with defined boundaries are of particular interest for their unique properties and prebiotic significance. Dynamic covalent libraries (DCvLs) and their underlying constitutional dynamic networks (CDNs) have been shown to be appropriate for studying adaptation to several processes, including compartmentalization. However, microcompartments (e.g., micelles) provide specific environments for the selective protection from interfering reactions such as hydrolysis and an enhanced chemical promiscuity due to the interface, governing different processes of network modulation. Different interactions between the micelles and the library constituents lead to dynamic sensing, resulting in different expressions of the network through pattern generation. The constituents integrated into the micelles are protected from hydrolysis and hence preferentially expressed in the network composition at the cost of constitutionally linked members. In the present work, micellar integration was observed for two processes: internal uptake based on hydrophobic forces and interfacial localization relying on attractive electrostatic interactions. The latter drives a complex triple adaptation of the network with feedback on the shape of the self-assembled entity. Our results demonstrate how microcompartments can enforce the expression of constituents of CDNs by reducing the hydrolysis of uptaken members, unravelling processes that govern the response of reactions networks. Such studies open the way toward using DCvLs and CDNs to understand the emergence of complexity within reaction networks by their interactions with microenvironments.
Collapse
Affiliation(s)
- Tanguy Rieu
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Artem Osypenko
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| |
Collapse
|
3
|
Liu K, Blokhuis A, van Ewijk C, Kiani A, Wu J, Roos WH, Otto S. Light-driven eco-evolutionary dynamics in a synthetic replicator system. Nat Chem 2024; 16:79-88. [PMID: 37653230 DOI: 10.1038/s41557-023-01301-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Darwinian evolution involves the inheritance and selection of variations in reproducing entities. Selection can be based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a reciprocal feedback on evolutionary dynamics. The onset of such eco-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits eco-evolutionary dynamics has remained elusive. Here we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a co-factor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator becomes dominant. This study shows how behaviour analogous to eco-evolutionary dynamics-which until now has been restricted to biology-can be created using an artificial minimal replicator system.
Collapse
Affiliation(s)
- Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Alex Blokhuis
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Chris van Ewijk
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Armin Kiani
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Juntian Wu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
4
|
Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett 2023; 597:2879-2896. [PMID: 37884438 DOI: 10.1002/1873-3468.14766] [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: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.
Collapse
Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Sarah Fisher
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Cesar Menor-Salvan
- Department of Biología de Sistemas, Universidad de Alcalá, Madrid, Spain
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| | | |
Collapse
|
7
|
Villarreal LP, Witzany G. Social Networking of Quasi-Species Consortia drive Virolution via Persistence. AIMS Microbiol 2021; 7:138-162. [PMID: 34250372 PMCID: PMC8255905 DOI: 10.3934/microbiol.2021010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Robertson CC, Kosikova T, Philp D. Encoding Multiple Reactivity Modes within a Single Synthetic Replicator. J Am Chem Soc 2020; 142:11139-11152. [PMID: 32414236 DOI: 10.1021/jacs.0c03527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Establishing programmable and self-sustaining replication networks in pools of chemical reagents is a key challenge in systems chemistry. Self-replicating templates are formed from two constituent components with complementary recognition and reactive sites via a slow bimolecular pathway and a fast template-directed pathway. Here, we re-engineer one of the components of a synthetic replicator to encode an additional recognition function, permitting the assembly of a binary complex between the components that mediates replicator formation through a template-independent pathway, which achieves maximum rate acceleration at early time points in the replication process. The complementarity between recognition sites creates a key conformational equilibrium between the catalytically inert product, formed via the template-independent pathway, and the catalytically active replicator that mediates the template-directed pathway. Consequently, the rapid formation of the catalytically inert isomer kick-starts replication through the template-directed pathway. Through kinetic analyses, we demonstrate that the presence of the two recognition-mediated reactivity modes results in enhanced template formation in comparison to that of systems capable of exploiting only a single recognition-mediated pathway. Finally, kinetic simulations reveal that the conformational equilibrium and both the relative and absolute efficiencies of the recognition-mediated pathways affect the extent to which self-replicating systems can benefit from this additional template-independent reactivity mode. These results allow us to formulate the rules that govern the coupling of replication processes to alternative recognition-mediated reactivity modes. The interplay between template-directed and template-independent pathways for replicator formation has significant relevance to ongoing efforts to design programmable and adaptable replicator networks.
Collapse
Affiliation(s)
- Craig C Robertson
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| |
Collapse
|
10
|
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Solà J, Jimeno C, Alfonso I. Exploiting complexity to implement function in chemical systems. Chem Commun (Camb) 2020; 56:13273-13286. [DOI: 10.1039/d0cc04170j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.
Collapse
Affiliation(s)
- Jordi Solà
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ciril Jimeno
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| |
Collapse
|
13
|
Abstract
One of the grand challenges in contemporary systems chemistry research is to mimic life-like functions using simple synthetic molecular networks. This is particularly true for systems that are out of chemical equilibrium and show complex dynamic behaviour, such as multi-stability, oscillations and chaos. We report here on thiodepsipeptide-based non-enzymatic networks propelled by reversible replication processes out of equilibrium, displaying bistability. Accordingly, we present quantitative analyses of the bistable behaviour, featuring a phase transition from the simple equilibration processes taking place in reversible dynamic chemistry into the bistable region. This behaviour is observed only when the system is continuously fueled by a reducing agent that keeps it far from equilibrium, and only when operating within a specifically defined parameter space. We propose that the development of biomimetic bistable systems will pave the way towards the study of more elaborate functions, such as information transfer and signalling.
Collapse
|
14
|
Wagner N, Hochberg D, Peacock-Lopez E, Maity I, Ashkenasy G. Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior. Life (Basel) 2019; 9:life9020045. [PMID: 31163645 PMCID: PMC6617095 DOI: 10.3390/life9020045] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 12/05/2022] Open
Abstract
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of these simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems.
Collapse
Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra Ajalvir Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain.
| | | | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
- Present address: Institute for Macromolecular Chemistry, Albert Ludwigs University of Freiburg, D-79104 Freiburg, Germany.
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| |
Collapse
|
15
|
Kosikova T, Philp D. Two Synthetic Replicators Compete To Process a Dynamic Reagent Pool. J Am Chem Soc 2019; 141:3059-3072. [PMID: 30668914 DOI: 10.1021/jacs.8b12077] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complementary building blocks, comprising a set of four aromatic aldehydes and a set of four nucleophiles-three anilines and one hydroxylamine-combine through condensation reactions to afford a dynamic covalent library (DCL) consisting of the eight starting materials and 16 condensation products. One of the aldehydes and, consequently, all of the DCL members derived from this compound bear an amidopyridine recognition site. Exposure of this DCL to two maleimides, Mp and Mm, each equipped with a carboxylic acid recognition site, results in the formation of a series of products through irreversible 1,3-dipolar cycloaddition reactions with the four nitrones present in the DCL. However, only the two cycloadducts in the product pool that incorporate both recognition sites, Tp and Tm, are self-replicators that can harness the DCL as feedstock for their own formation, facilitating their own synthesis via autocatalytic and cross-catalytic pathways. The ability of these replicators to direct their own formation from the components present in the dynamic reagent pool in response to the input of instructions in the form of preformed replicators is demonstrated through a series of quantitative 19F{1H} NMR spectroscopy experiments. Simulations establish the critical relationships between the kinetic and thermodynamic parameters of the replicators, the initial reagent concentrations, and the presence or absence of the DCL and their influence on the competition between Tp and Tm. Thus, we establish the rules that govern the behavior of the competing replicators under conditions where their formation is coupled tightly to the processing of a DCL.
Collapse
Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , KY16 9ST Fife , United Kingdom
| | - Douglas Philp
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh , St Andrews , KY16 9ST Fife , United Kingdom
| |
Collapse
|
16
|
Rink WM, Thomas F. De Novo Designed α-Helical Coiled-Coil Peptides as Scaffolds for Chemical Reactions. Chemistry 2018; 25:1665-1677. [DOI: 10.1002/chem.201802849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 01/31/2023]
Affiliation(s)
- W. Mathis Rink
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Straße 3a 37075 Göttingen Germany
| |
Collapse
|
17
|
Bai Y, Chotera A, Taran O, Liang C, Ashkenasy G, Lynn DG. Achieving biopolymer synergy in systems chemistry. Chem Soc Rev 2018; 47:5444-5456. [PMID: 29850753 DOI: 10.1039/c8cs00174j] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.
Collapse
Affiliation(s)
- Yushi Bai
- Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, USA.
| | | | | | | | | | | |
Collapse
|
18
|
Roberts DA, Pilgrim BS, Sirvinskaite G, Ronson TK, Nitschke JR. Covalent Post-assembly Modification Triggers Multiple Structural Transformations of a Tetrazine-Edged Fe4L6 Tetrahedron. J Am Chem Soc 2018; 140:9616-9623. [DOI: 10.1021/jacs.8b05082] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Derrick A. Roberts
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Ben S. Pilgrim
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Giedre Sirvinskaite
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Tanya K. Ronson
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Jonathan R. Nitschke
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| |
Collapse
|
19
|
Kosikova T, Philp D. Exploring the emergence of complexity using synthetic replicators. Chem Soc Rev 2018; 46:7274-7305. [PMID: 29099123 DOI: 10.1039/c7cs00123a] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.
Collapse
Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | | |
Collapse
|
20
|
Sadownik JW, Kosikova T, Philp D. Generating System-Level Responses from a Network of Simple Synthetic Replicators. J Am Chem Soc 2017; 139:17565-17573. [PMID: 29087701 DOI: 10.1021/jacs.7b09735] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The creation of reaction networks capable of exhibiting responses that are properties of entire systems represents a significant challenge for the chemical sciences. The system-level behavior of a reaction network is linked intrinsically to its topology and the functional connections between its nodes. A simple network of chemical reactions constructed from four reagents, in which each reagent reacts with exactly two others, can exhibit up-regulation of two products even when only a single chemical reaction is addressed catalytically. We implement a system with this topology using two maleimides and two nitrones of different sizes-either short or long and each bearing complementary recognition sites-that react pairwise through 1,3-dipolar cycloaddition reactions to create a network of four length-segregated replicating templates. Comprehensive 1H NMR spectroscopy experiments unravel the network topology, confirming that, in isolation, three out of four templates self-replicate, with the shortest template exhibiting the highest efficiency. The strongest template effects within the network are the mutually cross-catalytic relationships between the two templates of intermediate size. The network topology is such that the addition of different preformed templates as instructions to a mixture of all starting materials elicits system-level behavior. Instruction with a single template up-regulates the formation of two templates in a predictable manner. These results demonstrate that the rules governing system-level behavior can be unraveled through the application of wholly synthetic networks with well-defined chemistries and interactions.
Collapse
Affiliation(s)
- Jan W Sadownik
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| |
Collapse
|
21
|
Komáromy D, Tezcan M, Schaeffer G, Marić I, Otto S. Effector-Triggered Self-Replication in Coupled Subsystems. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dávid Komáromy
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Meniz Tezcan
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ivana Marić
- 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
| |
Collapse
|
22
|
Komáromy D, Tezcan M, Schaeffer G, Marić I, Otto S. Effector-Triggered Self-Replication in Coupled Subsystems. Angew Chem Int Ed Engl 2017; 56:14658-14662. [DOI: 10.1002/anie.201707191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dávid Komáromy
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Meniz Tezcan
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ivana Marić
- 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
| |
Collapse
|
23
|
Morrow SM, Bissette AJ, Fletcher SP. Potential for minimal self-replicating systems in a dynamic combinatorial library of equilibrating imines. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.06.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
24
|
Matysiak BM, Nowak P, Cvrtila I, Pappas CG, Liu B, Komáromy D, Otto S. Antiparallel Dynamic Covalent Chemistries. J Am Chem Soc 2017; 139:6744-6751. [PMID: 28440073 PMCID: PMC5438195 DOI: 10.1021/jacs.7b02575] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ability to design reaction networks with high, but addressable complexity is a necessary prerequisite to make advanced functional chemical systems. Dynamic combinatorial chemistry has proven to be a useful tool in achieving complexity, however with some limitations in controlling it. Herein we introduce the concept of antiparallel chemistries, in which the same functional group can be channeled into one of two reversible chemistries depending on a controllable parameter. Such systems allow both for achieving complexity, by combinatorial chemistry, and addressing it, by switching from one chemistry to another by controlling an external parameter. In our design the two antiparallel chemistries are thiol-disulfide exchange and thio-Michael addition, sharing the thiol as the common building block. By means of oxidation and reduction the system can be reversibly switched from predominantly thio-Michael chemistry to predominantly disulfide chemistry, as well as to any intermediate state. Both chemistries operate in water, at room temperature, and at mildly basic pH, which makes them a suitable platform for further development of systems chemistry.
Collapse
Affiliation(s)
- Bartosz M Matysiak
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Piotr Nowak
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivica Cvrtila
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dávid Komáromy
- 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
| |
Collapse
|
25
|
Wagner N, Mukherjee R, Maity I, Peacock-Lopez E, Ashkenasy G. Bistability and Bifurcation in Minimal Self-Replication and Nonenzymatic Catalytic Networks. Chemphyschem 2017; 18:1842-1850. [PMID: 28112462 DOI: 10.1002/cphc.201601293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/23/2017] [Indexed: 11/08/2022]
Abstract
Bistability and bifurcation, found in a wide range of biochemical networks, are central to the proper function of living systems. We investigate herein recent model systems that show bistable behavior based on nonenzymatic self-replication reactions. Such models were used before to investigate catalytic growth, chemical logic operations, and additional processes of self-organization leading to complexification. By solving for their steady-state solutions by using various analytical and numerical methods, we analyze how and when these systems yield bistability and bifurcation and discover specific cases and conditions producing bistability. We demonstrate that the onset of bistability requires at least second-order catalysis and results from a mismatch between the various forward and reverse processes. Our findings may have far-reaching implications in understanding early evolutionary processes of complexification, emergence, and potentially the origin of life.
Collapse
Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Rakesh Mukherjee
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | | | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| |
Collapse
|
26
|
Bottero I, Huck J, Kosikova T, Philp D. A Synthetic Replicator Drives a Propagating Reaction-Diffusion Front. J Am Chem Soc 2016; 138:6723-6. [PMID: 27177046 DOI: 10.1021/jacs.6b03372] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple synthetic autocatalytic replicator is capable of establishing and driving the propagation of a reaction-diffusion front within a 50 μL syringe. This replicator templates its own synthesis through a 1,3-dipolar cycloaddition reaction between a nitrone component, equipped with a 9-ethynylanthracene optical tag, and a maleimide. Kinetic studies using NMR and UV-vis spectroscopies confirm that the replicator forms efficiently and with high diastereoselectivity, and this replication process brings about a dramatic change in optical properties of the sample-a change in the color of the fluorescence in the sample from yellow to blue. The addition of a small amount of the preformed replicator at a specific location within a microsyringe, filled with the reaction building blocks, results in the initiation and propagation of a reaction-diffusion front. The realization of a replicator capable of initiating a reaction-diffusion front provides a platform for the examination of interconnected replicating networks under out-of-equilibrium conditions involving diffusion processes.
Collapse
Affiliation(s)
- Ilaria Bottero
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Jürgen Huck
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews , North Haugh, St Andrews, Fife KY16 9ST, U.K
| |
Collapse
|
27
|
Mukherjee R, Cohen-Luria R, Wagner N, Ashkenasy G. A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template-Directed Ligation. Angew Chem Int Ed Engl 2015; 54:12452-6. [DOI: 10.1002/anie.201503898] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/21/2015] [Indexed: 11/08/2022]
|
28
|
Mukherjee R, Cohen-Luria R, Wagner N, Ashkenasy G. A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template-Directed Ligation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503898] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
29
|
Nowak P, Colomb-Delsuc M, Otto S, Li J. Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library. J Am Chem Soc 2015; 137:10965-9. [PMID: 26192814 DOI: 10.1021/jacs.5b04380] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Self-assembly of a specific member of a dynamic combinatorial library (DCL) may lead to self-replication of this molecule. However, if the concentration of the potential replicator in the DCL fails to exceed its critical aggregation concentration (CAC), then self-replication will not occur. We now show how addition of a template can raise the concentration of a library member-template complex beyond its CAC, leading to the onset of self-replication. Once in existence, the replicator aggregates promote further replication also in the absence of the template that induced the initial emergence of the replicator.
Collapse
Affiliation(s)
- Piotr Nowak
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Mathieu Colomb-Delsuc
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jianwei Li
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
30
|
Wagner N, Ashkenasy G. How Catalytic Order Drives the Complexification of Molecular Replication Networks. Isr J Chem 2015. [DOI: 10.1002/ijch.201400198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
31
|
Leonetti G, Otto S. Solvent composition dictates emergence in dynamic molecular networks containing competing replicators. J Am Chem Soc 2015; 137:2067-72. [PMID: 25584629 DOI: 10.1021/ja512644f] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In Darwinian evolution, species that are better adapted to their environment win the competition for common resources from less well-adapted competitors. Thus, in such scenarios the nature of the environment may dictate the outcome of the competition. We investigated to what degree these biological principles acting at the level of species extend to the molecular level into systems based on fully synthetic self-replicating molecules. We now report two systems in which two replicators compete for a common building block and where the environment dictates which of the two replicators wins. We observed that subtle changes in the environment can lead to dramatic differences in the outcome of the competition.
Collapse
Affiliation(s)
- Giulia Leonetti
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | |
Collapse
|
32
|
Thapaliya ER, Captain B, Raymo FM. Plasmonic Acceleration of a Photochemical Replicator. ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201402211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
33
|
Dadon Z, Wagner N, Alasibi S, Samiappan M, Mukherjee R, Ashkenasy G. Competition and Cooperation in Dynamic Replication Networks. Chemistry 2014; 21:648-54. [DOI: 10.1002/chem.201405195] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Indexed: 11/09/2022]
|
34
|
Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
Collapse
Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
| |
Collapse
|
35
|
Thapaliya ER, Swaminathan S, Captain B, Raymo FM. Autocatalytic Fluorescence Photoactivation. J Am Chem Soc 2014; 136:13798-804. [DOI: 10.1021/ja5068383] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ek Raj Thapaliya
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Subramani Swaminathan
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Burjor Captain
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Françisco M. Raymo
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| |
Collapse
|
36
|
|
37
|
Bissette AJ, Fletcher SP. Mechanisms of Autocatalysis. Angew Chem Int Ed Engl 2013; 52:12800-26. [DOI: 10.1002/anie.201303822] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Indexed: 12/17/2022]
|
38
|
Hamieh S, Saggiomo V, Nowak P, Mattia E, Ludlow RF, Otto S. A “Dial-A-Receptor” Dynamic Combinatorial Library. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305744] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
39
|
Hamieh S, Saggiomo V, Nowak P, Mattia E, Ludlow RF, Otto S. A “Dial-A-Receptor” Dynamic Combinatorial Library. Angew Chem Int Ed Engl 2013; 52:12368-72. [DOI: 10.1002/anie.201305744] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Indexed: 01/28/2023]
|
40
|
Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A High-Resolution Structure that Provides Insight into Coiled-Coil Thiodepsipeptide Dynamic Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303900] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
41
|
Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A high-resolution structure that provides insight into coiled-coil thiodepsipeptide dynamic chemistry. Angew Chem Int Ed Engl 2013; 52:9944-7. [PMID: 23929823 DOI: 10.1002/anie.201303900] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/16/2013] [Indexed: 01/29/2023]
Abstract
Stable and reactive: A crystal structure at 1.35 Å of a thioester coiled-coil protein reveals high similarity to all-peptide-bond proteins. In these assemblies, the thioester bonds are kept reactive towards thiol molecules in the mixture. This enables efficient domain exchange between proteins in response to changes in folding conditions or introduction of external templates.
Collapse
Affiliation(s)
- Zehavit Dadon
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 84105 (Israel)
| | | | | | | | | |
Collapse
|
42
|
Li J, Nowak P, Otto S. Dynamic Combinatorial Libraries: From Exploring Molecular Recognition to Systems Chemistry. J Am Chem Soc 2013; 135:9222-39. [DOI: 10.1021/ja402586c] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jianwei Li
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Piotr Nowak
- 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
| |
Collapse
|
43
|
Eisenberg M, Shumacher I, Cohen-Luria R, Ashkenasy G. Dynamic combinatorial libraries of artificial repeat proteins. Bioorg Med Chem 2013; 21:3450-7. [PMID: 23582443 DOI: 10.1016/j.bmc.2013.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/10/2013] [Accepted: 03/11/2013] [Indexed: 10/27/2022]
Abstract
Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (~14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.
Collapse
Affiliation(s)
- Margarita Eisenberg
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | | | | | | |
Collapse
|
44
|
Abstract
Since its inception in the mid-1990s, dynamic combinatorial chemistry (DCC), the chemistry of complex systems under thermodynamic control, has proved valuable in identifying unexpected molecules with remarkable binding properties and in providing effective synthetic routes to complex species. Essentially, in this approach, one designs the experiment rather than the molecule. DCC has also provided us with insights into how some chemical systems respond to external stimuli. Using examples from the work of our laboratory and others, this Account shows how the concept of DCC, inspired by the evolution of living systems, has found an increasing range of applications in diverse areas and has evolved conceptually and experimentally. A dynamic combinatorial library (DCL) is a thermodynamically controlled mixture of interconverting species that can respond to various stimuli. The Cambridge version of dynamic combinatorial chemistry was initially inspired by the mammalian immune system and was conceived as a way to create and identify new unpredictable receptors. For example, an added template can select and stabilize a strongly binding member of the library which is then amplified at the expense of the unsuccessful library members, minimizing the free energy of the system. But researchers have exploited DCC in a variety of other ways: over the past two decades, this technique has contributed to the evolution of chemistry and to applications in the diverse fields of catalysis, fragrance release, and responsive materials. Among these applications, researchers have built intricate and well-defined architectures such as catenanes or hydrogen-bonded nanotubes, using the ability of complex chemical systems to reach a high level of organization. In addition, DCC has proved a powerful tool for the study of complex molecular networks and systems. The use of DCC is improving our understanding of chemical and biological systems. The study of folding or self-replicating macrocycles in DCLs has served as a model for appreciating how complex organisations such as life can emerge from a pool of simple chemicals. Today, DCC is no longer restricted to thermodynamic control, and new systems have recently appeared in which kinetic and thermodynamic control coexist. Expanding the realm of DCC to unexplored and promising new territories, these hybrid systems show that the concept of dynamic combinatorial chemistry continues to evolve.
Collapse
Affiliation(s)
- Fabien B. L. Cougnon
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Jeremy K. M. Sanders
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| |
Collapse
|
45
|
Samiappan M, Alasibi S, Cohen-Luria R, Shanzer A, Ashkenasy G. Allosteric effects in coiled-coil proteins folding and lanthanide-ion binding. Chem Commun (Camb) 2012; 48:9577-9. [DOI: 10.1039/c2cc35166h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|