1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Gutiérrez López MÁ, Tan ML, Frontera A, Matile S. The Origin of Anion-π Autocatalysis. JACS Au 2023; 3:1039-1051. [PMID: 37124310 PMCID: PMC10131205 DOI: 10.1021/jacsau.2c00656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 05/03/2023]
Abstract
The autocatalysis of epoxide-opening ether cyclizations on the aromatic surface of anion-π catalysts stands out as a leading example of emergent properties expected from the integration of unorthodox interactions into catalysis. A working hypothesis was proposed early on, but the mechanism of anion-π autocatalysis has never been elucidated. Here, we show that anion-π autocatalysis is almost independent of peripheral crowding in substrate and product. Inaccessible asymmetric anion-π autocatalysis and sometimes erratic reproducibility further support that the origin of anion-π autocatalysis is more complex than originally assumed. The apparent long-distance communication without physical contact calls for the inclusion of water between substrate and product on the catalytic aromatic surface. Efficient anion-π autocatalysis around equimolar amounts but poor activity in dry solvents and with excess water indicate that this inclusion of water requires high precision. Computational models suggest that two water molecules transmit dual substrate activation by the product and serve as proton shuttles along antiparallel but decoupled hydrogen-bonded chains to delocalize and stabilize evolving charge density in the transition state by "anion-π double bonds". This new transition-state model of anion-π autocatalysis provides a plausible mechanism that explains experimental results and brings anion-π catalysis to an unprecedented level of sophistication.
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Affiliation(s)
- M. Ángeles Gutiérrez López
- Department
of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
- National
Centre of Competence in Research (NCCR) Molecular Systems Engineering
(MSE), CH-4002 Basel, Switzerland
| | - Mei-Ling Tan
- Department
of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
- National
Centre of Competence in Research (NCCR) Molecular Systems Engineering
(MSE), CH-4002 Basel, Switzerland
| | - Antonio Frontera
- Departament
de Química, Universitat de les Illes
Balears, SP-07122 Palma de Mallorca, Spain
| | - Stefan Matile
- Department
of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
- National
Centre of Competence in Research (NCCR) Molecular Systems Engineering
(MSE), CH-4002 Basel, Switzerland
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4
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Hao X, Li TR, Chen H, Gini A, Zhang X, Rosset S, Mazet C, Tiefenbacher K, Matile S. Bioinspired Ether Cyclizations within a π-Basic Capsule Compared to Autocatalysis on π-Acidic Surfaces and Pnictogen-Bonding Catalysts. Chemistry 2021; 27:12215-12223. [PMID: 34060672 PMCID: PMC8456975 DOI: 10.1002/chem.202101548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 12/15/2022]
Abstract
While the integration of supramolecular principles in catalysis attracts increasing attention, a direct comparative assessment of the resulting systems catalysts to work out distinct characteristics is often difficult. Herein is reported how the broad responsiveness of ether cyclizations to diverse inputs promises to fill this gap. Cyclizations in the confined, π-basic and Brønsted acidic interior of supramolecular capsules, for instance, are found to excel with speed (exceeding general Brønsted acid and hydrogen-bonding catalysts by far) and selective violations of the Baldwin rules (as extreme as the so far unique pnictogen-bonding catalysts). The complementary cyclization on π-acidic aromatic surfaces remains unique with regard to autocatalysis, which is shown to be chemo- and diastereoselective with regard to product-like co-catalysts but, so far, not enantioselective.
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Affiliation(s)
- Xiaoyu Hao
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1121, Geneva, Switzerland.,NCCR Molecular Systems Engineering BPR 1095, Mattenstrasse 24a, CH-4058, Basel, Switzerland.,College of Materials, Chemistry and Chemical Engineering, Chengdu University of Technology, 1 Dongsan Road Erxianqiao, Chengdu, 610059, P.R. China
| | - Tian-Ren Li
- NCCR Molecular Systems Engineering BPR 1095, Mattenstrasse 24a, CH-4058, Basel, Switzerland.,Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4058, Basel, Switzerland
| | - Hao Chen
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1121, Geneva, Switzerland.,NCCR Molecular Systems Engineering BPR 1095, Mattenstrasse 24a, CH-4058, Basel, Switzerland
| | - Andrea Gini
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1121, Geneva, Switzerland.,NCCR Molecular Systems Engineering BPR 1095, Mattenstrasse 24a, CH-4058, Basel, Switzerland
| | - Xiang Zhang
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1121, Geneva, Switzerland.,NCCR Molecular Systems Engineering BPR 1095, Mattenstrasse 24a, CH-4058, Basel, Switzerland.,Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Science, Northwest A&F University, Xianyang Shi, Yangling, 712100, P. R. China
| | - Stéphane Rosset
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1121, Geneva, Switzerland
| | - Clément Mazet
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1121, Geneva, Switzerland
| | - Konrad Tiefenbacher
- NCCR Molecular Systems Engineering BPR 1095, Mattenstrasse 24a, CH-4058, Basel, Switzerland.,Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1121, Geneva, Switzerland.,NCCR Molecular Systems Engineering BPR 1095, Mattenstrasse 24a, CH-4058, Basel, Switzerland
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Novichkov AI, Hanopolskyi AI, Miao X, Shimon LJW, Diskin-Posner Y, Semenov SN. Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization. Nat Commun 2021; 12:2994. [PMID: 34016981 DOI: 10.1038/s41467-021-23206-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/26/2021] [Indexed: 11/08/2022] Open
Abstract
Autocatalytic and oscillatory networks of organic reactions are important for designing life-inspired materials and for better understanding the emergence of life on Earth; however, the diversity of the chemistries of these reactions is limited. In this work, we present the thiol-assisted formation of guanidines, which has a mechanism analogous to that of native chemical ligation. Using this reaction, we designed autocatalytic and oscillatory reaction networks that form substituted guanidines from thiouronium salts. The thiouronium salt-based oscillator show good stability of oscillations within a broad range of experimental conditions. By using nitrile-containing starting materials, we constructed an oscillator where the concentration of a bicyclic derivative of dihydropyrimidine oscillates. Moreover, the mixed thioester and thiouronium salt-based oscillator show unique responsiveness to chemical cues. The reactions developed in this work expand our toolbox for designing out-of-equilibrium chemical systems and link autocatalytic and oscillatory chemistry to the synthesis of guanidinium derivatives and the products of their transformations including analogs of nucleobases. So far, only a few chemical oscillators based on organic reactions have been developed. Here, the authors report both autocatalytic and oscillatory reaction networks that form substituted guanidines from thiouronium salts; when coupled to cascade cyclization, this reaction network produces oscillations in the production of pyrimidine-based heterocycles.
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6
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Paraja M, Hao X, Matile S. Polyether Natural Product Inspired Cascade Cyclizations: Autocatalysis on π-Acidic Aromatic Surfaces. Angew Chem Int Ed Engl 2020; 59:15093-15097. [PMID: 32181559 DOI: 10.1002/anie.202000681] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Indexed: 01/03/2023]
Abstract
Anion-π catalysis functions by stabilizing anionic transition states on aromatic π surfaces, thus providing a new approach to molecular transformation. The delocalized nature of anion-π interactions suggests that they serve best in stabilizing long-distance charge displacements. Aiming therefore for an anionic cascade reaction that is as charismatic as the steroid cyclization is for conventional cation-π biocatalysis, reported here is the anion-π-catalyzed epoxide-opening ether cyclizations of oligomers. Only on π-acidic aromatic surfaces having a positive quadrupole moment, such as hexafluorobenzene to naphthalenediimides, do these polyether cascade cyclizations proceed with exceptionally high autocatalysis (rate enhancements kauto /kcat >104 m-1 ). This distinctive characteristic adds complexity to reaction mechanisms (Goldilocks-type substrate concentration dependence, entropy-centered substrate destabilization) and opens intriguing perspectives for future developments.
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Affiliation(s)
- Miguel Paraja
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Xiaoyu Hao
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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7
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Affiliation(s)
- Miguel Paraja
- Department of Organic Chemistry University of Geneva Geneva Switzerland
| | - Xiaoyu Hao
- Department of Organic Chemistry University of Geneva Geneva Switzerland
| | - Stefan Matile
- Department of Organic Chemistry University of Geneva Geneva Switzerland
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8
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Gräwe A, Ranglack J, Weber W, Stein V. Engineering artificial signalling functions with proteases. Curr Opin Biotechnol 2020; 63:1-7. [DOI: 10.1016/j.copbio.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 01/01/2023]
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Abstract
In a previous paper [M. Dittner and B. Hartke, J. Chem. Theory Comput. 14, 3547 (2018)], we introduced a preliminary version of our GOCAT (globally optimal catalyst) concept in which electrostatic catalysts are designed for arbitrary reactions by global optimization of distributed point charges that surround the reaction. In this first version, a pre-defined reaction path was kept fixed. This unrealistic assumption allowed for only small catalytic effects. In the present work, we extend our GOCAT framework by a sophisticated and robust on-the-fly reaction path optimization, plus further concomitant algorithm adaptions. This allows smaller and larger excursions from a pre-defined reaction path under the influence of the GOCAT point-charge surrounding, all the way to drastic mechanistic changes. In contrast to the restricted first GOCAT version, this new version is able to address real-life catalysis. We demonstrate this by applying it to the electrostatic catalysis of a prototypical Diels-Alder reaction. Without using any prior information, this procedure re-discovers theoretically and experimentally established features of electrostatic catalysis of this very reaction, including a field-dependent transition from the synchronous, concerted textbook mechanism to a zwitterionic two-step mechanism, and diastereomeric discrimination by suitable electric field components.
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Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| | - Bernd Hartke
- Institute for Physical Chemistry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
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10
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Maguire OR, Wong ASY, Baltussen MG, van Duppen P, Pogodaev AA, Huck WTS. Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network. Chemistry 2020; 26:1676-1682. [PMID: 31808965 DOI: 10.1002/chem.201904725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/28/2019] [Indexed: 12/31/2022]
Abstract
Current efforts to design functional molecular systems have overlooked the importance of coupling out-of-equilibrium behaviour with changes in the environment. Here, the authors use an oscillating reaction network and demonstrate that the application of environmental forcing, in the form of periodic changes in temperature and in the inflow of the concentration of one of the network components, removes the dependency of the periodicity of this network on temperature or flow rates and enforces a stable periodicity across a wide range of conditions. Coupling a system to a dynamic environment can thus be used as a simple tool to regulate the output of a network. In addition, the authors show that coupling can also induce an increase in behavioural complexity to include quasi-periodic oscillations.
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Affiliation(s)
- Oliver R Maguire
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Albert S Y Wong
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Mathieu G Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Peer van Duppen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Aleksandr A Pogodaev
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
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Bayley H, Maguire OR, Huck WT. On the importance of reaction networks for synthetic living systems. Emerg Top Life Sci 2019; 3:517-27. [DOI: 10.1042/etls20190016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/11/2022]
Abstract
The goal of creating a synthetic cell necessitates the development of reaction networks which will underlie all of its behaviours. Recent developments in in vitro systems, based upon both DNA and enzymes, have created networks capable of a range of behaviours e.g. information processing, adaptation and diffusive signalling. These networks are based upon reaction motifs that when combined together produce more complex behaviour. We highlight why it is inevitable that networks, based on enzymes or enzyme-like catalysts, will be required for the construction of a synthetic cell. We outline several of the challenges, including (a) timing, (b) regulation and (c) energy distribution, that must be overcome in order to transition from the simple networks we have today to much more complex networks capable of a variety of behaviours and which could find application one day within a synthetic cell.
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12
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Prabhu GRD, Witek HA, Urban PL. Chemical clocks, oscillations, and other temporal effects in analytical chemistry: oddity or viable approach? Analyst 2018; 143:3514-3525. [PMID: 29850665 DOI: 10.1039/c7an01926b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most analytical methods are based on "analogue" inputs from sensors of light, electric potentials, or currents. The signals obtained by such sensors are processed using certain calibration functions to determine concentrations of the target analytes. The signal readouts are normally done after an optimised and fixed time period, during which an assay mixture is incubated. This minireview covers another-and somewhat unusual-analytical strategy, which relies on the measurement of time interval between the occurrences of two distinguishable states in the assay reaction. These states manifest themselves via abrupt changes in the properties of the assay mixture (e.g. change of colour, appearance or disappearance of luminescence, change in pH, variations in optical activity or mechanical properties). In some cases, a correlation between the time of appearance/disappearance of a given property and the analyte concentration can be also observed. An example of an assay based on time measurement is an oscillating reaction, in which the period of oscillations is linked to the concentration of the target analyte. A number of chemo-chronometric assays, relying on the existing (bio)transformations or artificially designed reactions, were disclosed in the past few years. They are very attractive from the fundamental point of view but-so far-only few of them have be validated and used to address real-world problems. Then, can chemo-chronometric assays become a practical tool for chemical analysis? Is there a need for further development of such assays? We are aiming to answer these questions.
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Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Rd., Hsinchu, 30010, Taiwan
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Affiliation(s)
- Sergey N. Semenov
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford Street MA 02138 USA
- Institute for Molecules and Materials; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Department of Organic Chemistry; Weizmann Institute of Science; Rehovot 76100 Israel
| | - Alar Ainla
- INL - International Iberian Nanotechnology Laboratory; Avenida Mestre José Veiga s/n 4715-330 Braga Portugal
| | - Ekaterina V. Skorb
- SCAMT Laboratory; ITMO University; St. Petersburg 197101 Russian Federation
| | - Sjoerd G. J. Postma
- Institute for Molecules and Materials; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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Abstract
![]()
Systems chemistry
aims to emulate the functional behavior observed
in living systems by constructing chemical reaction networks (CRNs)
with well-defined dynamic properties. Future expansion of the complexity
of these systems would require external control to tune behavior and
temporal organization of such CRNs. In this work, we design and implement
a photolabile probe, which upon irradiation strengthens the negative
feedback loop of a CRN that produces oscillations of trypsin under
out-of-equilibrium conditions. By changing the timing and duration
of irradiation, we can tailor the temporal response of the network.
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Affiliation(s)
- Aleksandr A Pogodaev
- Institute for Molecules and Materials, Radboud University, Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Albert S Y Wong
- Institute for Molecules and Materials, Radboud University, Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Affiliation(s)
- Yasunori Okamoto
- Department of Chemistry; University of Basel; Spitalstrasse 51 4056 Basel Switzerland
| | - Thomas R. Ward
- Department of Chemistry; University of Basel; Spitalstrasse 51 4056 Basel Switzerland
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16
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Abstract
Cross-regulation of complex biochemical reaction networks is an essential feature of living systems. In a biomimetic spirit, we report on our efforts to program the temporal activation of an artificial metalloenzyme via cross-regulation by a natural enzyme. In the presence of urea, urease slowly releases ammonia that reversibly inhibits an artificial transfer hydrogenase. Addition of an acid, which acts as fuel, allows to maintain the system out of equilibrium.
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Affiliation(s)
- Yasunori Okamoto
- Department of ChemistryUniversity of BaselSpitalstrasse 514056BaselSwitzerland
| | - Thomas R. Ward
- Department of ChemistryUniversity of BaselSpitalstrasse 514056BaselSwitzerland
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19
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Abstract
A new discipline of "systems chemistry" is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.
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Affiliation(s)
- Albert S Y Wong
- Institute for Molecular Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecular Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Maltanava HM, Poznyak SK, Andreeva DV, Quevedo MC, Bastos AC, Tedim J, Ferreira MGS, Skorb EV. Light-Induced Proton Pumping with a Semiconductor: Vision for Photoproton Lateral Separation and Robust Manipulation. ACS Appl Mater Interfaces 2017; 9:24282-24289. [PMID: 28654237 DOI: 10.1021/acsami.7b05209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Energy-transfer reactions are the key for living open systems, biological chemical networking, and the development of life-inspired nanoscale machineries. It is a challenge to find simple reliable synthetic chemical networks providing a localization of the time-dependent flux of matter. In this paper, we look to photocatalytic reaction on TiO2 from different angles, focusing on proton generation and introducing a reliable, minimal-reagent-consuming, stable inorganic light-promoted proton pump. Localized illumination was applied to a TiO2 surface in solution for reversible spatially controlled "inorganic photoproton" isometric cycling, the lateral separation of water-splitting reactions. The proton flux is pumped during the irradiation of the surface of TiO2 and dynamically maintained at the irradiated surface area in the absence of any membrane or predetermined material structure. Moreover, we spatially predetermine a transient acidic pH value on the TiO2 surface in the irradiated area with the feedback-driven generation of a base as deactivator. Importantly we describe how to effectively monitor the spatial localization of the process by the in situ scanning ion-selective electrode technique (SIET) measurements for pH and the scanning vibrating electrode technique (SVET) for local photoelectrochemical studies without additional pH-sensitive dye markers. This work shows the great potential for time- and space-resolved water-splitting reactions for following the investigation of pH-stimulated processes in open systems with their flexible localization on a surface.
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Affiliation(s)
- Hanna M Maltanava
- The Research Institute for Physical Chemical Problems, Belarusian State University , Minsk 220030, Belarus
| | - Sergey K Poznyak
- The Research Institute for Physical Chemical Problems, Belarusian State University , Minsk 220030, Belarus
| | - Daria V Andreeva
- Center for Soft and Living Matter, Institute of Basic Science Ulsan, National Institute of Science and Technology , Ulsan 44919, Republic of Korea
| | - Marcela C Quevedo
- Department of Materials and Ceramic Engineering, CICECO, University of Aveiro , Aveiro 3810-193, Portugal
| | - Alexandre C Bastos
- Department of Materials and Ceramic Engineering, CICECO, University of Aveiro , Aveiro 3810-193, Portugal
| | - João Tedim
- Department of Materials and Ceramic Engineering, CICECO, University of Aveiro , Aveiro 3810-193, Portugal
| | - Mário G S Ferreira
- Department of Materials and Ceramic Engineering, CICECO, University of Aveiro , Aveiro 3810-193, Portugal
| | - Ekaterina V Skorb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies (SCAMT), ITMO University , St. Petersburg 197101, Russian Federation
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge 02138, Massachusetts, United States
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Hakim AS, Omara ST, Syame SM, Fouad EA. Serotyping, antibiotic susceptibility, and virulence genes screening of Escherichia coli isolates obtained from diarrheic buffalo calves in Egyptian farms. Vet World 2017; 10:769-773. [PMID: 28831220 PMCID: PMC5553145 DOI: 10.14202/vetworld.2017.769-773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/23/2017] [Indexed: 01/01/2023] Open
Abstract
AIM In Egypt as in many other countries, river water buffalo (Bubalus bubalis) is considered an important source of high-quality milk and meat supply. The objective of this study was to investigate serotypes, virulence genes, and antibiotic resistance determinants profiles of Escherichia coli isolated from buffalo at some places in Egypt; noticibly, this issue was not discussed in the country yet. MATERIALS AND METHODS A number of 58 rectal samples were collected from diarrheic buffalo calves in different regions in Egypt, and bacteriological investigated for E. coli existence. The E. coli isolates were biochemically, serologicaly identified, tested for antibiotic susceptibility, and polymerase chain reaction (PCR) analyzed for the presence of antibiotic resistance determinants and virulence genes. RESULTS Overall 14 isolates typed as E. coli (24.1%); 6 were belonged to serogroup O78 (10.3%), followed by O125 (4 isolates, 6.9%), then O158 (3 isolates, 5.2%) and one isolate O8 (1.7%), among them, there were 5 E. coli isolates showed a picture of hemolysis (35.7%). The isolates exhibited a high resistance to β lactams over 60%, followed by sulfa (50%) and aminoglucoside (42.8%) group, in the same time the isolates were sensitive to quinolone, trimethoprim-sulfamethoxazole, tetracycline (100%), and cephalosporine groups (71.4%). A multiplex PCR was applied to the 14 E. coli isolates revealed that all were carrying at least one gene, as 10 carried blaTEM (71.4%), 8 Sul1 (57.1%), and 6 aadB (42.8%), and 9 isolates could be considered multidrug resistant (MDR) by an incidence of 64.3%. A PCR survey was stratified for the most important E. coli virulence genes, and showed the presence of Shiga toxins in 9 isolates carried either one or the two Stx genes (64.3%), 5 isolates carried hylA gene (35.7%), and eae in 2 isolates only (14.3%), all isolates carried at least one virulence gene except two (85.7%). CONCLUSION The obtained data displayed that in Egypt, buffalo as well as other ruminants could be a potential source of MDR pathogenic E. coli variants which have a public health importance.
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Affiliation(s)
- Ashraf S Hakim
- Department of Microbiology and Immunology, National Research Centre, Dokki, Cairo, Egypt
| | - Shimaa T Omara
- Department of Microbiology and Immunology, National Research Centre, Dokki, Cairo, Egypt
| | - Sohier M Syame
- Department of Microbiology and Immunology, National Research Centre, Dokki, Cairo, Egypt
| | - Ehab A Fouad
- Department of Microbiology and Immunology, National Research Centre, Dokki, Cairo, Egypt
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Abstract
Living systems rely on complex networks of chemical reactions to control the concentrations of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. One of the greatest challenges in chemistry is the creation of such functionality from chemical reactions. A key limitation is our lack of understanding of how molecular structure impacts on the dynamics of chemical reaction networks, preventing the design of networks that are robust (i.e., function in a large parameter space) and resilient (i.e., reach their out-of-equilibrium function rapidly). Here we demonstrate that reaction rates of individual reactions in the network can control the dynamics by which the system reaches limit cycle oscillations, thereby gaining information on the key parameters that govern the dynamics of these networks. We envision that these principles will be incorporated into the design of network motifs, enabling chemists to develop "molecular software" to create functional behavior in chemical systems.
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Affiliation(s)
- Albert S Y Wong
- Institute for Molecules and Materials, Radboud University Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Aleksandr A Pogodaev
- Institute for Molecules and Materials, Radboud University Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ilia N Vialshin
- Institute for Molecules and Materials, Radboud University Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Britta Helwig
- Institute for Molecules and Materials, Radboud University Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Postma SGJ, Vialshin IN, Gerritsen CY, Bao M, Huck WTS. Preprogramming Complex Hydrogel Responses using Enzymatic Reaction Networks. Angew Chem Int Ed Engl 2017; 56:1794-1798. [DOI: 10.1002/anie.201610875] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Sjoerd G. J. Postma
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Ilia N. Vialshin
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Casper Y. Gerritsen
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Min Bao
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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Postma SGJ, Vialshin IN, Gerritsen CY, Bao M, Huck WTS. Preprogramming Complex Hydrogel Responses using Enzymatic Reaction Networks. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sjoerd G. J. Postma
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Ilia N. Vialshin
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Casper Y. Gerritsen
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Min Bao
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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25
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Abstract
A broad overview of functional aspects in biological and synthetic out-of-equilibrium systems.
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Affiliation(s)
- Rémi Merindol
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
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26
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Abstract
We describe a biochemical timer composed of three biocatalytic reactions involving three types of adenylate nucleotides: adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP). The timer is triggered by a small amount of ATP or ADP. An abrupt increase in the ATP concentration (following numerous amplification cycles) leads to a sudden increase of luminescence from the reaction mixture. The time point when the luminescence appears is found to be a function of the initial concentration of the triggering nucleotide (5.0 × 10(-8)-1.0 × 10(-6) M), even in the presence of a complex biological matrix. The mechanism of the observed dependence of the time of luminescence increase on the concentration has been confirmed with simple kinetic models. Due to the biocompatibility of the proposed trienzymatic reaction scheme (sensitivity to common nucleotides and occurrence in a neutral pH aqueous environment), the scheme can be used in bioengineered systems that require modulation of the response time (light emission) by concentration.
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Affiliation(s)
- Ting-Ru Chen
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, 300, Taiwan
| | - Ching-Fong Hsu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, 300, Taiwan
| | - Chih-Lin Chen
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, 300, Taiwan
| | - Henryk A. Witek
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, 300, Taiwan
| | - Pawel L. Urban
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, 300, Taiwan
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