1
|
Kurpik G, Walczak A, Dydio P, Stefankiewicz AR. Multi-Stimuli-Responsive Network of Multicatalytic Reactions using a Single Palladium/Platinum Catalyst. Angew Chem Int Ed Engl 2024; 63:e202404684. [PMID: 38877818 DOI: 10.1002/anie.202404684] [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: 03/07/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/16/2024]
Abstract
Given her unrivalled proficiency in the synthesis of all molecules of life, nature has been an endless source of inspiration for developing new strategies in organic chemistry and catalysis. However, one feature that remains thus far beyond chemists' grasp is her unique ability to adapt the productivity of metabolic processes in response to triggers that indicate the temporary need for specific metabolites. To demonstrate the remarkable potential of such stimuli-responsive systems, we present a metabolism-inspired network of multicatalytic processes capable of selectively synthesising a range of products from simple starting materials. Specifically, the network is built of four classes of distinct catalytic reactions-cross-couplings, substitutions, additions, and reductions, involving three organic starting materials-terminal alkyne, aryl iodide, and hydrosilane. All starting materials are either introduced sequentially or added to the system at the same time, with no continuous influx of reagents or efflux of products. All processes in the system are catalysed by a multifunctional heteronuclear PdII/PtII complex, whose performance can be controlled by specific additives and external stimuli. The reaction network exhibits a substantial degree of orthogonality between different pathways, enabling the controllable synthesis of ten distinct products with high efficiency and selectivity through simultaneous triggering and suppression mechanisms.
Collapse
Affiliation(s)
- Gracjan Kurpik
- Center for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Anna Walczak
- Center for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Paweł Dydio
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
- University of Strasbourg, CNRS, ISIS UMR 7006, 8 Allée Gaspard Monge, 67000, Strasbourg, France
| | - Artur R Stefankiewicz
- Center for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| |
Collapse
|
2
|
Singh A, Parvin P, Saha B, Das D. Non-equilibrium self-assembly for living matter-like properties. Nat Rev Chem 2024:10.1038/s41570-024-00640-z. [PMID: 39179623 DOI: 10.1038/s41570-024-00640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
The soft and wet machines of life emerged as the spatially enclosed ensemble of biomolecules with replicating capabilities integrated with metabolic reaction cycles that operate at far-from-equilibrium. A thorough step-by-step synthetic integration of these elements, namely metabolic and replicative properties all confined and operating far-from-equilibrium, can set the stage from which we can ask questions related to the construction of chemical-based evolving systems with living matter-like properties - a monumental endeavour of systems chemistry. The overarching concept of this Review maps the discoveries on this possible integration of reaction networks, self-reproduction and compartmentalization under non-equilibrium conditions. We deconvolute the events of reaction networks and transient compartmentalization and extend the discussion towards self-reproducing systems that can be sustained under non-equilibrium conditions. Although enormous challenges lie ahead in terms of molecular diversity, information transfer, adaptation and selection that are required for open-ended evolution, emerging strategies to generate minimal metabolic cycles can extend our growing understanding of the chemical emergence of the biosphere of Earth.
Collapse
Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Payel Parvin
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Bapan Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
| |
Collapse
|
3
|
Duez Q, van de Wiel J, van Sluijs B, Ghosh S, Baltussen MG, Derks MTGM, Roithová J, Huck WTS. Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry. J Am Chem Soc 2024; 146:20778-20787. [PMID: 39013149 PMCID: PMC11295183 DOI: 10.1021/jacs.4c04218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is often a bottleneck. Here, we report on the interface between a continuous stirred-tank reactor, in which an immobilized enzymatic network made of 12 enzymes is compartmentalized, and an ion mobility-mass spectrometer. Feeding uniformly 13C-labeled inputs to the enzymatic network generates all isotopically labeled reaction intermediates and products, which are individually detected by ion mobility-mass spectrometry (IMS-MS) based on their mass-to-charge ratios and inverse ion mobilities. The metabolic flux can be continuously and quantitatively monitored by diluting the ERN output with nonlabeled standards of known concentrations. The real-time quantitative data obtained by IMS-MS are then harnessed to train a model of network kinetics, which proves sufficiently predictive to control the ERN output after a single optimally designed experiment. The high resolution of the time-course data provided by this approach is an important stepping stone to design and control sizable and intricate ERNs.
Collapse
Affiliation(s)
| | | | - Bob van Sluijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Souvik Ghosh
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Max T. G. M. Derks
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| |
Collapse
|
4
|
Wen X, Zhang C, Tian Y, Miao Y, Liu S, Xu JJ, Ye D, He J. Smart Molecular Imaging and Theranostic Probes by Enzymatic Molecular In Situ Self-Assembly. JACS AU 2024; 4:2426-2450. [PMID: 39055152 PMCID: PMC11267545 DOI: 10.1021/jacsau.4c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Enzymatic molecular in situ self-assembly (E-MISA) that enables the synthesis of high-order nanostructures from synthetic small molecules inside a living subject has emerged as a promising strategy for molecular imaging and theranostics. This strategy leverages the catalytic activity of an enzyme to trigger probe substrate conversion and assembly in situ, permitting prolonging retention and congregating many molecules of probes in the targeted cells or tissues. Enhanced imaging signals or therapeutic functions can be achieved by responding to a specific enzyme. This E-MISA strategy has been successfully applied for the development of enzyme-activated smart molecular imaging or theranostic probes for in vivo applications. In this Perspective, we discuss the general principle of controlling in situ self-assembly of synthetic small molecules by an enzyme and then discuss the applications for the construction of "smart" imaging and theranostic probes against cancers and bacteria. Finally, we discuss the current challenges and perspectives in utilizing the E-MISA strategy for disease diagnoses and therapies, particularly for clinical translation.
Collapse
Affiliation(s)
- Xidan Wen
- Department
of Nuclear Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital
of Medical School, Nanjing University, Nanjing 210008, China
- State
Key Laboratory of Analytical Chemistry for Life Science, Chemistry
and Biomedicine Innovation Center (ChemBIC), School of Chemistry and
Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Chao Zhang
- Department
of Neurosurgery, Zhujiang Hospital, Southern
Medical University, Guangzhou 510282, China
| | - Yuyang Tian
- State
Key Laboratory of Analytical Chemistry for Life Science, Chemistry
and Biomedicine Innovation Center (ChemBIC), School of Chemistry and
Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Yinxing Miao
- State
Key Laboratory of Analytical Chemistry for Life Science, Chemistry
and Biomedicine Innovation Center (ChemBIC), School of Chemistry and
Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Shaohai Liu
- State
Key Laboratory of Analytical Chemistry for Life Science, Chemistry
and Biomedicine Innovation Center (ChemBIC), School of Chemistry and
Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Jing-Juan Xu
- State
Key Laboratory of Analytical Chemistry for Life Science, Chemistry
and Biomedicine Innovation Center (ChemBIC), School of Chemistry and
Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Deju Ye
- State
Key Laboratory of Analytical Chemistry for Life Science, Chemistry
and Biomedicine Innovation Center (ChemBIC), School of Chemistry and
Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Jian He
- Department
of Nuclear Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital
of Medical School, Nanjing University, Nanjing 210008, China
| |
Collapse
|
5
|
Zhang Z, Howlett MG, Silvester E, Kukura P, Fletcher SP. A Chemical Reaction Network Drives Complex Population Dynamics in Oscillating Self-Reproducing Vesicles. J Am Chem Soc 2024; 146:18262-18269. [PMID: 38917079 PMCID: PMC11240260 DOI: 10.1021/jacs.4c00860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
We report chemically fueled oscillations of vesicles. The population cycling of vesicles is driven by their self-reproduction and collapse within a biphasic reaction network involving the interplay of molecular and supramolecular events. We studied the oscillations on the molecular and supramolecular scales and tracked vesicle populations in time by interferometric scattering microscopy and dynamic light scattering. Complex supramolecular events were observed during oscillations─including vesicle reproduction, growth, and decomposition─and differences in the number, size, and mass of aggregates can often be observed within and between pulses. This system's dynamic behavior is reminiscent of a reproductive cycle in living cells.
Collapse
Affiliation(s)
- Zhiheng Zhang
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Michael G. Howlett
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Emma Silvester
- The
Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K.
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
| | - Philipp Kukura
- The
Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Stephen P. Fletcher
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| |
Collapse
|
6
|
Li X, Fomitskaya P, Smaliak VA, Smith BS, Skorb EV, Semenov SN. Selenium catalysis enables negative feedback organic oscillators. Nat Commun 2024; 15:3316. [PMID: 38632338 PMCID: PMC11024130 DOI: 10.1038/s41467-024-47714-6] [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: 01/19/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
The construction of materials regulated by chemical reaction networks requires regulatory motifs that can be stacked together into systems with desired properties. Multiple autocatalytic reactions producing thiols are known. However, negative feedback loop motifs are unavailable for thiol chemistry. Here, we develop a negative feedback loop based on the selenocarbonates. In this system, thiols induce the release of aromatic selenols that catalyze the oxidation of thiols by organic peroxides. This negative feedback loop has two important features. First, catalytic oxidation of thiols follows Michaelis-Menten-like kinetics, thus increasing nonlinearity for the negative feedback. Second, the strength of the negative feedback can be tuned by varying substituents in selenocarbonates. When combined with the autocatalytic production of thiols in a flow reactor, this negative feedback loop induces sustained oscillations. The availability of this negative feedback motif enables the future construction of oscillatory, homeostatic, adaptive, and other regulatory circuits in life-inspired systems and materials.
Collapse
Affiliation(s)
- Xiuxiu Li
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
- Department of Chemistry and Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Southern University of Science and Technology, Shenzhen, China
| | - Polina Fomitskaya
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Viktoryia A Smaliak
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Barbara S Smith
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Ekaterina V Skorb
- Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russia
| | - Sergey N Semenov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
7
|
Naz M, Zhang L, Chen C, Yang S, Dou H, Mann S, Li J. Self-assembly of stabilized droplets from liquid-liquid phase separation for higher-order structures and functions. Commun Chem 2024; 7:79. [PMID: 38594355 PMCID: PMC11004187 DOI: 10.1038/s42004-024-01168-5] [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: 12/31/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
Dynamic microscale droplets produced by liquid-liquid phase separation (LLPS) have emerged as appealing biomaterials due to their remarkable features. However, the instability of droplets limits the construction of population-level structures with collective behaviors. Here we first provide a brief background of droplets in the context of materials properties. Subsequently, we discuss current strategies for stabilizing droplets including physical separation and chemical modulation. We also discuss the recent development of LLPS droplets for various applications such as synthetic cells and biomedical materials. Finally, we give insights on how stabilized droplets can self-assemble into higher-order structures displaying coordinated functions to fully exploit their potentials in bottom-up synthetic biology and biomedical applications.
Collapse
Affiliation(s)
- Mehwish Naz
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China
| | - Lin Zhang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China
| | - Chong Chen
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, Turku, 20520, Finland
| | - Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China.
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China.
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
| | - Jianwei Li
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, Turku, 20520, Finland.
| |
Collapse
|
8
|
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
|
9
|
Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
Collapse
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
| |
Collapse
|
10
|
Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
Collapse
Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- 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
| |
Collapse
|
11
|
Grelich-Mucha M, Bachelart T, Torbeev V, Ożga K, Berlicki Ł, Olesiak-Bańska J. Amyloid engineering - how terminal capping modifies morphology and secondary structure of supramolecular peptide aggregates. Biomater Sci 2024; 12:1590-1602. [PMID: 38323504 DOI: 10.1039/d3bm01641b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The effects of peptide N- and C-termini on aggregation behavior have been scarcely studied. Herein, we examine (105-115) peptide fragments of transthyretin (TTR) containing various functional groups at both termini and study their impact on the morphology and the secondary structure. We synthesized TTR(105-115) peptides functionalized with α-amino (H-), N-acetyl-α-amino (Ac-) or N,N-dimethyl-α-amino (DiMe-) groups at the N-terminus, and with amide (-NH2) or carboxyl (-OH) functions at the C-terminus. We also investigated quasi-racemic mixtures by mixing the L-enantiomers with the D-enantiomer capped by H- and -NH2 groups. We observed that fibril formation is promoted by the sufficient number of hydrogen bonds at peptides' termini. Moreover, the final morphology of the aggregates can be controlled by the functional groups at the N-terminus. Remarkably, all quasi-racemic mixtures resulted in the robust formation of fibrils. Overall, this work illustrates how modifications of peptide termini may help to engineer supramolecular aggregates with a predicted morphology.
Collapse
Affiliation(s)
- Manuela Grelich-Mucha
- Institute of Advanced Materials, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Thomas Bachelart
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400 Illkirch, France
| | - Vladimir Torbeev
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400 Illkirch, France
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Bańska
- Institute of Advanced Materials, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
| |
Collapse
|
12
|
Shklyaev OE, Balazs AC. Interlinking spatial dimensions and kinetic processes in dissipative materials to create synthetic systems with lifelike functionality. NATURE NANOTECHNOLOGY 2024; 19:146-159. [PMID: 38057363 DOI: 10.1038/s41565-023-01530-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/21/2023] [Indexed: 12/08/2023]
Abstract
Biological systems spontaneously convert energy input into the actions necessary to survive. Motivated by the efficacy of these processes, researchers aim to forge materials systems that exhibit the self-sustained and autonomous functionality found in nature. Success in this effort will require synthetic analogues of the following: a metabolism to generate energy, a vasculature to transport energy and materials, a nervous system to transmit 'commands', a musculoskeletal system to translate commands into physical action, regulatory networks to monitor the entire enterprise, and a mechanism to convert 'nutrients' into growing materials. Design rules must interconnect the material's structural and kinetic properties over ranges of length (that can vary from the nano- to mesoscale) and timescales to enable local energy dissipations to power global functionality. Moreover, by harnessing dynamic interactions intrinsic to the material, the system itself can perform the work needed for its own functionality. Here, we assess the advances and challenges in dissipative materials design and at the same time aim to spur developments in next-generation functional, 'living' materials.
Collapse
Affiliation(s)
- Oleg E Shklyaev
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anna C Balazs
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
13
|
Hayakawa I, Isogai T, Takanishi J, Asai S, Ando C, Tsutsumi T, Watanabe K, Sakakura A, Tsunematsu Y. Synthesis and biological evaluation of coprinoferrin, an acylated tripeptide hydroxamate siderophore. Org Biomol Chem 2024; 22:831-837. [PMID: 38175167 DOI: 10.1039/d3ob01850d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Coprinoferrin (CPF), originally isolated from a genetically engineered strain (ΔlaeA) of the mushroom fungus Coprinopsis cinerea, is an acylated tripeptide hydroxamate consisting of tandem aligned N5-hexanoyl-N5-hydroxy-L-ornithine with modifications of N-acetyl and C-carboxamide. These unique chemical properties make CPF an iron(III) binder (siderophore), which helps in iron acquisition from the environment and promotes hyphal growth as well as fruiting body formation in C. cinerea. However, CPF's detailed mode of action remains enigmatic. In this study, we have accomplished the synthesis of CPF from N-Boc-L-glutamic acid 5-benzyl ester. The physicochemical characteristics, spectroscopic features, and biological activity observed in the synthetic CPF closely match those of natural CPF. This alignment provides unequivocal confirmation of the proposed chemical structure, facilitating a deeper understanding of its physiological role in nature, particularly in fruiting body formation.
Collapse
Affiliation(s)
- Ichiro Hayakawa
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
| | - Tomoki Isogai
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
| | - Jun Takanishi
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Shihori Asai
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Chika Ando
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan.
| | - Tomohiro Tsutsumi
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Akira Sakakura
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
| | - Yuta Tsunematsu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan.
| |
Collapse
|
14
|
Dev D, Wagner N, Pramanik B, Sharma B, Maity I, Cohen-Luria R, Peacock-Lopez E, Ashkenasy G. A Peptide-Based Oscillator. J Am Chem Soc 2023; 145:26279-26286. [PMID: 37984498 DOI: 10.1021/jacs.3c09377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.
Collapse
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
| |
Collapse
|
15
|
Leathard AS, Beales PA, Taylor AF. Design of oscillatory dynamics in numerical simulations of compartment-based enzyme systems. CHAOS (WOODBURY, N.Y.) 2023; 33:123128. [PMID: 38149992 DOI: 10.1063/5.0180256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023]
Abstract
Enzymatic reactions that yield non-neutral products are known to involve feedback due to the bell-shaped pH-rate curve of the enzyme. Compartmentalizing the reaction has been shown to lead to transport-driven oscillations in theory; however, there have been few reproducible experimental examples. Our objective was to determine how the conditions could be optimized to achieve pH oscillations. We employed numerical simulations to investigate the hydrolysis of ethyl acetate in a confined esterase enzyme system, examining the influence of key factors on its behavior. Specific parameter ranges that lead to bistability and self-sustained pH oscillations and the importance of fast base transport for oscillations in this acid-producing system are highlighted. Suggestions are made to expand the parameter space for the occurrence of oscillations, including modifying the maximum of the enzyme pH-rate curve and increasing the negative feedback rate. This research not only sheds light on the programmable nature of enzyme-driven pH regulation but also furthers knowledge on the optimal design of such feedback systems for experimentalists.
Collapse
Affiliation(s)
- Anna S Leathard
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Paul A Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Annette F Taylor
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| |
Collapse
|
16
|
Wang H, Cheng Z, Yuan L, Ren L, Pan C, Epstein IR, Gao Q. Role of Fast and Slow Inhibitors in Oscillatory Rhythm Design. J Am Chem Soc 2023; 145:23152-23159. [PMID: 37844139 DOI: 10.1021/jacs.3c07076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In biological or abiotic systems, rhythms occur, owing to the coupling between positive and negative feedback loops in a reaction network. Using the Semenov-Whitesides oscillatory network for thioester hydrolysis as a prototype, we experimentally and theoretically analyzed the role of fast and slow inhibitors in oscillatory reaction networks. In the presence of positive feedback, a single fast inhibitor generates a time delay, resulting in two saddle-node bifurcations and bistability in a continuously stirred tank reactor. A slow inhibitor produces a node-focus bifurcation, resulting in damped oscillations. With both fast and slow inhibitors present, the node-focus bifurcation repeatedly modulates the saddle-node bifurcations, producing stable periodic oscillations. These fast and slow inhibitions result in a pair of time delays between steeply ascending and descending dynamics, which originate from the positive and negative feedbacks, respectively. This pattern can be identified in many chemical relaxation oscillators and oscillatory models, e.g., the bromate-sulfite pH oscillatory system, the Belousov-Zhabotinsky reaction, the trypsin oscillatory system, and the Boissonade-De Kepper model. This study provides a novel understanding of chemical and biochemical rhythms and suggests an approach to designing such behavior.
Collapse
Affiliation(s)
- Hongzhang Wang
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Zhenfang Cheng
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Ling Yuan
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Lin Ren
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, Zhejiang, P. R. China
| | - Changwei Pan
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| | - Irving R Epstein
- Department of Chemistry and Volen Center for Complex Systems, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Qingyu Gao
- College of Chemical Engineering, China University of Mining and Technology, Xuzhou221116, Jiangsu, P. R. China
| |
Collapse
|
17
|
Li Z, Wang J, Willner I. Alternate Strategies to Induce Dynamically Modulated Transient Transcription Machineries. ACS NANO 2023; 17:18266-18279. [PMID: 37669432 PMCID: PMC10540262 DOI: 10.1021/acsnano.3c05336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
Emulating native transient transcription machineries modulating temporal gene expression by synthetic circuits is a major challenge in the area of systems chemistry. Three different methods to operate transient transcription machineries and to modulate the gated transcription processes of target RNAs are introduced. One method involves the design of a reaction module consisting of transcription templates being triggered by promoter fuel strands transcribing target RNAs and in parallel generating functional DNAzymes in the transcription templates, modulating the dissipative depletion of the active templates and the transient operation of transcription circuits. The second approach involves the application of a reaction module consisting of two transcription templates being activated by a common fuel promoter strand. While one transcription template triggers the transcription of the target RNA, the second transcription template transcribes the anti-fuel strand, displacing the promoter strand associated with the transcription templates, leading to the depletion of the transcription templates and to the dynamic transient modulation of the transcription process. The third strategy involves the assembly of a reaction module consisting of a reaction template triggered by a fuel promoter strand transcribing the target RNA. The concomitant nickase-stimulated depletion of the promoter strand guides the transient modulation of the transcription process. Via integration of two parallel fuel-triggered transcription templates in the three transcription reaction modules and application of template-specific blocker units, the parallel and gated transiently modulated transcription of two different RNA aptamers is demonstrated. The nickase-stimulated transiently modulated transcription reaction module is applied as a functional circuit guiding the dynamic expression of gated, transiently operating, catalytic DNAzymes.
Collapse
Affiliation(s)
| | | | - Itamar Willner
- The Institute of Chemistry, The Center
for Nanoscience and Nanotechnology, The
Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
18
|
Ter Harmsel M, Maguire OR, Runikhina SA, Wong ASY, Huck WTS, Harutyunyan SR. A catalytically active oscillator made from small organic molecules. Nature 2023; 621:87-93. [PMID: 37673989 PMCID: PMC10482680 DOI: 10.1038/s41586-023-06310-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 06/12/2023] [Indexed: 09/08/2023]
Abstract
Oscillatory systems regulate many biological processes, including key cellular functions such as metabolism and cell division, as well as larger-scale processes such as circadian rhythm and heartbeat1-4. Abiotic chemical oscillations, discovered originally in inorganic systems5,6, inspired the development of various synthetic oscillators for application as autonomous time-keeping systems in analytical chemistry, materials chemistry and the biomedical field7-17. Expanding their role beyond that of a pacemaker by having synthetic chemical oscillators periodically drive a secondary function would turn them into significantly more powerful tools. However, this is not trivial because the participation of components of the oscillator in the secondary function might jeopardize its time-keeping ability. We now report a small molecule oscillator that can catalyse an independent chemical reaction in situ without impairing its oscillating properties. In a flow system, the concentration of the catalytically active product of the oscillator shows sustained oscillations and the catalysed reaction is accelerated only during concentration peaks. Augmentation of synthetic oscillators with periodic catalytic action allows the construction of complex systems that, in the future, may benefit applications in automated synthesis, systems and polymerization chemistry and periodic drug delivery.
Collapse
Affiliation(s)
- Matthijs Ter Harmsel
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Oliver R Maguire
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Sofiya A Runikhina
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Albert S Y Wong
- Department of Molecules and Materials, University of Twente, Enschede, the Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
| | | |
Collapse
|
19
|
Zhu C, Zhou Z, Gao XJ, Tao Y, Cao X, Xu Y, Shen Y, Liu S, Zhang Y. Cascade nanozymatic network mimicking cells with selective and linear perception of H 2O 2. Chem Sci 2023; 14:6780-6791. [PMID: 37350812 PMCID: PMC10284138 DOI: 10.1039/d3sc01714a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
A single stimulus leading to multiple responses is an essential function of many biological networks, which enable complex life activities. However, it is challenging to duplicate a similar chemical reaction network (CRN) using non-living chemicals, aiming at the disclosure of the origin of life. Herein, we report a nanozyme-based CRN with feedback and feedforward functions for the first time. It demonstrates multiple responses at different modes and intensities upon a single H2O2 stimulus. In the two-electron cascade oxidation of 3,3',5,5'-tetramethylbenzidine (TMB), the endogenous product H2O2 competitively inhibited substrates in the first one-electron oxidation reaction on a single-atom nanozyme (Co-N-CNTs) and strikingly accelerated the second one-electron oxidation reaction under a micellar nanozyme. As a proof-of-concept, we further confined the nanozymatic network to a microfluidic chip as a simplified artificial cell. It exhibited remarkable selectivity and linearity in the perception of H2O2 stimulus against more than 20 interferences in a wide range of concentrations (0.01-100 mM) and offered an instructive platform for studying primordial life-like processes.
Collapse
Affiliation(s)
- Caixia Zhu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Medical School, Southeast University Nanjing 211189 China
| | - Zhixin Zhou
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Medical School, Southeast University Nanjing 211189 China
| | - Xuejiao J Gao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University Nanchang 330022 China
| | - Yanhong Tao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University Nanchang 330022 China
| | - Xuwen Cao
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Medical School, Southeast University Nanjing 211189 China
| | - Yuan Xu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Medical School, Southeast University Nanjing 211189 China
| | - Yanfei Shen
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Medical School, Southeast University Nanjing 211189 China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Medical School, Southeast University Nanjing 211189 China
| | - Yuanjian Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Medical School, Southeast University Nanjing 211189 China
| |
Collapse
|
20
|
Zhou H, Cheng R, Quarrell M, Shchukin D. Autonomic self-regulating systems based on polyelectrolyte microcapsules and microgel particles. J Colloid Interface Sci 2023; 638:403-411. [PMID: 36758253 DOI: 10.1016/j.jcis.2023.01.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/11/2023] [Accepted: 01/22/2023] [Indexed: 01/29/2023]
Abstract
Biological systems possess unique non-equilibrium functions, maintaining tight manipulation of their surroundings through inter-communication of multiple components and self-regulatory capability organized over different length scales. However, most artificial materials are incapable of communicating and self-regulating behavior due to their limited number of component and direct responsive modes. Herein, a new integrated self-regulation system is developed utilizing stimuli-responsive polyelectrolyte capsules as building blocks. The combination of stimuli-responsive capsules and enzyme immobilized microgels is designed to mimic life systems and its programmable interactive communications and self-regulation behavior is demonstrated through communication-feedback mechanism. Polyelectrolyte capsules can sense changes of their surrounding, then start the internal communication by releasing energy-rich cargo mimicking the behavior of the cells. The microgel particles subsequently complete closed-loop communication through providing negative feedback on capsules by enzymatic reaction and actuating pH-regulation of the whole system. Different communication modes and pH-regulation behaviors could be achieved by adjusting spatial and kinetic conditions. Proposed intelligent system is highly customizable due to the wide selection of encapsulated cargos, stimuli-responsive blocks and reaction networks, and would have broad influences in areas ranging from medical implants that assist in stabilizing body functions to microreactor system that regulate catalytic reactions.
Collapse
Affiliation(s)
- Hongda Zhou
- Stephenson Institute for Renewable Energy and Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom.
| | - Rui Cheng
- HH Wills Physics Laboratory, Bristol Centre for Functional Nanomaterials, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - Matthew Quarrell
- Stephenson Institute for Renewable Energy and Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Dmitry Shchukin
- Stephenson Institute for Renewable Energy and Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom.
| |
Collapse
|
21
|
van Duppen P, Daines E, Robinson WE, Huck WTS. Dynamic Environmental Conditions Affect the Composition of a Model Prebiotic Reaction Network. J Am Chem Soc 2023; 145:7559-7568. [PMID: 36961990 PMCID: PMC10080678 DOI: 10.1021/jacs.3c00908] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Prebiotic environments are dynamic, containing a range of periodic and aperiodic variations in reaction conditions. However, the impact of the temporal dynamics of environmental conditions upon prebiotic chemical reaction networks has not been investigated. Here, we demonstrate how the magnitude and rate of temporal fluctuations of the catalysts Ca2+ and hydroxide control the product distributions of the formose reaction. Surprisingly, the product compositions of the formose reaction under dynamic conditions deviate significantly from those under steady state conditions. We attribute these compositional changes to the non-uniform propagation of fluctuations through the network, thereby shaping reaction outcomes. An examination of temporal concentration patterns showed that collections of compounds responded collectively to perturbations, indicating that key gating reactions branching from the Breslow cycle may be important responsive features of the formose reaction. Our findings show how the compositions of prebiotic reaction networks were shaped by sequential environmental events, illustrating the necessity for considering the temporal traits of prebiotic environments that supported the origin of life.
Collapse
Affiliation(s)
- Peer van Duppen
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Elena Daines
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - William E Robinson
- 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
| |
Collapse
|
22
|
Ivanov NM, Baltussen MG, Regueiro CLF, Derks MTGM, Huck WTS. Computing Arithmetic Functions Using Immobilised Enzymatic Reaction Networks. Angew Chem Int Ed Engl 2023; 62:e202215759. [PMID: 36562219 PMCID: PMC10108092 DOI: 10.1002/anie.202215759] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Living systems use enzymatic reaction networks to process biochemical information and make decisions in response to external or internal stimuli. Herein, we present a modular and reusable platform for molecular information processing using enzymes immobilised in hydrogel beads and compartmentalised in a continuous stirred tank reactor. We demonstrate how this setup allows us to perform simple arithmetic operations, such as addition, subtraction and multiplication, using various concentrations of substrates or inhibitors as inputs and the production of a fluorescent molecule as the readout.
Collapse
Affiliation(s)
- Nikita M Ivanov
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| | - Mathieu G Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| | | | - Max T G M Derks
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| |
Collapse
|
23
|
Manna RK, Shklyaev OE, Balazs AC. Chemically Driven Multimodal Locomotion of Active, Flexible Sheets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:780-789. [PMID: 36602946 DOI: 10.1021/acs.langmuir.2c02666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The inhibitor-promoter feedback loop is a vital component in regulatory pathways that controls functionality in living systems. In this loop, the production of chemical A at one site promotes the production of chemical B at another site, but B inhibits the production of A. In solution, differences in the volumes of the reactants and products of this reaction can generate buoyancy-driven fluid flows, which will deform neighboring soft material. To probe the intrinsic interrelationship among chemistry, hydrodynamics, and fluid-structure interactions, we model a bio-inspired system where a flexible sheet immersed in solution encompasses two spatially separated catalytic patches, which drive the A-B inhibitor-promotor reaction. The convective rolls of fluid generated above the patches can circulate inward or outward depending on the chemical environment. Within the regime displaying chemical oscillations, the dynamic fluid-structure interactions morph the shape of the sheet to periodically "fly", "crawl", or "swim" along the bottom of the confining chamber, revealing an intimate coupling between form and function in this system. The oscillations in the sheet's motion in turn affect the chemical oscillations in the solution. In the regime with non-oscillatory chemistry, the induced flow still morphs the shape of the sheet, but now, the fluid simply translates the sheet along the length of the chamber. The findings reveal the potential for enzymatic reactions in the body to generate hydrodynamic behavior that modifies the shape of neighboring soft tissue, which in turn modifies both the fluid dynamics and the enzymatic reaction. The findings indicate that this non-linear dynamic behavior can be playing a critical role in the functioning of regulatory pathways in living systems.
Collapse
Affiliation(s)
- Raj Kumar Manna
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania15260, United States
| | - Oleg E Shklyaev
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania15260, United States
| | - Anna C Balazs
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania15260, United States
| |
Collapse
|
24
|
Dong J, Willner I. Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis. ACS NANO 2023; 17:687-696. [PMID: 36576858 PMCID: PMC9836355 DOI: 10.1021/acsnano.2c10108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Transient transcription machineries play important roles in the dynamic modulation of gene expression and the sequestered regulation of cellular networks. The present study emulates such processes by designing artificial reaction modules consisting of transcription machineries that guide the transient synthesis of catalytic DNAzymes, the transient operation of gated DNAzymes, and the temporal activation of an intercommunicated DNAzyme cascade. The reaction modules rely on functional constituents that lead to the triggered activation of transcription machineries in the presence of the nucleoside triphosphates oligonucleotide fuel, yielding the transient formation and dissipative depletion of the intermediate DNAzyme(s) products. The kinetics of the transient DNAzyme networks are computationally simulated, allowing to predict and experimentally validate the performance of the systems under different auxiliary conditions. The study advances the field of systems chemistry by introducing transcription machinery-based networks for the dynamic control over transient catalysis─a primary step toward life-like cellular assemblies.
Collapse
|
25
|
Rifaie-Graham O, Yeow J, Najer A, Wang R, Sun R, Zhou K, Dell TN, Adrianus C, Thanapongpibul C, Chami M, Mann S, de Alaniz JR, Stevens MM. Photoswitchable gating of non-equilibrium enzymatic feedback in chemically communicating polymersome nanoreactors. Nat Chem 2023; 15:110-118. [PMID: 36344820 PMCID: PMC9836937 DOI: 10.1038/s41557-022-01062-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 09/14/2022] [Indexed: 11/09/2022]
Abstract
The circadian rhythm generates out-of-equilibrium metabolite oscillations that are controlled by feedback loops under light/dark cycles. Here we describe a non-equilibrium nanosystem comprising a binary population of enzyme-containing polymersomes capable of light-gated chemical communication, controllable feedback and coupling to macroscopic oscillations. The populations consist of esterase-containing polymersomes functionalized with photo-responsive donor-acceptor Stenhouse adducts (DASA) and light-insensitive semipermeable urease-loaded polymersomes. The DASA-polymersome membrane becomes permeable under green light, switching on esterase activity and decreasing the pH, which in turn initiates the production of alkali in the urease-containing population. A pH-sensitive pigment that absorbs green light when protonated provides a negative feedback loop for deactivating the DASA-polymersomes. Simultaneously, increased alkali production deprotonates the pigment, reactivating esterase activity by opening the membrane gate. We utilize light-mediated fluctuations of pH to perform non-equilibrium communication between the nanoreactors and use the feedback loops to induce work as chemomechanical swelling/deswelling oscillations in a crosslinked hydrogel. We envision possible applications in artificial organelles, protocells and soft robotics.
Collapse
Affiliation(s)
- Omar Rifaie-Graham
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Jonathan Yeow
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Adrian Najer
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Richard Wang
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Rujie Sun
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Kun Zhou
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Tristan N Dell
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Christopher Adrianus
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Chalaisorn Thanapongpibul
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Mohamed Chami
- BioEM lab, Biozentrum, University of Basel, Basel, Switzerland
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK
| | - Javier Read de Alaniz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK.
| |
Collapse
|
26
|
Zhang H, Zeng H, Eklund A, Guo H, Priimagi A, Ikkala O. Feedback-controlled hydrogels with homeostatic oscillations and dissipative signal transduction. NATURE NANOTECHNOLOGY 2022; 17:1303-1310. [PMID: 36443600 PMCID: PMC9747616 DOI: 10.1038/s41565-022-01241-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/14/2022] [Indexed: 05/06/2023]
Abstract
Driving systems out of equilibrium under feedback control is characteristic for living systems, where homeostasis and dissipative signal transduction facilitate complex responses. This feature not only inspires dissipative dynamic functionalities in synthetic systems but also poses great challenges in designing novel pathways. Here we report feedback-controlled systems comprising two coupled hydrogels driven by constant light, where the system can be tuned to undergo stable homeostatic self-oscillations or damped steady states of temperature. We demonstrate that stable temperature oscillations can be utilized for dynamic colours and cargo transport, whereas damped steady states enable signal transduction pathways. Here mechanical triggers cause temperature changes that lead to responses such as bending motions inspired by the single-touch mechanoresponse in Mimosa pudica and the frequency-gated snapping motion inspired by the plant arithmetic in the Venus flytrap. The proposed concepts suggest generalizable feedback pathways for dissipative dynamic materials and interactive soft robotics.
Collapse
Affiliation(s)
- Hang Zhang
- Department of Applied Physics, Aalto University, Espoo, Finland
| | - Hao Zeng
- Smart Photonic Materials, Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
| | - Amanda Eklund
- Department of Applied Physics, Aalto University, Espoo, Finland
| | - Hongshuang Guo
- Smart Photonic Materials, Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Arri Priimagi
- Smart Photonic Materials, Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
| | - Olli Ikkala
- Department of Applied Physics, Aalto University, Espoo, Finland.
| |
Collapse
|
27
|
Goswami S, Reja A, Pal S, Singh A, Das D. Nonequilibrium Amyloid Polymers Exploit Dynamic Covalent Linkage to Temporally Control Charge-Selective Catalysis. J Am Chem Soc 2022; 144:19248-19252. [PMID: 36219699 DOI: 10.1021/jacs.2c09262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extant proteins exploit thermodynamically activated negatively charged coenzymes and hydrotropes to temporally access mechanistically important conformations that regulate vital biological functions, from metabolic reactions to expression modulation. Herein, we show that a short amyloid peptide can bind to a small molecular coenzyme by exploiting reversible covalent linkage to polymerize and access catalytically proficient nonequilibrium amyloid microphases. Subsequent hydrolysis of the activated coenzyme leads to depolymerization, realizing a variance of the surface charge of the assembly as a function of time. Such temporal change of surface charge dynamically modulates catalytic activities of the transient assemblies as observed in highly evolved modern-day biocatalysts.
Collapse
Affiliation(s)
- Surashree Goswami
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Abhishek Singh
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| |
Collapse
|
28
|
Slootbeek AD, van Haren MHI, Smokers IBA, Spruijt E. Growth, replication and division enable evolution of coacervate protocells. Chem Commun (Camb) 2022; 58:11183-11200. [PMID: 36128910 PMCID: PMC9536485 DOI: 10.1039/d2cc03541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
Living and proliferating cells undergo repeated cycles of growth, replication and division, all orchestrated by complex molecular networks. How a minimal cell cycle emerged and helped primitive cells to evolve remains one of the biggest mysteries in modern science, and is an active area of research in chemistry. Protocells are cell-like compartments that recapitulate features of living cells and may be seen as the chemical ancestors of modern life. While compartmentalization is not strictly required for primitive, open-ended evolution of self-replicating systems, it gives such systems a clear identity by setting the boundaries and it can help them overcome three major obstacles of dilution, parasitism and compatibility. Compartmentalization is therefore widely considered to be a central hallmark of primitive life, and various types of protocells are actively investigated, with the ultimate goal of developing a protocell capable of autonomous proliferation by mimicking the well-known cell cycle of growth, replication and division. We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are. Considerations are given for designing chemical networks in coacervates that can lead to sustained growth, selective replication and controlled division, in a way that they are linked together like in the cell cycle. Ultimately, such a system may undergo evolution by natural selection of certain phenotypes, leading to adaptation and the gain of new functions, and we end with a brief discussion of the opportunities for coacervates to facilitate this.
Collapse
Affiliation(s)
- Annemiek D Slootbeek
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| |
Collapse
|
29
|
Wang X, Wu S, Tang TYD, Tian L. Engineering strategies for sustainable synthetic cells. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
30
|
Li Z, Wang J, Willner I. Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs. SCIENCE ADVANCES 2022; 8:eabq5947. [PMID: 35977022 PMCID: PMC9385147 DOI: 10.1126/sciadv.abq5947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Following transient spatiotemporal misregulation of gene expression programs by native transcription machineries, we introduce a versatile biomimetic concept to design transient dynamic transcription machineries, revealing gated and cascaded temporal transcription of RNAs. The concept is based on the engineering of the reaction module consisting of malachite green (MG) and/or DFHBI {(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2,3-dimethyl-4H-imidazol-4-one} DNA scaffolds, T7 RNA polymerase (RNAP) aptamer transcription scaffold, and the inhibited T7 RNAP-aptamer complex. In the presence of the counter RNAP aptamer strand and ribonucleoside triphosphates, the triggered activation of the three transcription scaffolds are activated, leading to the transcription of the MG and/or DFHBI RNA aptamer and to the transcription of the RNAP aptamer acting as an autoinhibitor that leads to the transient temporal, dissipative, and blockage of all transcription. By appropriate design of the transcription scaffolds and the inhibitors/coupler, transient gated and cascaded transcription processes are demonstrated, and a bimodal transcription module synthesizing a transient operating ribozyme is introduced.
Collapse
|
31
|
Nakamoto M, Kitano S, Matsusaki M. Biomacromolecule-Fueled Transient Volume Phase Transition of a Hydrogel. Angew Chem Int Ed Engl 2022; 61:e202205125. [PMID: 35441476 DOI: 10.1002/anie.202205125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Indexed: 12/15/2022]
Abstract
A metabolic cycle-inspired hydrogel which exhibits the biomacromolecule-fueled transient volume phase transition is reported. This hydrogel has the affinity and digestive capacity for a fuel α-poly-L-lysine by incorporating acrylic acid and trypsin. The hydrogel captured fuel and transiently shrank owing to the construction of electrostatic cross-linkages. This process was inherently connected with the digestion of these cross-linkages and the release of oligo-lysine as waste, which induced the reswelling of the hydrogel at equilibrium. The transient volume change of the hydrogel realized the fuel-stimulated transient release of a payload. This study provides a strategy for engineering materials with biomacromolecule-fueled dynamic functions under the out-of-equilibrium condition.
Collapse
Affiliation(s)
- Masahiko Nakamoto
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shiro Kitano
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Michiya Matsusaki
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.,Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| |
Collapse
|
32
|
Schaffter SW, Chen KL, O'Brien J, Noble M, Murugan A, Schulman R. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nat Chem 2022; 14:1224-1232. [PMID: 35927329 DOI: 10.1038/s41557-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/16/2022] [Indexed: 01/01/2023]
Abstract
Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network's various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.
Collapse
Affiliation(s)
- Samuel W Schaffter
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuan-Lin Chen
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jackson O'Brien
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Madeline Noble
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Arvind Murugan
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Rebecca Schulman
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. .,Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
33
|
Howlett MG, Engwerda AHJ, Scanes RJH, Fletcher SP. An autonomously oscillating supramolecular self-replicator. Nat Chem 2022; 14:805-810. [PMID: 35618766 DOI: 10.1038/s41557-022-00949-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/13/2022] [Indexed: 01/24/2023]
Abstract
A key goal of chemistry is to develop synthetic systems that mimic biology, such as self-assembling, self-replicating models of minimal life forms. Oscillations are often observed in complex biological networks, but oscillating, self-replicating species are unknown, and how to control autonomous supramolecular-level oscillating systems is also not yet established. Here we show how a population of self-assembling self-replicators can autonomously oscillate, so that simple micellar species repeatedly appear and disappear in time. The interplay of molecular and supramolecular events is key to observing oscillations: the repeated formation and disappearance of compartments is connected to a reaction network where molecular-level species are formed and broken down. The dynamic behaviour of our system across different length scales offers the opportunities for mass transport, as we demonstrate via reversible dye uptake. We believe these findings will inspire new biomimetic systems and may unlock nanotechnology systems such as (supra)molecular pumps, where compartment formation is controlled in time and space.
Collapse
|
34
|
Robinson WE, Daines E, van Duppen P, de Jong T, Huck WTS. Environmental conditions drive self-organization of reaction pathways in a prebiotic reaction network. Nat Chem 2022; 14:623-631. [PMID: 35668214 DOI: 10.1038/s41557-022-00956-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/26/2022] [Indexed: 11/09/2022]
Abstract
The evolution of life from the prebiotic environment required a gradual process of chemical evolution towards greater molecular complexity. Elaborate prebiotically relevant synthetic routes to the building blocks of life have been established. However, it is still unclear how functional chemical systems evolved with direction using only the interaction between inherent molecular chemical reactivity and the abiotic environment. Here we demonstrate how complex systems of chemical reactions exhibit well-defined self-organization in response to varying environmental conditions. This self-organization allows the compositional complexity of the reaction products to be controlled as a function of factors such as feedstock and catalyst availability. We observe how Breslow's cycle contributes to the reaction composition by feeding C2 building blocks into the network, alongside reaction pathways dominated by formaldehyde-driven chain growth. The emergence of organized systems of chemical reactions in response to changes in the environment offers a potential mechanism for a chemical evolution process that bridges the gap between prebiotic chemical building blocks and the origin of life.
Collapse
Affiliation(s)
- William E Robinson
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Elena Daines
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Peer van Duppen
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Thijs de Jong
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, Netherlands.
| |
Collapse
|
35
|
Baltussen MG, van de Wiel J, Fernández Regueiro CL, Jakštaitė M, Huck WTS. A Bayesian Approach to Extracting Kinetic Information from Artificial Enzymatic Networks. Anal Chem 2022; 94:7311-7318. [PMID: 35549162 PMCID: PMC9134183 DOI: 10.1021/acs.analchem.2c00659] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to create artificial enzymatic networks capable of increasingly complex behavior, an improved methodology in understanding and controlling the kinetics of these networks is needed. Here, we introduce a Bayesian analysis method allowing for the accurate inference of enzyme kinetic parameters and determination of most likely reaction mechanisms, by combining data from different experiments and network topologies in a single probabilistic analysis framework. This Bayesian approach explicitly allows us to continuously improve our parameter estimates and behavior predictions by iteratively adding new data to our models, while automatically taking into account uncertainties introduced by the experimental setups or the chemical processes in general. We demonstrate the potential of this approach by characterizing systems of enzymes compartmentalized in beads inside flow reactors. The methods we introduce here provide a new approach to the design of increasingly complex artificial enzymatic networks, making the design of such networks more efficient, and robust against the accumulation of experimental errors.
Collapse
Affiliation(s)
- Mathieu G Baltussen
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen van de Wiel
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ, Nijmegen, The Netherlands
| | | | - Miglė Jakštaitė
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ, Nijmegen, The Netherlands
| |
Collapse
|
36
|
Nakamoto M, Kitano S, Matsusaki M. Biomacromolecule‐Fueled Transient Volume Phase Transition of a Hydrogel. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Masahiko Nakamoto
- Division of Applied Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
| | - Shiro Kitano
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
| | - Michiya Matsusaki
- Division of Applied Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
| |
Collapse
|
37
|
Lewis RW, Klemm B, Macchione M, Eelkema R. Fuel-driven macromolecular coacervation in complex coacervate core micelles. Chem Sci 2022; 13:4533-4544. [PMID: 35656128 PMCID: PMC9019912 DOI: 10.1039/d2sc00805j] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022] Open
Abstract
Fuel-driven macromolecular coacervation is an entry into the transient formation of highly charged, responsive material phases. In this work, we used a chemical reaction network (CRN) to drive the coacervation of macromolecular species readily produced using radical polymerisation methods. The CRN enables transient quaternization of tertiary amine substrates, driven by the conversion of electron deficient allyl acetates and thiol or amine nucleophiles. By incorporating tertiary amine functionality into block copolymers, we demonstrate chemical triggered complex coacervate core micelle (C3M) assembly and disassembly. In contrast to most dynamic coacervate systems, this CRN operates at constant physiological pH without the need for complex biomolecules. By varying the allyl acetate fuel, deactivating nucleophile and reagent ratios, we achieved both sequential signal-induced C3M (dis)assembly, as well as transient non-equilibrium (dis)assembly. We expect that timed and signal-responsive control over coacervate phase formation at physiological pH will find application in nucleic acid delivery, nano reactors and protocell research. We apply an allyl acetate fuelled chemical reaction network (CRN) to control the coacervation of macromolecular species at constant physiological pH without the need for complex biomolecules.![]()
Collapse
Affiliation(s)
- Reece W Lewis
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Benjamin Klemm
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Mariano Macchione
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| |
Collapse
|
38
|
Guindani C, da Silva LC, Cao S, Ivanov T, Landfester K. Synthetic Cells: From Simple Bio-Inspired Modules to Sophisticated Integrated Systems. Angew Chem Int Ed Engl 2022; 61:e202110855. [PMID: 34856047 PMCID: PMC9314110 DOI: 10.1002/anie.202110855] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/08/2021] [Indexed: 12/01/2022]
Abstract
Bottom-up synthetic biology is the science of building systems that mimic the structure and function of living cells from scratch. To do this, researchers combine tools from chemistry, materials science, and biochemistry to develop functional and structural building blocks to construct synthetic cell-like systems. The many strategies and materials that have been developed in recent decades have enabled scientists to engineer synthetic cells and organelles that mimic the essential functions and behaviors of natural cells. Examples include synthetic cells that can synthesize their own ATP using light, maintain metabolic reactions through enzymatic networks, perform gene replication, and even grow and divide. In this Review, we discuss recent developments in the design and construction of synthetic cells and organelles using the bottom-up approach. Our goal is to present representative synthetic cells of increasing complexity as well as strategies for solving distinct challenges in bottom-up synthetic biology.
Collapse
Affiliation(s)
- Camila Guindani
- Chemical Engineering ProgramCOPPEFederal University of Rio de Janeiro, PEQ/COPPE/UFRJ, CEP 21941-972Rio de JaneiroRJBrazil
| | - Lucas Caire da Silva
- Department of Physical Chemistry of PolymersMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Shoupeng Cao
- Department of Physical Chemistry of PolymersMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Tsvetomir Ivanov
- Department of Physical Chemistry of PolymersMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Katharina Landfester
- Department of Physical Chemistry of PolymersMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| |
Collapse
|
39
|
Kriukov DV, Koyuncu AH, Wong ASY. History Dependence in a Chemical Reaction Network Enables Dynamic Switching. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107523. [PMID: 35257479 DOI: 10.1002/smll.202107523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/02/2022] [Indexed: 06/14/2023]
Abstract
This work describes an enzymatic autocatalytic network capable of dynamic switching under out-of-equilibrium conditions. The network, wherein a molecular fuel (trypsinogen) and an inhibitor (soybean trypsin inhibitor) compete for a catalyst (trypsin), is kept from reaching equilibria using a continuous flow stirred tank reactor. A so-called 'linear inhibition sweep' is developed (i.e., a molecular analogue of linear sweep voltammetry) to intentionally perturb the competition between autocatalysis and inhibition, and used to demonstrate that a simple molecular system, comprising only three components, is already capable of a variety of essential neuromorphic behaviors (hysteresis, synchronization, resonance, and adaptation). This research provides the first steps in the development of a strategy that uses the principles in systems chemistry to transform chemical reaction networks into platforms capable of neural network computing.
Collapse
Affiliation(s)
- Dmitrii V Kriukov
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
| | - A Hazal Koyuncu
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
| | - Albert S Y Wong
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
- MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
- BRAINS (Center for Brain-inspired Nano Systems), University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
| |
Collapse
|
40
|
Guindani C, Silva LC, Cao S, Ivanov T, Landfester K. Synthetic Cells: From Simple Bio‐Inspired Modules to Sophisticated Integrated Systems. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Camila Guindani
- Chemical Engineering Program COPPE Federal University of Rio de Janeiro, PEQ/COPPE/UFRJ, CEP 21941-972 Rio de Janeiro RJ Brazil
| | - Lucas Caire Silva
- Department of Physical Chemistry of Polymers Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Shoupeng Cao
- Department of Physical Chemistry of Polymers Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Tsvetomir Ivanov
- Department of Physical Chemistry of Polymers Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Katharina Landfester
- Department of Physical Chemistry of Polymers Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| |
Collapse
|
41
|
Chatterjee A, Reja A, Pal S, Das D. Systems chemistry of peptide-assemblies for biochemical transformations. Chem Soc Rev 2022; 51:3047-3070. [PMID: 35316323 DOI: 10.1039/d1cs01178b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.
Collapse
Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| |
Collapse
|
42
|
Afrose SP, Mahato C, Sharma P, Roy L, Das D. Nonequilibrium Catalytic Supramolecular Assemblies of Melamine- and Imidazole-Based Dynamic Building Blocks. J Am Chem Soc 2022; 144:673-678. [PMID: 34990140 DOI: 10.1021/jacs.1c11457] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The development of synthetic nonequilibrium systems has gathered increasing attention due to their potential to illustrate the dynamic, complex, and emergent traits of biological systems. Simple building blocks capable of interacting via dynamic covalent chemistry and physical assembly in a reaction network under nonequilibrium conditions can contribute to our understanding of complex systems of life and its origin. Herein, we have demonstrated the nonequilibrium generation of catalytic supramolecular assemblies from simple heterocycle melamine driven by a thermodynamically activated ester. Utilizing a reversible covalent linkage, an imidazole moiety was recruited by the assemblies to access a catalytic transient state that dissipated energy via accelerated hydrolysis of the activated ester. The nonequilibrium assemblies were further capable of temporally binding to a hydrophobic guest to modulate its photophysical properties. Notably, the presence of an exogenous aromatic base augmented the lifetime of the catalytic microphases, reflecting their higher kinetic stability.
Collapse
Affiliation(s)
- Syed Pavel Afrose
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Chiranjit Mahato
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Pooja Sharma
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Lisa Roy
- Institute of Chemical Technology Mumbai-IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension Centre, Bhubaneswar 751013, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| |
Collapse
|
43
|
Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non-Equilibrium Conditions. Angew Chem Int Ed Engl 2022; 61:e202111857. [PMID: 34767668 DOI: 10.1002/anie.202111857] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 11/07/2022]
Abstract
Herein, we report the substrate induced generation of a transient catalytic microenvironment from a single amino acid functionalized fatty acid in presence of a cofactor hemin. The catalytic state accessed under non-equilibrium conditions showed acceleration of peroxidase activity resulting in degradation of the substrate and subsequently led to disassembly. Equilibrated systems could not access the three-dimensional microphases and showed substantially lower catalytic activity. Further, the assembled state showed latent catalytic function (promiscuity) to hydrolyze a precursor to yield the same substrate. Consequently, the assembly demonstrated protometabolism by exploiting the peroxidase-hydrolase cascade to augment the lifetime and the mechanical properties of the catalytic state.
Collapse
Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Antara Reja
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Subhajit Bal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Baishakhi Tikader
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Dibyendu Das
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| |
Collapse
|
44
|
Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non‐Equilibrium Conditions**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Baishakhi Tikader
- Department of Chemistry Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| |
Collapse
|
45
|
Cho CJ, Niederholtmeyer H, Seo H, Bhattacharya A, Devaraj NK. Functionalizing lipid sponge droplets with DNA. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202100045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christy J. Cho
- University of California San Diego Chemistry and Biochemistry UNITED STATES
| | - Henrike Niederholtmeyer
- Max-Planck-Institut für terrestrische Mikrobiologie: Max-Planck-Institut fur terrestrische Mikrobiologie Cell-free Synthetic Biology Group Karl-von-Frisch-Str. 10 35043 Marburg GERMANY
| | - Hyeonglim Seo
- University of California San Diego Chemistry and Biochemistry UNITED STATES
| | | | - Neal K. Devaraj
- University of California San Diego Chemistry and Biochemistry UNITED STATES
| |
Collapse
|
46
|
Priyanka, Shandilya E, Brar SK, Mahato RR, Maiti S. Spatiotemporal dynamics of self-assembled structures in enzymatically induced agonistic and antagonistic conditions. Chem Sci 2021; 13:274-282. [PMID: 35059177 PMCID: PMC8694342 DOI: 10.1039/d1sc05353a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/20/2021] [Indexed: 12/20/2022] Open
Abstract
Predicting and designing systems with dynamic self-assembly properties in a spatiotemporal fashion is an important research area across disciplines ranging from understanding the fundamental non-equilibrium features of life to the fabrication of next-generation materials with life-like properties. Herein, we demonstrate a spatiotemporal dynamics pattern in the self-assembly behavior of a surfactant from an unorganized assembly, induced by adenosine triphosphate (ATP) and enzymes responsible for the degradation or conversion of ATP. We report the different behavior of two enzymes, alkaline phosphatase (ALP) and hexokinase (HK), towards adenosine triphosphate (ATP)-driven surfactant assembly, which also results in contrasting spatiotemporal dynamic assembly behavior. Here, ALP acts antagonistically, resulting in transient self-assemblies, whereas HK shows agonistic action with the ability to sustain the assemblies. This dynamic assembly behavior was then used to program the time-dependent emergence of a self-assembled structure in a two-dimensional space by maintaining concentration gradients of the enzymes and surfactant at different locations, demonstrating a new route for obtaining 'spatial' organizational adaptability in a self-organized system of interacting components for the incorporation of programmed functionality.
Collapse
Affiliation(s)
- Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Surinder Kaur Brar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| |
Collapse
|
47
|
Ura T, Tomita S, Shiraki K. Dynamic behavior of liquid droplets with enzyme compartmentalization triggered by sequential glycolytic enzyme reactions. Chem Commun (Camb) 2021; 57:12544-12547. [PMID: 34755724 DOI: 10.1039/d1cc04596b] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Dynamic droplet formation via liquid-liquid phase separation (LLPS) is believed to be involved in the regulation of various biological processes. Here, a model LLPS system coupled with a sequential glycolytic enzymatic reaction was developed to reproduce the dynamic control of liquid droplets; (i) the droplets, which consist of poly-L-lysine and nucleotides, compartmentalize two different enzymes (hexokinase and glucose-6-phosphate dehydrogenase) individually, accelerating the overall reaction, and (ii) each enzymatic reaction triggers the formation, dissolution and long-term retention of the droplets by converting the scaffold nucleotides. This model system will offer a new aspect of enzymes associated with LLPS in living cells.
Collapse
Affiliation(s)
- Tomoto Ura
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan. .,Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
| |
Collapse
|
48
|
Scott WA, Gharakhanian EG, Bell AG, Evans D, Barun E, Houk KN, Deming TJ. Active Controlled and Tunable Coacervation Using Side-Chain Functional α-Helical Homopolypeptides. J Am Chem Soc 2021; 143:18196-18203. [PMID: 34669392 DOI: 10.1021/jacs.1c07925] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the development of new side-chain amino acid-functionalized α-helical homopolypeptides that reversibly form coacervate phases in aqueous media. The designed multifunctional nature of the side-chains was found to provide a means to actively control coacervation via mild, biomimetic redox chemistry as well as allow response to physiologically relevant environmental changes in pH, temperature, and counterions. These homopolypeptides were found to possess properties that mimic many of those observed in natural coacervate forming intrinsically disordered proteins. Despite ordered α-helical conformations that are thought to disfavor coacervation, molecular dynamics simulations of a polypeptide model revealed a high degree of side-chain conformational disorder and hydration around the ordered backbone, which may explain the ability of these polypeptides to form coacervates. Overall, the modular design, uniform nature, and ordered chain conformations of these polypeptides were found to provide a well-defined platform for deconvolution of molecular elements that influence biopolymer coacervation and tuning of coacervate properties for downstream applications.
Collapse
Affiliation(s)
- Wendell A Scott
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Eric G Gharakhanian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Alexandra G Bell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ehab Barun
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Timothy J Deming
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
49
|
Maity I, Sharma C, Lossada F, Walther A. Feedback and Communication in Active Hydrogel Spheres with pH Fronts: Facile Approaches to Grow Soft Hydrogel Structures. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Indrajit Maity
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
- Freiburg Institute for Advanced Studies University of Freiburg Freiburg Germany
| | - Charu Sharma
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Francisco Lossada
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Andreas Walther
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| |
Collapse
|
50
|
Maity I, Sharma C, Lossada F, Walther A. Feedback and Communication in Active Hydrogel Spheres with pH Fronts: Facile Approaches to Grow Soft Hydrogel Structures. Angew Chem Int Ed Engl 2021; 60:22537-22546. [PMID: 34347941 PMCID: PMC8518392 DOI: 10.1002/anie.202109735] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 12/12/2022]
Abstract
Compartmentalized reaction networks regulating signal processing, communication and pattern formation are central to living systems. Towards achieving life-like materials, we compartmentalized urea-urease and more complex urea-urease/ester-esterase pH-feedback reaction networks into hydrogel spheres and investigate how fuel-driven pH fronts can be sent out from these spheres and regulated by internal reaction networks. Membrane characteristics are installed by covering urease spheres with responsive hydrogel shells. We then encapsulate the two networks (urea-urease and ester-esterase) separately into different hydrogel spheres to devise communication, pattern formation and attraction. Moreover, these pH fronts and patterns can be used for self-growing hydrogels, and for developing complex geometries from non-injectable hydrogels without 3D printing tools. This study opens possibilities for compartmentalized feedback reactions and their use in next generation materials fabrication.
Collapse
Affiliation(s)
- Indrajit Maity
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
- Freiburg Institute for Advanced StudiesUniversity of FreiburgFreiburgGermany
| | - Charu Sharma
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Francisco Lossada
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Andreas Walther
- A3BMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| |
Collapse
|