1
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Singh A, Parvin P, Saha B, Das D. Non-equilibrium self-assembly for living matter-like properties. Nat Rev Chem 2024:10.1038/s41570-024-00640-z. [PMID: 39179623 DOI: 10.1038/s41570-024-00640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
The soft and wet machines of life emerged as the spatially enclosed ensemble of biomolecules with replicating capabilities integrated with metabolic reaction cycles that operate at far-from-equilibrium. A thorough step-by-step synthetic integration of these elements, namely metabolic and replicative properties all confined and operating far-from-equilibrium, can set the stage from which we can ask questions related to the construction of chemical-based evolving systems with living matter-like properties - a monumental endeavour of systems chemistry. The overarching concept of this Review maps the discoveries on this possible integration of reaction networks, self-reproduction and compartmentalization under non-equilibrium conditions. We deconvolute the events of reaction networks and transient compartmentalization and extend the discussion towards self-reproducing systems that can be sustained under non-equilibrium conditions. Although enormous challenges lie ahead in terms of molecular diversity, information transfer, adaptation and selection that are required for open-ended evolution, emerging strategies to generate minimal metabolic cycles can extend our growing understanding of the chemical emergence of the biosphere of Earth.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Payel Parvin
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Bapan Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
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2
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Bassan R, Mondal B, Varshney M, Roy S. 1-Naphthylacetic acid appended amino acids-based hydrogels: probing of the supramolecular catalysis of ester hydrolysis reaction. NANOSCALE ADVANCES 2024; 6:3399-3409. [PMID: 38933855 PMCID: PMC11197428 DOI: 10.1039/d4na00268g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/07/2024] [Indexed: 06/28/2024]
Abstract
A 1-naphthaleneacetic acid-appended phenylalanine-derivative (Nap-F) forms a stable hydrogel with a minimum gelation concentration (MGC) of 0.7% w/v (21 mM) in phosphate buffer of pH 7.4. Interestingly, Nap-F produces two-component [Nap-F + H = Nap-FH, Nap-F + K = Nap-FK and Nap-F + R = Nap-FR], three-component [Nap-F + H + K = Nap-FH-K, Nap-F + H + R = Nap-FH-R and Nap-F + K + R = Nap-FK-R] and four-component [Nap-F + H + K + R = Nap-FH-K-R] hydrogels in water with all three natural basic amino acids (H = histidine, K = lysine and R = arginine) at various combinations below its MGC. Nap-F-hydrogel forms a nice entangled nanofibrillar network structure as evidenced by field emission scanning electron microscopy (FE-SEM). Interestingly, lysine-based co-assembled two- (Nap-FK), three- (Nap-FH-K and Nap-FK-R) and four-component (Nap-FH-K-R) xerogels exhibit helical nanofibrillar morphology, which was confirmed by circular dichroism spectroscopy, FE-SEM and TEM imaging. However, histidine and arginine-based two-component (Nap-FH and Nap-FR) and three-component (Nap-FH-R) co-assembled xerogels exhibiting straight nanofibrillar morphology. In their co-assembled states, these two-, three- and four-component supramolecular hydrogels show promising esterase-like activity below their MGCs. The enhanced catalytic activity of helical fibers compared to obtained straight fibers (other than lysine-based assembled systems) suggests that the helical fibrillar nanostructure is involved in ordering the esterase-like although all supramolecular assemblies are chemically different from one another.
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Affiliation(s)
- Ruchika Bassan
- Department of Chemistry, Birla Institute of Technology and Science-Pilani K K Birla Goa Campus, NH 17B, Zuarinagar Sancoale Goa 403726 India
| | - Biplab Mondal
- School of Biological Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata-700034 West Bengal India
| | - Mayank Varshney
- Senior Application Scientist, Characterization Division, Anton Paar India Pvt. Ltd. 582, Phase V, Udyog Vihar Industrial Area Gurgaon 122016 Haryana India
| | - Subhasish Roy
- Department of Chemistry, Birla Institute of Technology and Science-Pilani K K Birla Goa Campus, NH 17B, Zuarinagar Sancoale Goa 403726 India
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3
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Arad E, Jelinek R. Catalytic physiological amyloids. Methods Enzymol 2024; 697:77-112. [PMID: 38816136 DOI: 10.1016/bs.mie.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Amyloid fibrils have been identified in many protein systems, mostly linked to progression and cytotoxicity in neurodegenerative diseases and other pathologies, but have also been observed in normal physiological systems. A growing body of work has shown that amyloid fibrils can catalyze chemical reactions. Most studies have focused on catalysis by de-novo synthetic amyloid-like peptides; however, recent studies reveal that physiological, native amyloids are catalytic as well. Here, we discuss methodologies and major experimental aspects pertaining to physiological catalytic amyloids. We highlight analyzes of kinetic parameters related to the catalytic activities of amyloid fibrils, structure-function considerations, characterization of the catalytic active sites, and deciphering of catalytic mechanisms.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel; Department of Chemical Engineering, Columbia University in the City of New York, New York, NY, United States.
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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4
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Vela-Gallego S, Lewandowski B, Möhler J, Puente A, Gil-Cantero D, Wennemers H, de la Escosura A. Modifying the Catalytic Activity of Lipopeptide Assemblies with Nucleobases. Chemistry 2024; 30:e202303395. [PMID: 37877614 DOI: 10.1002/chem.202303395] [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: 10/16/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 10/26/2023]
Abstract
Biohybrid catalysts that operate in aqueous media are intriguing for systems chemistry. In this paper, we investigate whether control over the self-assembly of biohybrid catalysts can tune their properties. As a model, we use the catalytic activity of functional hybrid molecules consisting of a catalytic H-dPro-Pro-Glu tripeptide, derivatized with fatty acid and nucleobase moieties. This combination of simple biological components merged the catalytic properties of the peptide with the self-assembly of the lipid, and the structural ordering of the nucleobases. The biomolecule hybrids self-assemble in aqueous media into fibrillar assemblies and catalyze the reaction between butanal and nitrostyrene. The interactions between the nucleobases enhanced the order of the supramolecular structures and affected their catalytic activity and stereoselectivity. The results point to the significant control and ordering that nucleobases can provide in the self-assembly of biologically inspired supramolecular catalysts.
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Affiliation(s)
- Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
| | - Bartosz Lewandowski
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Jasper Möhler
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Alonso Puente
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
| | - David Gil-Cantero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología / CSIC, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Helma Wennemers
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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5
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Dai K, Pol MD, Saile L, Sharma A, Liu B, Thomann R, Trefs JL, Qiu D, Moser S, Wiesler S, Balzer BN, Hugel T, Jessen HJ, Pappas CG. Spontaneous and Selective Peptide Elongation in Water Driven by Aminoacyl Phosphate Esters and Phase Changes. J Am Chem Soc 2023; 145:26086-26094. [PMID: 37992133 DOI: 10.1021/jacs.3c07918] [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: 11/24/2023]
Abstract
Nature chose phosphates to activate amino acids, where reactive intermediates and complex machinery drive the construction of polyamides. Outside of biology, the pathways and mechanisms that allow spontaneous and selective peptide elongation in aqueous abiotic systems remain unclear. Herein we work to uncover those pathways by following the systems chemistry of aminoacyl phosphate esters, synthetic counterparts of aminoacyl adenylates. The phosphate esters act as solubility tags, making hydrophobic amino acids and their oligomers soluble in water and enabling selective elongation and different pathways to emerge. Thus, oligomers up to dodecamers were synthesized in one flask and on the minute time scale, where consecutive additions activated autonomous phase changes. Depending on the pathway, the resulting phases initially carry nonpolar peptides and amphiphilic oligomers containing phosphate esters. During elongation and phosphate release, shorter oligomers dominate in solution, while the aggregated phase favors the presence of longer oligomers due to their self-assembly propensity. Furthermore we demonstrated that the solution phases can be isolated and act as a new environment for continuous elongation, by adding various phosphate esters. These findings suggest that the systems chemistry of aminoacyl phosphate esters can activate a selection mechanism for peptide bond formation by merging aqueous synthesis and self-assembly.
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Affiliation(s)
- Kun Dai
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Mahesh D Pol
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Lenard Saile
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Arti Sharma
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bin Liu
- College of Materials and Chemical Engineering, China Three Gorges University, Yichang, Hubei 443002, China
| | - Ralf Thomann
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
| | - Johanna L Trefs
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Sandra Moser
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Stefan Wiesler
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Bizan N Balzer
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Thorsten Hugel
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Henning J Jessen
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Charalampos G Pappas
- DFG Cluster of Excellence livMatS @FIT─Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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6
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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7
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Sadihov-Hanoch H, Bandela AK, Chotera-Ouda A, Ben David O, Cohen-Luria R, Lynn DG, Ashkenasy G. Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras. SOFT MATTER 2023; 19:3940-3945. [PMID: 37211859 DOI: 10.1039/d2sm01528e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.
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Affiliation(s)
- Hava Sadihov-Hanoch
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Anil Kumar Bandela
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Agata Chotera-Ouda
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Oshrat Ben David
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, USA
| | - Gonen Ashkenasy
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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8
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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.
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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
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9
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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10
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Arad E, Jelinek R. Catalytic amyloids. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Zhang J, Liu J, Li H, Li X, Zhao Y, Zhao P, Cui J, Yang B, Song Y, Zheng Y. Programming Hydrogels with Complex Transient Behaviors via Autocatalytic Cascade Reactions. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20073-20082. [PMID: 35439417 DOI: 10.1021/acsami.2c03177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
It is challenging to design complex synthetic life-like systems that can show both autoevolution and fuel-driven transient behaviors. Here, we report a new class of chemical reaction networks (CRNs) to construct life-like polymer hydrogels. The CRNs are constituted of autocatalytic cascade reactions and fuel-driven reaction networks. The reactions start with only two compounds, that is, thiol of 4-arm-PEG-SH and thiuram disulfides, and undergo thiol oxidation (k1), disulfide metathesis (k2), and thionate hydrolysis-coupling reactions (k3) subsequently, leading to a four-state autonomous transition of sol(I) → soft gel → sol(II) → stiff gel. Moreover, thiuram disulfides can be applied as a fuel to drive the repeated occurrence of metathesis and hydrolysis-coupling reactions, generating dissipative stiff gel → sol(II) → stiff gel cycles. Systematic kinetics studies reveal that the event and lifetime of every transient state could be delicately tailored-up by varying the thiuram disulfide concentration, pH of the system, and thiuram structures. Since the consecutive transient behaviors are precisely predictable, we envision the strategy's potential in guiding the molecular designs of autonomous and adaptive materials for many fields.
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Affiliation(s)
- Jingyi Zhang
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, P. R. China
| | - Jian Liu
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, P. R. China
| | - Huizeng Li
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049 Beijing, P. R. China
| | - Xiaohe Li
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, P. R. China
| | - Yuanfeng Zhao
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, P. R. China
| | - Peng Zhao
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, P. R. China
| | - Jiaxi Cui
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Bo Yang
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, P. R. China
| | - Yanlin Song
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049 Beijing, P. R. China
| | - Yijun Zheng
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, P. R. China
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12
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Xu J, Gao T, Sheng L, Wang Y, Lou C, Wang H, Liu Y, Cao A. Conformationally engineering flexible peptides on silver nanoparticles. iScience 2022; 25:104324. [PMID: 35601913 PMCID: PMC9117549 DOI: 10.1016/j.isci.2022.104324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022] Open
Abstract
Molecular conformational engineering is to engineer flexible non-functional molecules into unique conformations to create novel functions just like natural proteins fold. Obviously, it is a grand challenge with tremendous opportunities. Based on the facts that natural proteins are only marginally stable with a net stabilizing energy roughly equivalent to the energy of two hydrogen bonds, and the energy barriers for the adatom diffusion of some metals are within a similar range, we propose that metal nanoparticles can serve as a general replacement of protein scaffolds to conformationally engineer protein fragments on the surface of nanoparticles. To prove this hypothesis, herein, we successfully restore the antigen-recognizing function of the flexible peptide fragment of a natural anti-lysozyme antibody on the surface of silver nanoparticles, creating a silver nanoparticle-base artificial antibody (Silverbody). A plausible mechanism is proposed, and some general principles for conformational engineering are summarized to guide future studies in this area. A silver NP-based artificial antibody is created by conformational engineering Function emerges on NPs from non-functional peptide by mimicking the protein folding A general mechanism is proposed for the conformational engineering on metal NPs
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Affiliation(s)
- Jia Xu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Tiange Gao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Lingjie Sheng
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Yan Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Chenxi Lou
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Corresponding author
| | - Yuanfang Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Corresponding author
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13
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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.
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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.
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14
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Afrose SP, Mahato C, Sharma P, Roy L, Das D. Nonequilibrium Catalytic Supramolecular Assemblies of Melamine- and Imidazole-Based Dynamic Building Blocks. J Am Chem Soc 2022; 144:673-678. [PMID: 34990140 DOI: 10.1021/jacs.1c11457] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The development of synthetic nonequilibrium systems has gathered increasing attention due to their potential to illustrate the dynamic, complex, and emergent traits of biological systems. Simple building blocks capable of interacting via dynamic covalent chemistry and physical assembly in a reaction network under nonequilibrium conditions can contribute to our understanding of complex systems of life and its origin. Herein, we have demonstrated the nonequilibrium generation of catalytic supramolecular assemblies from simple heterocycle melamine driven by a thermodynamically activated ester. Utilizing a reversible covalent linkage, an imidazole moiety was recruited by the assemblies to access a catalytic transient state that dissipated energy via accelerated hydrolysis of the activated ester. The nonequilibrium assemblies were further capable of temporally binding to a hydrophobic guest to modulate its photophysical properties. Notably, the presence of an exogenous aromatic base augmented the lifetime of the catalytic microphases, reflecting their higher kinetic stability.
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Affiliation(s)
- Syed Pavel Afrose
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Chiranjit Mahato
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Pooja Sharma
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Lisa Roy
- Institute of Chemical Technology Mumbai-IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension Centre, Bhubaneswar 751013, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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15
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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.
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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
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16
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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
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17
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Pina AS, Morgado L, Duncan KL, Carvalho S, Carvalho HF, Barbosa AJM, de P. Mariz B, Moreira IP, Kalafatovic D, Morais Faustino BM, Narang V, Wang T, Pappas CG, Ferreira I, Roque ACA, Ulijn RV. Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity. Chem Sci 2022; 13:210-217. [PMID: 35059169 PMCID: PMC8694286 DOI: 10.1039/d1sc04420f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/05/2021] [Indexed: 12/16/2022] Open
Abstract
Phage-display screening on self-assembled tyrosine-phosphate ligands enables the identification of oligopeptides selective to dynamic supramolecular targets, with the lead peptide showing a preferred hairpin-like conformation and catalytic activity.
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Affiliation(s)
- Ana S. Pina
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Krystyna L. Duncan
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Sara Carvalho
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Henrique F. Carvalho
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Arménio J. M. Barbosa
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Beatriz de P. Mariz
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Inês P. Moreira
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Daniela Kalafatovic
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
| | - Bruno M. Morais Faustino
- CENIMAT/I3N, Department of Materials Science, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Vishal Narang
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
| | - Tong Wang
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Imaging Facility of CUNY ASRC, 85 St Nicholas Terrace, New York 10031, USA
| | - Charalampos G. Pappas
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Isabel Ferreira
- CENIMAT/I3N, Department of Materials Science, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - A. Cecília A. Roque
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Rein V. Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Hunter College of CUNY, Department of Chemistry and Biochemistry, 695 Park Avenue, New York 10065, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center of CUNY, New York 10016, USA
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18
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Kahana A, Maslov S, Lancet D. Dynamic lipid aptamers: non-polymeric chemical path to early life. Chem Soc Rev 2021; 50:11741-11746. [PMID: 34541591 DOI: 10.1039/d1cs00633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A widespread dogma asserts that life could not have emerged without biopolymers - RNA and proteins. However, the widely acknowledged implausibility of a spontaneous appearance and proliferation of these complex molecules in primordial messy chemistry casts doubt on this scenario. A proposed alternative is "Lipid-First", based on the evidence that lipid assemblies may spontaneously emerge in heterogeneous environments, and are shown to undergo growth and fission, and to portray autocatalytic self-copying. What seems undecided is whether lipid assemblies have protein-like capacities for stereospecific interactions, a sine qua non of life processes. This Viewpoint aims to alleviate such doubts, pointing to growing experimental evidence that lipid aggregates possess dynamic surface configurations capable of stereospecific molecular recognition. Such findings help support a possible key role of lipids in seeding life's origin.
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Affiliation(s)
- Amit Kahana
- Dept. of Molecular Genetics, the Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Svetlana Maslov
- Dept. of Molecular Genetics, the Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Doron Lancet
- Dept. of Molecular Genetics, the Weizmann Institute of Science, Rehovot 7610001, Israel.
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19
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Glionna C, Kumar V, Le Saux G, Pramanik B, Wagner N, Cohen-Luria R, Ashkenasy G, Ashkenasy N. Dynamic Surface Layer Coiled Coil Proteins Processing Analog-to-Digital Information. J Am Chem Soc 2021; 143:17441-17451. [PMID: 34652148 DOI: 10.1021/jacs.1c06356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Surface layer proteins perform multiple functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. However, mimicking the complex and dynamic behavior of such two-dimensional biochemical systems is challenging, and hence research has so far focused mainly on the design and manipulation of the structure and functionality of protein assemblies in solution. Motivated by the new opportunities that dynamic surface layer proteins may offer for modern technology, we herein demonstrate that immobilization of coiled coil proteins onto an inorganic surface facilitates complex behavior, manifested by reversible chemical reactions that can be rapidly monitored as digital surface readouts. Using multiple chemical triggers as inputs and several surface characteristics as outputs, we can realize reversible switching and logic gate operations that are read in parallel. Moreover, using the same coiled coil protein monolayers for derivatization of nanopores drilled into silicon nitride membranes facilitates control over ion and mass transport through the pores, thereby expanding the applicability of the dynamic coiled coil system for contemporary stochastic biosensing applications.
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Affiliation(s)
- Chiara Glionna
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Vinod Kumar
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Guillaume Le Saux
- Department of Materials Engineering, 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
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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20
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Sheehan F, Sementa D, Jain A, Kumar M, Tayarani-Najjaran M, Kroiss D, Ulijn RV. Peptide-Based Supramolecular Systems Chemistry. Chem Rev 2021; 121:13869-13914. [PMID: 34519481 DOI: 10.1021/acs.chemrev.1c00089] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.
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Affiliation(s)
- Fahmeed Sheehan
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Deborah Sementa
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Ankit Jain
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Mohit Kumar
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, Barcelona 08028, Spain
| | - Mona Tayarani-Najjaran
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Daniela Kroiss
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
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21
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Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks. Proc Natl Acad Sci U S A 2021; 118:2015285118. [PMID: 33622789 DOI: 10.1073/pnas.2015285118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.
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22
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Integration of photocatalytic and dark-operating catalytic biomimetic transformations through DNA-based constitutional dynamic networks. Nat Commun 2021; 12:4224. [PMID: 34244502 PMCID: PMC8270929 DOI: 10.1038/s41467-021-24512-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023] Open
Abstract
Nucleic acid-based constitutional dynamic networks (CDNs) have recently emerged as versatile tools to control a variety of catalytic processes. A key challenge in the application of these systems is achieving intercommunication between different CDNs to mimic the complex interlinked networks found in cellular biology. In particular, the possibility to interface photochemical ‘energy-harvesting’ processes with dark-operating ‘metabolic’ processes, in a similar way to plants, represents an up to now unexplored yet enticing research direction. The present study introduces two CDNs that allow the intercommunication of photocatalytic and dark-operating catalytic functions mediated by environmental components that facilitate the dynamic coupling of the networks. The dynamic feedback-driven intercommunication of the networks is accomplished via information transfer between the two CDNs effected by hairpin fuel strands in the environment of the system, leading to the coupling of the photochemical and dark-operating modules. Nucleic acid-based constitutional dynamic networks (CDNs) enable control of various catalytic processes, but it is challenging to achieve intercommunication between different CDNs and by that mimic complex cell biology networks. Here, the authors report two CDNs that control the integration of photochemical and dark-operating processes, and show their intercommunication afforded by environmental components.
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23
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Baruch-Leshem A, Chevallard C, Gobeaux F, Guenoun P, Daillant J, Fontaine P, Goldmann M, Kushmaro A, Rapaport H. Catalytically active peptides affected by self-assembly and residues order. Colloids Surf B Biointerfaces 2021; 203:111751. [DOI: 10.1016/j.colsurfb.2021.111751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 03/31/2021] [Accepted: 04/04/2021] [Indexed: 12/20/2022]
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24
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Indrajit Maity
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for Macromolecular Chemistry Freiburg Institute for Advanced Studies Albert Ludwigs University of Freiburg 79104 Freiburg Germany
| | - Dharm Dev
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Kingshuk Basu
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Nathaniel Wagner
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Gonen Ashkenasy
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
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25
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021; 60:4512-4517. [PMID: 33006406 PMCID: PMC7984337 DOI: 10.1002/anie.202012837] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 12/23/2022]
Abstract
Living cells exploit bistable and oscillatory behaviors as memory mechanisms, facilitating the integration of transient stimuli into sustained molecular responses that control downstream functions. Synthetic bistable networks have also been studied as memory entities, but have rarely been utilized to control orthogonal functions in coupled dynamic systems. We herein present a new cascade pathway, for which we have exploited a well-characterized switchable peptide-based replicating network, operating far from equilibrium, that yields two alternative steady-state outputs, which in turn serve as the input signals for consecutive processes that regulate various features of Au nanoparticle shape and assembly. This study further sheds light on how bridging together the fields of systems chemistry and nanotechnology may open up new opportunities for the dynamically controlled design of functional materials.
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Affiliation(s)
- Indrajit Maity
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
- Institute for Macromolecular ChemistryFreiburg Institute for Advanced StudiesAlbert Ludwigs University of Freiburg79104FreiburgGermany
| | - Dharm Dev
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Kingshuk Basu
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Nathaniel Wagner
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Gonen Ashkenasy
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
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26
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Chen Y, Tao K, Ji W, Makam P, Rencus-Lazar S, Gazit E. Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials. Protein Pept Lett 2021; 27:688-697. [PMID: 32048950 DOI: 10.2174/0929866527666200212123542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/29/2019] [Accepted: 12/09/2019] [Indexed: 11/22/2022]
Abstract
Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.
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Affiliation(s)
- Yu Chen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Wei Ji
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sigal Rencus-Lazar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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27
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Tan J, Zhang L, Hsieh MC, Goodwin JT, Grover MA, Lynn DG. Chemical control of peptide material phase transitions. Chem Sci 2021; 12:3025-3031. [PMID: 34164071 PMCID: PMC8179288 DOI: 10.1039/d0sc03666h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network. Substrate initiated assembly of a dynamic chemical network.![]()
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Affiliation(s)
- Junjun Tan
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Li Zhang
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Ming-Chien Hsieh
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA .,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - Jay T Goodwin
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - David G Lynn
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
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28
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Yue L, Wang S, Zhou Z, Willner I. Nucleic Acid Based Constitutional Dynamic Networks: From Basic Principles to Applications. J Am Chem Soc 2020; 142:21577-21594. [DOI: 10.1021/jacs.0c09891] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhixin Zhou
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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29
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Schaufelberger F, Seigel K, Ramström O. Hydrogen-Bond Catalysis of Imine Exchange in Dynamic Covalent Systems. Chemistry 2020; 26:15581-15588. [PMID: 32427370 DOI: 10.1002/chem.202001666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 12/28/2022]
Abstract
The reversibility of imine bonds has been exploited to great effect in the field of dynamic covalent chemistry, with applications such as preparation of functional systems, dynamic materials, molecular machines, and covalent organic frameworks. However, acid catalysis is commonly needed for efficient equilibration of imine mixtures. Herein, it is demonstrated that hydrogen bond donors such as thioureas and squaramides can catalyze the equilibration of dynamic imine systems under unprecedentedly mild conditions. Catalysis occurs in a range of solvents and in the presence of many sensitive additives, showing moderate to good rate accelerations for both imine metathesis and transimination with amines, hydrazines, and hydroxylamines. Furthermore, the catalyst proved simple to immobilize, introducing both reusability and extended control of the equilibration process.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden
| | - Karolina Seigel
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden
| | - Olof Ramström
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden.,Department of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA, 01854, USA.,Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182, Kalmar, Sweden
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30
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Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
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31
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32
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33
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34
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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35
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Datta LP, Manchineella S, Govindaraju T. Biomolecules-derived biomaterials. Biomaterials 2020; 230:119633. [DOI: 10.1016/j.biomaterials.2019.119633] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022]
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36
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Morales-Reina S, Giri C, Leclercq M, Vela-Gallego S, de la Torre I, Castón JR, Surin M, de la Escosura A. Programmed Recognition between Complementary Dinucleolipids To Control the Self-Assembly of Lipidic Amphiphiles. Chemistry 2020; 26:1082-1090. [PMID: 31729787 DOI: 10.1002/chem.201904217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/25/2019] [Indexed: 01/01/2023]
Abstract
One of the major goals in systems chemistry is to create molecular assemblies with emergent properties that are characteristic of life. An interesting approach toward this goal is based on merging different biological building blocks into synthetic systems with properties arising from the combination of their molecular components. The covalent linkage of nucleic acids (or their constituents: nucleotides, nucleosides and nucleobases) with lipids in the same hybrid molecule leads, for example, to the so-called nucleolipids. Herein, we describe nucleolipids with a very short sequence of two nucleobases per lipid, which, in combination with hydrophobic effects promoted by the lipophilic chain, allow control of the self-assembly of lipidic amphiphiles to be achieved. The present work describes a spectroscopic and microscopy study of the structural features and dynamic self-assembly of dinucleolipids that contain adenine or thymine moieties, either pure or in mixtures. This approach leads to different self-assembled nanostructures, which include spherical, rectangular and fibrillar assemblies, as a function of the sequence of nucleobases and chiral effects of the nucleolipids involved. We also show evidence that the resulting architectures can encapsulate hydrophobic molecules, revealing their potential as drug delivery vehicles or as compartments to host interesting chemistries in their interior.
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Affiliation(s)
- Sara Morales-Reina
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Chandan Giri
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel Materials, Center for Innovation in Materials and Polymers, University of Mons-UMONS, 20 Place du Parc, 7000, Mons, Belgium
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Isabel de la Torre
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Center for Innovation in Materials and Polymers, University of Mons-UMONS, 20 Place du Parc, 7000, Mons, Belgium
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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37
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Li Y, Chen H, Qu L, Bai R, Lan Y. Geometry, stability and aromaticity of β-diketiminate-coordinated alkaline-earth compounds. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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de la Escosura A. The Informational Substrate of Chemical Evolution: Implications for Abiogenesis. Life (Basel) 2019; 9:E66. [PMID: 31398942 PMCID: PMC6789672 DOI: 10.3390/life9030066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks.
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Affiliation(s)
- Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma of Madrid, Cantoblanco Campus, 28049 Madrid, Spain.
- Department of Organic Chemistry, Institute for Advanced Research in Chemistry (IAdChem), Cantoblanco Campus, 28049 Madrid, Spain.
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39
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Strazewski P. The Essence of Systems Chemistry. Life (Basel) 2019; 9:life9030060. [PMID: 31373279 PMCID: PMC6789438 DOI: 10.3390/life9030060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/06/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023] Open
Abstract
Systems Chemistry investigates the upkeep of specific interactions of an exceptionally broad choice of objects over longer periods of time than the average time of existence of the objects themselves. This maintenance of a dynamic state focuses on conditions where the objects are thermodynamically not very stable and should be rare or virtually inexistent. It does not matter whether they are homochirally enriched populations of chiral molecules, a specific composition of some sort of aggregate, supramolecules, or even a set of chemically relatively unstable molecules that constantly transform one into another. What does matter is that these specific interactions prevail in complex mixtures and eventually grow in numbers and frequency through the enhancing action of autocatalysis, which makes such systems ultimately resemble living cells and interacting living populations. Such chemical systems need to be correctly understood, but also intuitively described. They may be so complex that metaphors become practically more important, as a means of communication, than the precise and correct technical description of chemical models and complex molecular or supramolecular relations. This puts systems chemists on a tightrope walk of science communication, between the complex reality and an imaginative model world. This essay addresses, both, scientists who would like to read “A Brief History of Systems Chemistry”, that is, about its “essence”, and systems chemists who work with and communicate complex life-like chemical systems. I illustrate for the external reader a light mantra, that I call “to make more of it”, and I charily draw systems chemists to reflect upon the fact that chemists are not always good at drawing a clear line between a model and “the reality”: The real thing. We are in a constant danger of taking metaphors for real. Yet in real life, we do know very well that we cannot smoke with Magritte’s pipe, don’t we?
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Affiliation(s)
- Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France.
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40
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Yue L, Wang S, Willner I. Triggered reversible substitution of adaptive constitutional dynamic networks dictates programmed catalytic functions. SCIENCE ADVANCES 2019; 5:eaav5564. [PMID: 31093526 PMCID: PMC6510552 DOI: 10.1126/sciadv.aav5564] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/26/2019] [Indexed: 05/22/2023]
Abstract
The triggered substitution of networks and their resulting functions play an important mechanism in biological transformations, such as intracellular metabolic pathways and cell differentiation. We describe the triggered, cyclic, reversible intersubstitution of three nucleic acid-based constitutional dynamic networks (CDNs) and the programmed catalytic functions guided by the interconverting CDNs. The transitions between the CDNs are activated by nucleic acid strand displacement processes acting as triggers and counter triggers, leading to the adaptive substitution of the constituents and to emerging catalytic functions dictated by the compositions of the different networks. The quantitative evaluation of the compositions of the different CDNs is achieved by DNAzyme reporters and complementary electrophoresis experiments. By coupling a library of six hairpins to the interconverting CDNs, the CDN-guided, emerging, programmed activities of three different biocatalysts are demonstrated. The study has important future applications in the development of sensor systems, finite-state logic devices, and selective switchable catalytic assemblies.
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41
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Runnels CM, Lanier KA, Williams JK, Bowman JC, Petrov AS, Hud NV, Williams LD. Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers. J Mol Evol 2018; 86:598-610. [PMID: 30456440 PMCID: PMC6267704 DOI: 10.1007/s00239-018-9876-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/09/2018] [Indexed: 12/20/2022]
Abstract
Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We observe that all three biopolymer types are pre-organized, conditionally self-complementary, chemically unstable in aqueous media yet persistent because of kinetic trapping, with chiral monomers and directional chains. All three biopolymers are synthesized by dehydration reactions that are catalyzed by molecular motors driven by hydrolysis of phosphorylated nucleosides. All three biopolymers can access specific states that protect against hydrolysis. These protected states are folded, using self-complementary interactions among recurrent folding elements within a given biopolymer, or assembled, in associations between the same or different biopolymer types. Self-association in a hydrolytic environment achieves self-preservation. Heterogeneous association achieves partner-preservation. These universal properties support a model in which life's polymers emerged simultaneously and co-evolved in a common hydrolytic milieu where molecular persistence depended on folding and assembly. We believe that an understanding of the structure, function, and origins of any given type of biopolymer requires the context of other biopolymers.
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Affiliation(s)
- Calvin M Runnels
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kathryn A Lanier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Justin Krish Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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