1
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Brasnett C, Kiani A, Sami S, Otto S, Marrink SJ. Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations. Commun Chem 2024; 7:151. [PMID: 38961263 PMCID: PMC11222477 DOI: 10.1038/s42004-024-01234-y] [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: 11/21/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Biomolecular condensates are phase separated systems that play an important role in the spatio-temporal organisation of cells. Their distinct physico-chemical nature offers a unique environment for chemical reactions to occur. The compartmentalisation of chemical reactions is also believed to be central to the development of early life. To demonstrate how molecular dynamics may be used to capture chemical reactions in condensates, here we perform reactive molecular dynamics simulations using the coarse-grained Martini forcefield. We focus on the formation of rings of benzene-1,3-dithiol inside a synthetic peptide-based condensate, and find that the ring size distribution shifts to larger macrocycles compared to when the reaction takes place in an aqueous environment. Moreover, reaction rates are noticeably increased when the peptides simultaneously undergo phase separation, hinting that condensates may act as chaperones in recruiting molecules to reaction hubs.
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Affiliation(s)
- Christopher Brasnett
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Armin Kiani
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Selim Sami
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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2
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Komáromy D, Monzón DM, Marić I, Monreal Santiago G, Ottelé J, Altay M, Schaeffer G, Otto S. Generalist versus Specialist Self-Replicators. Chemistry 2024; 30:e202303837. [PMID: 38294075 DOI: 10.1002/chem.202303837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide-based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide-containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide-based replicator and hexameric ethyleneoxide-based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators.
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Affiliation(s)
- Dávid Komáromy
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Diego M Monzón
- Instituto de Bio-Orgánica "Antonio González" (IUBO-AG), Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, 38206, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Ivana Marić
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Guillermo Monreal Santiago
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jim Ottelé
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Meniz Altay
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gaël Schaeffer
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Sijbren Otto
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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3
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Sasselli IR, Coluzza I. Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly. J Chem Theory Comput 2024; 20:224-238. [PMID: 38113378 PMCID: PMC10782451 DOI: 10.1021/acs.jctc.3c01015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.
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Affiliation(s)
- Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research
and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Ivan Coluzza
- Ikerbasque,
Basque Foundation for Science, Plaza de Euskadi 5, 48009 Bilbao, Spain
- BCMaterials,
Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, 48940 Leioa, Spain
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4
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Sami S, Marrink SJ. Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. J Chem Theory Comput 2023. [PMID: 37327401 DOI: 10.1021/acs.jctc.2c01186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Chemical reactions are ubiquitous in both materials and the biophysical sciences. While coarse-grained (CG) molecular dynamics simulations are often needed to study the spatiotemporal scales present in these fields, chemical reactivity has not been explored thoroughly in CG models. In this work, a new approach to model chemical reactivity is presented for the widely used Martini CG Martini model. Employing tabulated potentials with a single extra particle for the angle dependence, the model provides a generic framework for capturing bonded topology changes using nonbonded interactions. As a first example application, the reactive model is used to study the macrocycle formation of benzene-1,3-dithiol molecules through the formation of disulfide bonds. We show that starting from monomers, macrocycles with sizes in agreement with experimental results are obtained using reactive Martini. Overall, our reactive Martini framework is general and can be easily extended to other systems. All of the required scripts and tutorials to explain its use are provided online.
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Affiliation(s)
- Selim Sami
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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5
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Du C, Li Z, Zhu X, Ouyang G, Liu M. Hierarchically self-assembled homochiral helical microtoroids. NATURE NANOTECHNOLOGY 2022; 17:1294-1302. [PMID: 36329269 PMCID: PMC9747612 DOI: 10.1038/s41565-022-01234-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 09/07/2022] [Indexed: 05/22/2023]
Abstract
Fabricating microscale helical structures from small molecules remains challenging due to the disfavoured torsion energy of twisted architectures and elusory chirality control at different hierarchical levels of assemblies. Here we report a combined solution-interface-directed assembly strategy for the formation of hierarchically self-assembled helical microtoroids with micrometre-scale lengths. A drop-evaporation assembly protocol on a solid substrate from pre-assembled intermediate colloids of enantiomeric binaphthalene bisurea compounds leads to microtoroids with preferred helicity, which depends on the molecular chirality of the starting enantiomers. Collective variable-temperature spectroscopic analyses, electron microscopy characterizations and theoretical simulations reveal a mechanism that simultaneously induces aggregation and cyclization to impart a favourable handedness to the final microtoroidal structures. We then use monodispersed luminescent helical toroids as chiral light-harvesting antenna and show excellent Förster resonance energy transfer ability to a co-hosted chiral acceptor dye, leading to unique circularly polarized luminescence. Our results shed light on the potential of the combined solution-interface-directed self-assembly approach in directing hierarchical chirality control and may advance the prospect of chiral superstructures at a higher length scale.
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Affiliation(s)
- Cong Du
- Beijing National Laboratory of Molecular Sciences and CAS Key Laboratory of Colloid, Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Zujian Li
- Beijing National Laboratory of Molecular Sciences and CAS Key Laboratory of Colloid, Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Xuefeng Zhu
- Beijing National Laboratory of Molecular Sciences and CAS Key Laboratory of Colloid, Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Guanghui Ouyang
- Beijing National Laboratory of Molecular Sciences and CAS Key Laboratory of Colloid, Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
| | - Minghua Liu
- Beijing National Laboratory of Molecular Sciences and CAS Key Laboratory of Colloid, Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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6
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Dhawan S, Singh H, Dutta S, Haridas V. Designer peptides as versatile building blocks for functional materials. Bioorg Med Chem Lett 2022; 68:128733. [PMID: 35421579 DOI: 10.1016/j.bmcl.2022.128733] [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: 02/11/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/02/2022]
Abstract
Peptides and pseudopeptides show distinct self-assembled nanostructures such as fibers, nanotubes, vesicles, micelles, toroids, helices and rods. The formation of such molecular communities through the collective behavior of molecules is not fully understood at a molecular level. All these self-assembled nanostructured materials have a wide range of applications such as drug delivery, gene delivery, biosensing, bioimaging, catalysis, tissue engineering, nano-electronics and sensing. Self-assembly is one of the most efficient and a simple strategy to generate complex functional materials. Owing to its significance, the last few decades witnessed a remarkable advancement in the field of self-assembling peptides with a plethora of new designer synthetic systems being discovered. These systems range from amphiphilic, cyclic, linear and polymeric peptides. This article presents only selected examples of such self-assembling peptides and pseudopeptides.
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Affiliation(s)
- Sameer Dhawan
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Souvik Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India.
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7
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Growing single crystals of two-dimensional covalent organic frameworks enabled by intermediate tracing study. Nat Commun 2022; 13:1370. [PMID: 35296677 PMCID: PMC8927472 DOI: 10.1038/s41467-022-29086-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/23/2022] [Indexed: 12/04/2022] Open
Abstract
Resolving single-crystal structures of two-dimensional covalent organic frameworks (2D COFs) is a great challenge, hindered in part by limited strategies for growing high-quality crystals. A better understanding of the growth mechanism facilitates development of methods to grow high-quality 2D COF single crystals. Here, we take a different perspective to explore the 2D COF growth process by tracing growth intermediates. We discover two different growth mechanisms, nucleation and self-healing, in which self-assembly and pre-arrangement of monomers and oligomers are important factors for obtaining highly crystalline 2D COFs. These findings enable us to grow micron-sized 2D single crystalline COF Py-1P. The crystal structure of Py-1P is successfully characterized by three-dimensional electron diffraction (3DED), which confirms that Py-1P does, in part, adopt the widely predicted AA stacking structure. In addition, we find the majority of Py-1P crystals (>90%) have a previously unknown structure, containing 6 stacking layers within one unit cell. Resolving single-crystal structures of two-dimensional covalent organic frameworks (2D COFs) is a great challenge. Here, the authors identify two different growth mechanisms of COFs, enabling the growth and structure determination of micron-sized 2D single-crystalline COFs.
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8
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Hendrikse SIS, Contreras-Montoya R, Ellis AV, Thordarson P, Steed JW. Biofunctionality with a twist: the importance of molecular organisation, handedness and configuration in synthetic biomaterial design. Chem Soc Rev 2021; 51:28-42. [PMID: 34846055 DOI: 10.1039/d1cs00896j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The building blocks of life - nucleotides, amino acids and saccharides - give rise to a large variety of components and make up the hierarchical structures found in Nature. Driven by chirality and non-covalent interactions, helical and highly organised structures are formed and the way in which they fold correlates with specific recognition and hence function. A great amount of effort is being put into mimicking these highly specialised biosystems as biomaterials for biomedical applications, ranging from drug discovery to regenerative medicine. However, as well as lacking the complexity found in Nature, their bio-activity is sometimes low and hierarchical ordering is missing or underdeveloped. Moreover, small differences in folding in natural biomolecules (e.g., caused by mutations) can have a catastrophic effect on the function they perform. In order to develop biomaterials that are more efficient in interacting with biomolecules, such as proteins, DNA and cells, we speculate that incorporating order and handedness into biomaterial design is necessary. In this review, we first focus on order and handedness found in Nature in peptides, nucleotides and saccharides, followed by selected examples of synthetic biomimetic systems based on these components that aim to capture some aspects of these ordered features. Computational simulations are very helpful in predicting atomic orientation and molecular organisation, and can provide invaluable information on how to further improve on biomaterial designs. In the last part of the review, a critical perspective is provided along with considerations that can be implemented in next-generation biomaterial designs.
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Affiliation(s)
- Simone I S Hendrikse
- Department of Chemical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia. .,School of Chemistry, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | | | - Amanda V Ellis
- Department of Chemical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Pall Thordarson
- School of Chemistry, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
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9
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Feng Y, Philp D. A Molecular Replication Process Drives Supramolecular Polymerization. J Am Chem Soc 2021; 143:17029-17039. [PMID: 34617739 DOI: 10.1021/jacs.1c06404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Supramolecular polymers are materials in which the connections between monomers in the polymer main chain are non-covalent bonds. This area has seen rapid expansion in the last two decades and has been exploited in several applications. However, suitable contiguous hydrogen-bond arrays can be difficult to synthesize, placing some limitations on the deployment of supramolecular polymers. We have designed a hydrogen-bonded polymer assembled from a bifunctional monomer composed of two replicating templates separated by a rigid spacer. This design allows the autocatalytic formation of the polymer main chain through the self-templating properties of the replicators and drives the synthesis of the bifunctional monomer from its constituent components in solution. The template-directed 1,3-dipolar cycloaddition reaction between nitrone and maleimide proceeds with high diastereoselectivity, affording the bifunctional monomer. The high binding affinity between the self-complementary replicating templates that allows the bifunctional monomer to polymerize in solution is derived from the positive cooperativity associated with this binding process. The assembly of the polymer in solution has been investigated by diffusion-ordered NMR spectroscopy. Both microcrystalline and thin films of the polymeric material can be prepared readily and have been characterized by powder X-ray diffraction and scanning electron microscopy. These results demonstrate that the approach described here is a valid one for the construction of supramolecular polymers and can be extended to systems where the rigid spacer between the replicating templates is replaced by one carrying additional function.
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Affiliation(s)
- Yuanning Feng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Douglas Philp
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
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10
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de Marco AL, Bochicchio D, Gardin A, Doni G, Pavan GM. Controlling Exchange Pathways in Dynamic Supramolecular Polymers by Controlling Defects. ACS NANO 2021; 15:14229-14241. [PMID: 34472834 PMCID: PMC8482751 DOI: 10.1021/acsnano.1c01398] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/26/2021] [Indexed: 05/23/2023]
Abstract
Supramolecular fibers composed of monomers that self-assemble directionally via noncovalent interactions are ubiquitous in nature, and of great interest in chemistry. In these structures, the constitutive monomers continuously exchange in-and-out the assembly according to a well-defined supramolecular equilibrium. However, unraveling the exchange pathways and their molecular determinants constitutes a nontrivial challenge. Here, we combine coarse-grained modeling, enhanced sampling, and machine learning to investigate the key factors controlling the monomer exchange pathways in synthetic supramolecular polymers having an intrinsic dynamic behavior. We demonstrate how the competition of directional vs. nondirectional interactions between the monomers controls the creation/annihilation of defects in the supramolecular polymers, from where monomers exchange proceeds. This competition determines the exchange pathway, dictating whether a fiber statistically swaps monomers from the tips or from all along its length. Finally, thanks to their generality, our models allow the investigation of molecular approaches to control the exchange pathways in these dynamic assemblies.
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Affiliation(s)
- Anna L. de Marco
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus
Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
- Department
of Physics, Universit degli studi di Genova, Via Dodecaneso 33, 16100 Genova, Italy
| | - Davide Bochicchio
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus
Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
- Department
of Physics, Universit degli studi di Genova, Via Dodecaneso 33, 16100 Genova, Italy
| | - Andrea Gardin
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Giovanni Doni
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus
Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Giovanni M. Pavan
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus
Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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11
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Teixeira R, Serra VV, Botequim D, Paulo PMR, Andrade SM, Costa SMB. Fluorescence Spectroscopy of Porphyrins and Phthalocyanines: Some Insights into Supramolecular Self-Assembly, Microencapsulation, and Imaging Microscopy. Molecules 2021; 26:4264. [PMID: 34299539 PMCID: PMC8306603 DOI: 10.3390/molecules26144264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/06/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022] Open
Abstract
The molecular interactions of anionic tetrasulfonate phenyl porphyrin (TPPS) with poly(amido amine) (PAMAM) dendrimers of generation 2.0 and 4.0 (G2 and G4, respectively) forming H- or J-aggregates, as well as with human and bovine serum albumin proteins (HSA and BSA), were reviewed in the context of self-assembly molecular complementarity. The spectroscopic studies were extended to the association of aluminum phthtalocyanine (AlPCS4) detected with a PAMAM G4 dendrimer with fluorescence studies in both steady state and dynamic state, as well as due to the fluorescence quenching associated to electron-transfer with a distribution of lifetimes. The functionalization of TPPS with peripheral substituents enables the assignment of spontaneous pH-induced aggregates with different and well-defined morphologies. Other work reported in the literature, in particular with soft self-assembly materials, fall in the same area with particular interest for the environment. The microencapsulation of TPPS studies into polyelectrolyte capsules was developed quite recently and aroused much interest, which is well supported and complemented by the extensive data reported on the Imaging Microscopy section of the Luminescence of Porphyrins and Phthalocyanines included in the present review.
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Affiliation(s)
- Raquel Teixeira
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Vanda Vaz Serra
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - David Botequim
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Pedro M R Paulo
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Suzana M Andrade
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Sílvia M B Costa
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
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12
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Komáromy D, Tiemersma-Wegman T, Kemmink J, Portale G, Adamski PR, Blokhuis A, Aalbers FS, Marić I, Santiago GM, Ottelé J, Sood A, Saggiomo V, Liu B, van der Meulen P, Otto S. Stoichiometry alone can steer supramolecular systems on complex free energy surfaces with high selectivity. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Liu B, Beatty MA, Pappas CG, Liu K, Ottelé J, Otto S. Self‐Sorting in Dynamic Combinatorial Libraries Leads to the Co‐Existence of Foldamers and Self‐Replicators. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Meagan A. Beatty
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Charalampos G. Pappas
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Kai Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
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14
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Liu B, Beatty MA, Pappas CG, Liu K, Ottelé J, Otto S. Self-Sorting in Dynamic Combinatorial Libraries Leads to the Co-Existence of Foldamers and Self-Replicators. Angew Chem Int Ed Engl 2021; 60:13569-13573. [PMID: 33949062 PMCID: PMC8252005 DOI: 10.1002/anie.202101052] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 12/27/2022]
Abstract
Nature segregates fundamental tasks such as information storage/transmission and catalysis between two different compound classes (e.g. polynucleotides for replication and folded polyamides for catalysis). This division of labor is likely a product of evolution, raising the question of how simpler systems in which replicators and folded macromolecules co-exist may emerge in the transition from chemistry to biology. In synthetic systems, achieving co-existence of replicators and foldamers in a single molecular network remains an unsolved problem. Previous work on dynamic molecular networks has given rise to either self-replicating fibers or well-defined foldamer structures (or completely un-sorted complex systems). We report a system in which two cross-reactive dithiol (nucleobase- and peptide-based) building blocks self-sort into a replicator fiber and foldamer that both emerge spontaneously and co-exist. The self-sorting behavior remains prevalent across different building block ratios as two phases of emergence occur: replicator growth followed by foldamer formation. This is attributed to the autocatalytic formation of the replicator fiber, followed by enrichment of the system in the remaining building block, which is subsequently incorporated into a foldamer.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Meagan A Beatty
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
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15
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Lau CYJ, Mastrobattista E. Programming supramolecular peptide materials by modulating the intermediate steps in the complex assembly pathway: Implications for biomedical applications. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2020.101396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Chan KH, Lim J, Jee JE, Aw JH, Lee SS. Peptide-Peptide Co-Assembly: A Design Strategy for Functional Detection of C-peptide, A Biomarker of Diabetic Neuropathy. Int J Mol Sci 2020; 21:ijms21249671. [PMID: 33352955 PMCID: PMC7766332 DOI: 10.3390/ijms21249671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/29/2022] Open
Abstract
Diabetes-related neuropathy is a debilitating condition that may be averted if it can be detected early. One possible way this can be achieved at low cost is to utilise peptides to detect C-peptide, a biomarker of diabetic neuropathy. This depends on peptide-peptide co-assembly, which is currently in a nascent stage of intense study. Instead, we propose a bead-based triple-overlay combinatorial strategy that can preserve inter-residue information during the screening process for a suitable complementary peptide to co-assemble with C-peptide. The screening process commenced with a pentapeptide general library, which revealed histidine to be an essential residue. Further screening with seven tetrapeptide focused libraries led to a table of self-consistent peptide sequences that included tryptophan and lysine at high frequencies. Three complementary nonapeptides (9mer com-peptides), wpkkhfwgq (Trp-D), kwkkhfwgq (Lys-D), and KWKKHFWGQ (Lys-L) (as a negative control) were picked from this table for co-assembly studies with C-peptide. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) and circular dichroism (CD) spectroscopies were utilized to study inter-peptide interactions and changes in secondary structures respectively. ATR-FTIR studies showed that there is indeed inter-peptide interaction between C-peptide and the tryptophan residues of the 9mer com-peptides. CD studies of unaggregated and colloidal C-peptide with the 9mer com-peptides suggest that the extent of co-assembly of C-peptide with Trp-D is greatest, followed by Lys-D and Lys-L. These results are promising and indicate that the presented strategy is viable for designing and evaluating longer complementary peptides, as well as complementary peptides for co-assembly with other polypeptides of interest and importance. We discuss the possibility of designing complementary peptides to inhibit toxic amyloidosis with this approach.
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Affiliation(s)
- Kiat Hwa Chan
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
- Correspondence: (K.H.C.); (S.S.L.)
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Joo Eun Jee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Jia Hui Aw
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
| | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
- Correspondence: (K.H.C.); (S.S.L.)
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17
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Wang L, Lv Y, Li C, Yang G, Fu B, Peng Q, Jian L, Hou D, Wang J, Zhao C, Yang P, Zhang K, Wang L, Wang Z, Wang H, Xu W. Transformable Dual-Inhibition System Effectively Suppresses Renal Cancer Metastasis through Blocking Endothelial Cells and Cancer Stem Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2004548. [PMID: 32881381 DOI: 10.1002/smll.202004548] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Tumor vasculature and cancer stem cells (CSCs) accelerate the development of metastatic renal cancer. Dual inhibition of vascular endothelium and CSCs is still a challenge due to their different pathological features. Herein, a transformable dual-inhibition system (TDS) based on a self-assembly peptide is proposed to construct nanofibrous barriers on the cell membrane in situ, which contributes to 1) reducing endothelial permeability and angiogenesis; and 2) inhibiting stemness and metastasis of CSCs in renal cancer. TDS specifically targets overexpressed receptor CD105 that provides the possibility to modulate both endothelial cells and CSCs for cancer therapy. Subsequently, owing to ligand-receptor interaction-induced transformation, the nanofibers form a barrier on the cell membrane. For vascular endothelium, TDS reduces the vascular permeability to 67.0% ± 4.7% and decreases angiogenesis to 62.0% ± 4.0%, thereby preventing the renal cancer metastasis. For human-derived CSCs, TDS inhibits stemness by reducing endogenic miR-19b and its transportation via CSCs-derived exosomes, which increases PTEN expression and consequently suppresses CSCs-mediated metastasis. In patient-derived xenograft mice, TDS significantly inhibits the tumorigenesis and angiogenesis. It also reduces the metastatic nodules in lung 5.0-fold compared with the control group. TDS opens up a promising avenue for suppressing the metastasis of cancer.
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Affiliation(s)
- Lu Wang
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
| | - Yulin Lv
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
| | - Cong Li
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
| | - Guang Yang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Bo Fu
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
| | - Qiang Peng
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
| | - Lingrui Jian
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
| | - Dayong Hou
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Jiaqi Wang
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Changhao Zhao
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Peipei Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Kuo Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Lei Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Ziqi Wang
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Hao Wang
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Wanhai Xu
- Department of Urology (Heilongjiang Key Laboratory of Scientific Research in Urology), The Fourth Hospital of Harbin Medical University, Harbin, 150001, China
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150001, China
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18
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Meneghin E, Biscaglia F, Volpato A, Bolzonello L, Pedron D, Frezza E, Ferrarini A, Gobbo M, Collini E. Biomimetic Nanoarchitectures for Light Harvesting: Self-Assembly of Pyropheophorbide-Peptide Conjugates. J Phys Chem Lett 2020; 11:7972-7980. [PMID: 32886518 PMCID: PMC8011917 DOI: 10.1021/acs.jpclett.0c02138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/04/2020] [Indexed: 05/27/2023]
Abstract
The biological light-harvesting process offers an unlimited source of inspiration. The high level of control, adaptation capability, and efficiency challenge humankind to create artificial biomimicking nanoarchitectures with the same performances to respond to our energy needs. Here, in the extensive search for design principles at the base of efficient artificial light harvesters, an approach based on self-assembly of pigment-peptide conjugates is proposed. The solvent-driven and controlled aggregation of the peptide moieties promotes the formation of a dense network of interacting pigments, giving rise to an excitonic network characterized by intense and spectrally wide absorption bands. The ultrafast dynamics of the nanosystems studied through two-dimensional electronic spectroscopy reveals that the excitation energy is funneled in an ultrafast time range (hundreds of femtoseconds) to a manifold of long-living dark states, thus suggesting the considerable potentiality of the systems as efficient harvesters.
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Affiliation(s)
- Elena Meneghin
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Francesca Biscaglia
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Andrea Volpato
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Luca Bolzonello
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Danilo Pedron
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Elisa Frezza
- Université
de Paris, CiTCoM, CNRS, F-75006 Paris, France
| | - Alberta Ferrarini
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Marina Gobbo
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Elisabetta Collini
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
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19
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Maity S, Ottelé J, Santiago GM, Frederix PWJM, Kroon P, Markovitch O, Stuart MCA, Marrink SJ, Otto S, Roos WH. Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization. J Am Chem Soc 2020; 142:13709-13717. [PMID: 32786814 PMCID: PMC7426903 DOI: 10.1021/jacs.0c02635] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Self-assembly features
prominently in fields ranging from materials
science to biophysical chemistry. Assembly pathways, often passing
through transient intermediates, can control the outcome of assembly
processes. Yet, the mechanisms of self-assembly remain largely obscure
due to a lack of experimental tools for probing these pathways at
the molecular level. Here, the self-assembly of self-replicators into
fibers is visualized in real-time by high-speed atomic force microscopy
(HS-AFM). Fiber growth requires the conversion of precursor molecules
into six-membered macrocycles, which constitute the fibers. HS-AFM
experiments, supported by molecular dynamics simulations, revealed
that aggregates of precursor molecules accumulate at the sides of
the fibers, which then diffuse to the fiber ends where growth takes
place. This mechanism of precursor reservoir formation, followed by
one-dimensional diffusion, which guides the precursor molecules to
the sites of growth, reduces the entropic penalty associated with
colocalizing precursors and growth sites and constitutes a new mechanism
for supramolecular polymerization.
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Affiliation(s)
- Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Guillermo Monreal Santiago
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Peter Kroon
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands.,Origins Center, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
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20
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Ottelé J, Hussain AS, Mayer C, Otto S. Chance emergence of catalytic activity and promiscuity in a self-replicator. Nat Catal 2020. [DOI: 10.1038/s41929-020-0463-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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21
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Emergence of light-driven protometabolism on recruitment of a photocatalytic cofactor by a self-replicator. Nat Chem 2020; 12:603-607. [PMID: 32591744 DOI: 10.1038/s41557-020-0494-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
Abstract
Establishing how life can emerge from inanimate matter is among the grand challenges of contemporary science. Chemical systems that capture life's essential characteristics-replication, metabolism and compartmentalization-offer a route to understanding this momentous process. The synthesis of life, whether based on canonical biomolecules or fully synthetic molecules, requires the functional integration of these three characteristics. Here we show how a system of fully synthetic self-replicating molecules, on recruiting a cofactor, acquires the ability to transform thiols in its environment into disulfide precursors from which the molecules can replicate. The binding of replicator and cofactor enhances the activity of the latter in oxidizing thiols into disulfides through photoredox catalysis and thereby accelerates replication by increasing the availability of the disulfide precursors. This positive feedback marks the emergence of light-driven protometabolism in a system that bears no resemblance to canonical biochemistry and constitutes a major step towards the highly challenging aim of creating a new and completely synthetic form of life.
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22
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Jain R, Roy S. Controlling Neuronal Cell Growth through Composite Laminin Supramolecular Hydrogels. ACS Biomater Sci Eng 2020; 6:2832-2846. [PMID: 33463249 DOI: 10.1021/acsbiomaterials.9b01998] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Designing an extracellular matrix mimic by biofunctionalization of polymeric scaffolds is a popular strategy and extremely crucial for facilitating the interactions between cells and the matrix. To this direction, supramolecular gels are gaining exponential attention over the last few years, owing to their potential biocompatibility and biodegradability. In spite of diverse biological roles of native laminin, the bioactivities of self-assembling laminin-derived short peptides were less explored. In this work, we have explored the minimalist design to develop hydrogel scaffolds based on IKVAV and YIGSR peptides individually and their composite matrix, which can provide structurally and functionally relevant materials for tissue engineering. Till date, composite supramolecular gels solely made up of self-assembling IKVAV and YIGSR peptides have never been reported. Such composite gels can be a closer mimic of natural laminin protein, which could mimic the essential functions of the short peptide fragments present on different chains of the extracellular matrix protein, laminin. Interestingly, we used a unique strategy of simple mixing of the two laminin mimetic peptides, which tend to induce coassembly with a self-sorted nanofibrous network with relatively enhanced mechanical strength. The physicochemical properties of the biofunctional hydrogels were studied using different microscopic, spectroscopic, and rheology techniques. To assess the bioactivity of laminin-derived scaffolds in controlling neuronal cell growth, its biocompatibility, cellular growth, and proliferation were quantified using C6 glial cells and SHSY5Y neuroblastoma cells. The live/dead staining further confirmed the adhesion and proliferation of the cells. A significant increase in neurite length provides clear evidence on mimicking the neurite extension function of native laminin protein by its short derivatives. Interestingly, similar β-III tubulin expression and cell cycle phases were observed, in comparison to control, which indicated normal cellular functioning of the cells cultured over short laminin hydrogel scaffolds. All bioassays suggested that Fmoc YIGSR promotes growth of neural cells to a greater extent and maintains healthier morphology, in comparison to hydrophobic Fmoc IKVAV, owing to the entangled longer fibrous network formed by YIGSR peptide. It is expected that thinner long fibers provide a more uniform surface and are more supportive for cell adhesion in comparison to hydrophobic, shorter fibers IKVAV peptide. However, in composite gels, the detrimental effect of hydrophobic IKVAV peptide could be reduced and better adhesion and proliferation could be achieved along with enhanced cell survival. These observations demonstrate the high potential of the laminin-derived hydrogels in tissue engineering and neuronal stem cell differentiation in future.
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Affiliation(s)
- Rashmi Jain
- Institute of Nano Science and Technology, Habitat Centre, Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Sangita Roy
- Institute of Nano Science and Technology, Habitat Centre, Phase-10, Sector-64, Mohali, Punjab 160062, India
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23
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Zhang S, Cortes W, Sasaki T, Asahina S, Natsuko A, Zhang Q, Zhang Y. Mechanoresponsive Alignment of Molecular Self-Assembled Negatively Charged Nanofibrils. ACS APPLIED BIO MATERIALS 2020; 3:1698-1704. [PMID: 35021658 DOI: 10.1021/acsabm.0c00011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inspired by the mechanoresponsive orientation of actin filaments in cell, we introduce a design paradigm of synthetic molecular self-assembling fibrils that respond to external mechanical force by transforming from a macroscopically disorder state to a highly ordered uniaxial aligned state. The incorporation of aromatic-containing amino acids and negatively charged amino acids lead to self-assembly motifs that transform into uniform nanofibrils in acidic solution. Adjusting the pH level of aqueous solution introduces optimal negative charge to the surface of self-assembling nanofibrils inducing long-range electrostatic repulsion forming a nematic phase. Upon external mechanical force, nanofibrils align in the force direction. Via evaporation casting in capillary confinement, the solvated synthetic self-assembling nanofibrils transform into scalable lamellar domains. Adjusting capillary geometry and drying procedure offers further parameters for tuning the mesoscale alignment of nanofibrils generating a variety of interference colors. The design paradigm of mechanoresponsive alignment of self-assembled nanofibrils as an addition of nanofabrication techniques is potentially employable for realizing biomimetic optical structures.
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Affiliation(s)
- Shijin Zhang
- Bioinspired Soft Matter Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan
| | - William Cortes
- Bioinspired Soft Matter Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan
| | - Toshio Sasaki
- Imaging Section, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Shunsuke Asahina
- SM Application Group, JEOL Ltd., Akishima, Tokyo 196-8558, Japan
| | - Asano Natsuko
- SM Application Group, JEOL Ltd., Akishima, Tokyo 196-8558, Japan
| | - Qizheng Zhang
- Bioinspired Soft Matter Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan
| | - Ye Zhang
- Bioinspired Soft Matter Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan
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24
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Tuning the gelation behavior of short laminin derived peptides via solvent mediated self-assembly. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 108:110483. [DOI: 10.1016/j.msec.2019.110483] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022]
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25
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Liu B, Pappas CG, Ottelé J, Schaeffer G, Jurissek C, Pieters PF, Altay M, Marić I, Stuart MCA, Otto S. Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids. J Am Chem Soc 2020; 142:4184-4192. [PMID: 32023041 PMCID: PMC7059183 DOI: 10.1021/jacs.9b10796] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
The conditions that led to the formation
of the first organisms
and the ways that life originates from a lifeless chemical soup are
poorly understood. The recent hypothesis of “RNA-peptide coevolution”
suggests that the current close relationship between amino acids and
nucleobases may well have extended to the origin of life. We now show
how the interplay between these compound classes can give rise to
new self-replicating molecules using a dynamic combinatorial approach.
We report two strategies for the fabrication of chimeric amino acid/nucleobase
self-replicating macrocycles capable of exponential growth. The first
one relies on mixing nucleobase- and peptide-based building blocks,
where the ligation of these two gives rise to highly specific chimeric
ring structures. The second one starts from peptide nucleic acid (PNA)
building blocks in which nucleobases are already linked to amino acids
from the start. While previously reported nucleic acid-based self-replicating
systems rely on presynthesis of (short) oligonucleotide sequences,
self-replication in the present systems start from units containing
only a single nucleobase. Self-replication is accompanied by self-assembly,
spontaneously giving rise to an ordered one-dimensional arrangement
of nucleobase nanostructures.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Christoph Jurissek
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Priscilla F Pieters
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Meniz Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivana Marić
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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26
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Kahana A, Lancet D. Protobiotic Systems Chemistry Analyzed by Molecular Dynamics. Life (Basel) 2019; 9:E38. [PMID: 31083329 PMCID: PMC6617412 DOI: 10.3390/life9020038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022] Open
Abstract
Systems chemistry has been a key component of origin of life research, invoking models of life's inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD's kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.
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Affiliation(s)
- Amit Kahana
- Dept. Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Doron Lancet
- Dept. Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610010, Israel.
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Liu B, Pappas CG, Zangrando E, Demitri N, Chmielewski PJ, Otto S. Complex Molecules That Fold Like Proteins Can Emerge Spontaneously. J Am Chem Soc 2019; 141:1685-1689. [PMID: 30562021 PMCID: PMC6356852 DOI: 10.1021/jacs.8b11698] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Folding can bestow macromolecules with various properties, as evident from nature's proteins. Until now complex folded molecules are the product either of evolution or of an elaborate process of design and synthesis. We now show that molecules that fold in a well-defined architecture of substantial complexity can emerge autonomously and selectively from a simple precursor. Specifically, we have identified a self-synthesizing macrocyclic foldamer with a complex and unprecedented secondary and tertiary structure that constructs itself highly selectively from 15 identical peptide-nucleobase subunits, using a dynamic combinatorial chemistry approach. Folding of the structure drives its synthesis in 95% yield from a mixture of interconverting molecules of different ring sizes in a one-step process. Single-crystal X-ray crystallography and NMR reveal a folding pattern based on an intricate network of noncovalent interactions involving residues spaced apart widely in the linear sequence. These results establish dynamic combinatorial chemistry as a powerful approach to developing synthetic molecules with folding motifs of a complexity that goes well beyond that accessible with current design approaches. The fact that such molecules can form autonomously implies that they may have played a role in the origin of life at earlier stages than previously thought possible.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry , Stratingh Institute , Nijenborgh 4, 9747 AG Groningen , The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry , Stratingh Institute , Nijenborgh 4, 9747 AG Groningen , The Netherlands
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , 34127 Trieste , Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste , S.S. 14 Km 163.5 in Area Science Park , 34149 Basovizza, Trieste , Italy
| | - Piotr J Chmielewski
- Department of Chemistry , University of Wrocław , F. Joliot-Curie 14, 50383 Wrocław , Poland
| | - Sijbren Otto
- Centre for Systems Chemistry , Stratingh Institute , Nijenborgh 4, 9747 AG Groningen , The Netherlands
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28
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Affiliation(s)
- Meniz Altay
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Yigit Altay
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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29
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Altay M, Altay Y, Otto S. Parasitic Behavior of Self-Replicating Molecules. Angew Chem Int Ed Engl 2018; 57:10564-10568. [PMID: 29856109 DOI: 10.1002/anie.201804706] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/16/2022]
Abstract
Self-replication plays a central role in the origin of life and in strategies to synthesize life de novo. Studies on self-replication have focused mostly on isolated systems, while the dynamics of systems containing multiple replicators have received comparatively little attention. Yet most evolutionary scenarios involve the interplay between different replicators. Here we report the emergence of parasitic behavior in a system containing self-replicators derived from two subtly different building blocks 1 and 2. Replicators from 2 form readily through cross-catalysis by pre-existing replicators made from 1. Once formed, the new replicators consume the original replicators to which they owe their existence. These results resemble parasitic and predatory behavior that is normally associated with living systems and show how such lifelike behavior has its roots in relatively simple systems of self-replicating molecules.
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Affiliation(s)
- Meniz Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Yigit Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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30
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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31
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Torchi A, Bochicchio D, Pavan GM. How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships From Coarse-Grained Simulations. J Phys Chem B 2018. [PMID: 29543455 DOI: 10.1021/acs.jpcb.8b00428] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in a controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at an experimental level. Here we show coarse-grained molecular dynamics simulations (<5 Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers. As a representative case, we focus on a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers, experimentally seen to undergo dynamic clustering following the superselective binding to a multivalent recruiter. Our simulations show that the dynamic reorganization of the supramolecular structure proceeds via monomer diffusion on the dynamic fiber surface (exchange within the fiber). Rationally changing the structure of the monomers to make the fiber surface more or less dynamic allows tuning the rate of response to the stimulus and of supramolecular reconfiguration. Simple in silico experiments draw a structure-dynamics-property relationship revealing the key factors underpinning the dynamic adaptivity and stimuli-responsiveness of these supramolecular polymers. We come out with clear evidence that to master the bioinspired properties of these fibers, it is necessary to control their intrinsic dynamics, while the high-resolution of our molecular models permits us to show how.
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Affiliation(s)
- Andrea Torchi
- Department of Innovative Technologies , University of Applied Sciences and Arts of Southern Switzerland , Galleria 2, Via Cantonale 2c , CH-6928 Manno , Switzerland
| | - Davide Bochicchio
- Department of Innovative Technologies , University of Applied Sciences and Arts of Southern Switzerland , Galleria 2, Via Cantonale 2c , CH-6928 Manno , Switzerland
| | - Giovanni M Pavan
- Department of Innovative Technologies , University of Applied Sciences and Arts of Southern Switzerland , Galleria 2, Via Cantonale 2c , CH-6928 Manno , Switzerland
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32
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Kosikova T, Philp D. Exploring the emergence of complexity using synthetic replicators. Chem Soc Rev 2018; 46:7274-7305. [PMID: 29099123 DOI: 10.1039/c7cs00123a] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.
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Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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Reja A, Biswas A, Yadav J, Dev D, Das AK. Induction of Supramolecular Helical Handedness in a Chemical Reaction Directed Self-Healable Soft Material. ChemistrySelect 2017. [DOI: 10.1002/slct.201702212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Antara Reja
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Ankan Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Jonu Yadav
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Dharm Dev
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
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