201
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Le Vay KK, Salibi E, Ghosh B, Tang TYD, Mutschler H. Ribozyme activity modulates the physical properties of RNA-peptide coacervates. eLife 2023; 12:e83543. [PMID: 37326308 DOI: 10.7554/elife.83543] [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: 09/18/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Condensed coacervate phases are now understood to be important features of modern cell biology, as well as valuable protocellular models in origin-of-life studies and synthetic biology. In each of these fields, the development of model systems with varied and tuneable material properties is of great importance for replicating properties of life. Here, we develop a ligase ribozyme system capable of concatenating short RNA fragments into long chains. Our results show that the formation of coacervate microdroplets with the ligase ribozyme and poly(L-lysine) enhances ribozyme rate and yield, which in turn increases the length of the anionic polymer component of the system and imparts specific physical properties to the droplets. Droplets containing active ribozyme sequences resist growth, do not wet or spread on unpassivated surfaces, and exhibit reduced transfer of RNA between droplets when compared to controls containing inactive sequences. These altered behaviours, which stem from RNA sequence and catalytic activity, constitute a specific phenotype and potential fitness advantage, opening the door to selection and evolution experiments based on a genotype-phenotype linkage.
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Affiliation(s)
- Kristian Kyle Le Vay
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Elia Salibi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Basusree Ghosh
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - T Y Dora Tang
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
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202
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Seo K, Ichihashi N. Investigation of Compatibility between DNA Replication, Transcription, and Translation for in Vitro Central Dogma. ACS Synth Biol 2023; 12:1813-1822. [PMID: 37271965 DOI: 10.1021/acssynbio.3c00130] [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: 06/06/2023]
Abstract
Recent advances in in vitro synthetic biology have made it possible to reconstitute various cellular functions in a test tube. However, the integration of these functions remains a major challenge. This study aimed to identify a suitable condition to achieve all three reactions that constitute the central dogma: transcription, translation, and DNA replication. Specifically, we investigated the effect of the concentrations of 11 nonprotein factors required for in vitro transcription, translation, and DNA replication on each of these reactions. Our results indicate that certain factors have opposing effects on the three reactions. For example, while dNTP is necessary for DNA replication, it inhibited translation, and both rNTP and tRNA, which are essential for transcription and translation, inhibited DNA replication with several DNA polymerases. We also found that these opposing effects were partially alleviated by optimizing the magnesium concentration. Using this knowledge, we successfully demonstrated transcription/translation-coupled DNA replication with higher levels of transcription and translation while maintaining a certain level of DNA replication. These findings not only provide useful insights for the development of a complex artificial system with the central dogma but also raise the question of how natural cells overcome the incompatibility between the three reactions.
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Affiliation(s)
- Kaito Seo
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
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203
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Mohd Nor Ihsan NS, Abdul Sani SF, Looi LM, Cheah PL, Chiew SF, Pathmanathan D, Bradley DA. A review: Exploring the metabolic and structural characterisation of beta pleated amyloid fibril in human tissue using Raman spectrometry and SAXS. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00059-7. [PMID: 37307955 DOI: 10.1016/j.pbiomolbio.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/12/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Amyloidosis is a deleterious condition caused by abnormal amyloid fibril build-up in living tissues. To date, 42 proteins that are linked to amyloid fibrils have been discovered. Amyloid fibril structure variation can affect the severity, progression rate, or clinical symptoms of amyloidosis. Since amyloid fibril build-up is the primary pathological basis for various neurodegenerative illnesses, characterization of these deadly proteins, particularly utilising optical techniques have been a focus. Spectroscopy techniques provide significant non-invasive platforms for the investigation of the structure and conformation of amyloid fibrils, offering a wide spectrum of analyses ranging from nanometric to micrometric size scales. Even though this area of study has been intensively explored, there still remain aspects of amyloid fibrillization that are not fully known, a matter hindering progress in treating and curing amyloidosis. This review aims to provide recent updates and comprehensive information on optical techniques for metabolic and proteomic characterization of β-pleated amyloid fibrils found in human tissue with thorough literature analysis of publications. Raman spectroscopy and SAXS are well established experimental methods for study of structural properties of biomaterials. With suitable models, they offer extended information for valid proteomic analysis under physiologically relevant conditions. This review points to evidence that despite limitations, these techniques are able to provide for the necessary output and proteomics indication in order to extrapolate the aetiology of amyloid fibrils for reliable diagnostic purposes. Our metabolic database may also contribute to elucidating the nature and function of the amyloid proteome in development and clearance of amyloid diseases.
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Affiliation(s)
- N S Mohd Nor Ihsan
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S F Abdul Sani
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - L M Looi
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - P L Cheah
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S F Chiew
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Dharini Pathmanathan
- Institute of Mathematical Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - D A Bradley
- Centre for Applied Physics and Radiation Technologies, Sunway University, 46150 PJ, Malaysia; Department of Physics, School of Mathematics & Physics, University of Surrey, Guildford, GU2 7XH, UK
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204
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Ji Y, Lin Y, Qiao Y. Plant Cell-Inspired Membranization of Coacervate Protocells with a Structured Polysaccharide Layer. J Am Chem Soc 2023. [PMID: 37267599 DOI: 10.1021/jacs.3c01326] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The design of compartmentalized colloids that exhibit biomimetic properties is providing model systems for developing synthetic cell-like entities (protocells). Inspired by the cell walls in plant cells, we developed a method to prepare membranized coacervates as protocell models by coating membraneless liquid-like microdroplets with a protective layer of rigid polysaccharides. Membranization not only endowed colloidal stability and prevented aggregation and coalescence but also facilitated selective biomolecule sequestration and chemical exchange across the membrane. The polysaccharide wall surrounding coacervate protocells acted as a stimuli-responsive structural barrier that enabled enzyme-triggered membrane lysis to initiate internalization and killing of Escherichia coli. The membranized coacervates were capable of spatial organization into structured tissue-like protocell assemblages, offering a means to mimic metabolism and cell-to-cell communication. We envision that surface engineering of protocells as developed in this work generates a platform for constructing advanced synthetic cell mimetics and sophisticated cell-like behaviors.
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Affiliation(s)
- Yanglimin Ji
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiyang Lin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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205
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Dagar S, Sarkar S, Rajamani S. Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles. ORIGINS LIFE EVOL B 2023; 53:43-60. [PMID: 37243884 DOI: 10.1007/s11084-023-09636-z] [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: 12/10/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.
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Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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206
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins. J Phys Chem B 2023; 127:4746-4760. [PMID: 37200094 PMCID: PMC10875986 DOI: 10.1021/acs.jpcb.3c01619] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory random coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google Colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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207
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Rao A, Roy S, Jain V, Pillai PP. Nanoparticle Self-Assembly: From Design Principles to Complex Matter to Functional Materials. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25248-25274. [PMID: 35715224 DOI: 10.1021/acsami.2c05378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The creation of matter with varying degrees of complexities and desired functions is one of the ultimate targets of self-assembly. The ability to regulate the complex interactions between the individual components is essential in achieving this target. In this direction, the initial success of controlling the pathways and final thermodynamic states of a self-assembly process is promising. Despite the progress made in the field, there has been a growing interest in pushing the limits of self-assembly processes. The main inception of this interest is that the intended self-assembled state, with varying complexities, may not be "at equilibrium (or at global minimum)", rendering free energy minimization unsuitable to form the desired product. Thus, we believe that a thorough understanding of the design principles as well as the ability to predict the outcome of a self-assembly process is essential to form a collection of the next generation of complex matter. The present review highlights the potent role of finely tuned interparticle interactions in nanomaterials to achieve the preferred self-assembled structures with the desired properties. We believe that bringing the design and prediction to nanoparticle self-assembly processes will have a similar effect as retrosynthesis had on the logic of chemical synthesis. Along with the guiding principles, the review gives a summary of the different types of products created from nanoparticle assemblies and the functional properties emerging from them. Finally, we highlight the reasonable expectations from the field and the challenges lying ahead in the creation of complex and evolvable matter.
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Affiliation(s)
- Anish Rao
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Sumit Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Vanshika Jain
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Pramod P Pillai
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
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208
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Ding D, Zhang SJ, Szostak JW. Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides. Nucleic Acids Res 2023:7184164. [PMID: 37247941 PMCID: PMC10359593 DOI: 10.1093/nar/gkad439] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023] Open
Abstract
The nonenzymatic copying of RNA is thought to have been necessary for the transition between prebiotic chemistry and ribozyme-catalyzed RNA replication in the RNA World. We have previously shown that a potentially prebiotic nucleotide activation pathway based on phospho-Passerini chemistry can lead to the efficient synthesis of 2-aminoimidazole activated mononucleotides when carried out under freeze-thaw cycling conditions. Such activated nucleotides react with each other to form 5'-5' 2-aminoimidazolium bridged dinucleotides, enabling template-directed primer extension to occur within the same reaction mixture. However, mononucleotides linked to oligonucleotides by a 5'-5' 2-aminoimidazolium bridge are superior substrates for nonenzymatic primer extension; their higher intrinsic reactivity and their higher template affinity enable faster template copying at lower substrate concentrations. Here we show that eutectic phase phospho-Passerini chemistry efficiently activates short oligonucleotides and promotes the formation of monomer-bridged-oligonucleotide species during freeze-thaw cycles. We then demonstrate that in-situ generated monomer-bridged-oligonucleotides lead to efficient nonenzymatic template copying in the same reaction mixture. Our demonstration that multiple steps in the pathway from activation chemistry to RNA copying can occur together in a single complex environment simplifies this aspect of the origin of life.
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Affiliation(s)
- Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA02114, USA
| | - Stephanie J Zhang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA02114, USA
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA02114, USA
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA02115, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL60637, USA
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209
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Chen X, Würbser MA, Boekhoven J. Chemically Fueled Supramolecular Materials. ACCOUNTS OF MATERIALS RESEARCH 2023; 4:416-426. [PMID: 37256081 PMCID: PMC10226104 DOI: 10.1021/accountsmr.2c00244] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/10/2023] [Indexed: 06/01/2023]
Abstract
In biology, the function of many molecules is regulated through nonequilibrium chemical reaction cycles. The prototypical example is the phosphorylation of an amino acid in an enzyme which induces a functional change, e.g., it folds or unfolds, assembles or disassembles, or binds a substrate. Such phosphorylation does not occur spontaneously but requires a phosphorylating agent with high chemical potential (for example, adenosine triphosphate (ATP)) to be converted into a molecule with lower chemical potential (adenosine diphosphate (ADP)). When this energy is used to regulate an assembly, we speak of chemically fueled assemblies; i.e., the molecule with high potential, the fuel, is used to regulate a self-assembly process. For example, the binding of guanosine triphosphate (GTP) to tubulin induces self-assembly. The bound GTP is hydrolyzed to guanosine diphosphate (GDP) upon assembly, which induces tubulin disassembly. The result is a dynamic assembly endowed with unique characteristics, such as time-dependent behavior and the ability to self-heal. These intriguing, unique properties have inspired supramolecular chemists to create similar chemically fueled molecular assemblies from the bottom up. While examples have been designed, they remain scarce partly because chemically fueled reaction cycles are rare and often complex. Thus, we recently developed a carbodiimide-driven reaction cycle that is versatile and easy to use, quantitatively understood, and does not suffer from side reactions. In the reaction cycle, a carboxylate precursor reacts with a carbodiimide to form an activated species like an anhydride or ester. The activated state reacts with water and thereby reverts to its precursor state; i.e., the activated state is deactivated. Effectively, the precursor catalyzes carbodiimides' conversion into waste and forms a transient activated state. We designed building blocks to regulate a range of assemblies and supramolecular materials at the expense of carbodiimide fuel. The simplicity and versatility of the reaction cycles have democratized and popularized the field of chemically fueled assemblies. In this Account, we describe what we have "learned" on our way. We introduce the field exemplified by biological nonequilibrium self-assembly. We describe the design of the carbodiimide-driven reaction cycle. Using examples from our group and others, we offer design rules for the building block's structure and strategies to create the desired morphology or supramolecular materials. The discussed morphologies include fibers, colloids, crystals, and oil- and coacervate-based droplets. We then demonstrate how these assemblies form supramolecular materials with unique material properties like the ability to self-heal. Besides, we discuss the concept of reciprocal coupling in which the assembly exerts feedback on its reaction cycle and we also offer examples of such feedback mechanisms. Finally, we close the Account with a discussion and an outlook on this field. This Account aims to provide our fundamental understanding and facilitate further progress toward conceptually new supramolecular materials.
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Affiliation(s)
- Xiaoyao Chen
- Department
of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching bei München, Germany
| | - Michaela A. Würbser
- Department
of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching bei München, Germany
| | - Job Boekhoven
- Department
of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching bei München, Germany
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210
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Peters S, Semenov DA, Hochleitner R, Trapp O. Synthesis of prebiotic organics from CO 2 by catalysis with meteoritic and volcanic particles. Sci Rep 2023; 13:6843. [PMID: 37231067 DOI: 10.1038/s41598-023-33741-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
The emergence of prebiotic organics was a mandatory step toward the origin of life. The significance of the exogenous delivery versus the in-situ synthesis from atmospheric gases is still under debate. We experimentally demonstrate that iron-rich meteoritic and volcanic particles activate and catalyse the fixation of CO2, yielding the key precursors of life-building blocks. This catalysis is robust and produces selectively aldehydes, alcohols, and hydrocarbons, independent of the redox state of the environment. It is facilitated by common minerals and tolerates a broad range of the early planetary conditions (150-300 °C, ≲ 10-50 bar, wet or dry climate). We find that up to 6 × 108 kg/year of prebiotic organics could have been synthesized by this planetary-scale process from the atmospheric CO2 on Hadean Earth.
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Affiliation(s)
- Sophia Peters
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
- Max Planck Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany
| | - Dmitry A Semenov
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
- Max Planck Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany
| | - Rupert Hochleitner
- Mineralogische Staatssammlung München, Theresienstr. 41, 80333, Munich, Germany
| | - Oliver Trapp
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.
- Max Planck Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany.
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211
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Wolfram M, Tiwari MK, Hassenkam T, Li M, Bjerrum MJ, Meldal M. Cascade autohydrolysis of Alzheimer's Aβ peptides. Chem Sci 2023; 14:4986-4996. [PMID: 37206405 PMCID: PMC10189894 DOI: 10.1039/d2sc06668h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/03/2023] [Indexed: 05/21/2023] Open
Abstract
Protein/peptide self-assembly into amyloid structures associates with major neurodegenerative disorders such as Alzheimer's disease (AD). Soluble assemblies (oligomers) of the Aβ peptide and their aggregates are perceived as neurotoxic species in AD. While screening for synthetic cleavage agents that could break down such aberrant assemblies through hydrolysis, we observed that the assemblies of Aβ oligopeptides, containing the nucleation sequence Aβ14-24 (H14QKLVFFAEDV24), could act as cleavage agents by themselves. Autohydrolysis showed a common fragment fingerprint among various mutated Aβ14-24 oligopeptides, Aβ12-25-Gly and Aβ1-28, and full-length Aβ1-40/42, under physiologically relevant conditions. Primary endoproteolytic autocleavage at the Gln15-Lys16, Lys16-Leu17 and Phe19-Phe20 positions was followed by subsequent exopeptidase self-processing of the fragments. Control experiments with homologous d-amino acid enantiomers Aβ12-25-Gly and Aβ16-25-Gly showed the same autocleavage pattern under similar reaction conditions. The autohydrolytic cascade reaction (ACR) was resilient to a broad range of conditions (20-37 °C, 10-150 μM peptide concentration at pH 7.0-7.8). Evidently, assemblies of the primary autocleavage fragments acted as structural/compositional templates (autocatalysts) for self-propagating autohydrolytic processing at the Aβ16-21 nucleation site, showing the potential for cross-catalytic seeding of the ACR in larger Aβ isoforms (Aβ1-28 and Aβ1-40/42). This result may shed new light on Aβ behaviour in solution and might be useful in the development of intervention strategies to decompose or inhibit neurotoxic Aβ assemblies in AD.
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Affiliation(s)
- Martin Wolfram
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Manish K Tiwari
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Tue Hassenkam
- Globe Institute, Section for Geobiology, Copenhagen University Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Ming Li
- Technical University of Denmark, The Danish Hydrocarbon Research and Technology Centre Elektrovej, 2800 Kongens Lyngby Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
| | - Morten Meldal
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark +45 27202355 +45 21308299
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212
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Yang C, Xiao H, Luo Z, Tang L, Dai B, Zhou N, Liang E, Wang G, Tang J. A light-fueled dissipative aggregation-induced emission system for time-dependent information encryption. Chem Commun (Camb) 2023; 59:5910-5913. [PMID: 37170996 DOI: 10.1039/d3cc01092a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A light-fueled dissipative aggregation-induced emission (LDAIE) system is successfully fabricated based on reversible electrostatic interactions between cationic AIE luminogens (AIEgens) and anionic spiropyran (ASP) transformed from sulfonato-merocyanine photoacid (SMEH) upon 420 nm light irradiation. The novel LDAIE system can exhibit reversible and spontaneous AIE fluorescence on/off, showing potential in time-dependent information encryption with self-erasing ability. This work opens new opportunities to fabricate a unique fluorescent anti-counterfeiting platform with high-level security.
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Affiliation(s)
- Caixia Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, P. R. China.
- College of Packaging and Material Engineering, Hunan University of Technology, Zhuzhou 412007, P. R. China
- College of Chemistry and Chemical Engineering Hunan Institute of Science and Technology Yueyang, Hunan Province 414006, P. R. China.
| | - Hangxiang Xiao
- College of Chemistry and Chemical Engineering Hunan Institute of Science and Technology Yueyang, Hunan Province 414006, P. R. China.
| | - Zichen Luo
- College of Chemistry and Chemical Engineering Hunan Institute of Science and Technology Yueyang, Hunan Province 414006, P. R. China.
| | - Li Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, P. R. China.
| | - Bailin Dai
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, P. R. China.
| | - Ningbo Zhou
- College of Chemistry and Chemical Engineering Hunan Institute of Science and Technology Yueyang, Hunan Province 414006, P. R. China.
- Key Laboratory of Hunan Province for Advanced Carbon-based Functional Materials, School of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang, 414006, P. R. China
| | - Enxiang Liang
- College of Chemistry and Chemical Engineering Hunan Institute of Science and Technology Yueyang, Hunan Province 414006, P. R. China.
- Key Laboratory of Hunan Province for Advanced Carbon-based Functional Materials, School of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang, 414006, P. R. China
| | - Guoxiang Wang
- College of Chemistry and Chemical Engineering Hunan Institute of Science and Technology Yueyang, Hunan Province 414006, P. R. China.
- Key Laboratory of Hunan Province for Advanced Carbon-based Functional Materials, School of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang, 414006, P. R. China
| | - Jianxin Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, P. R. China.
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213
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Abstract
The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Joseph B. Solomon
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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214
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Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. Chem Sci 2023; 14:4913-4922. [PMID: 37181767 PMCID: PMC10171074 DOI: 10.1039/d3sc00841j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a 'local energy'-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations.
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Affiliation(s)
- Ke Chen
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München Lichtenbergstraße 4 D-85747 Garching Germany
- Institute of Science and Technology Am Campus 1 3400 Klosterneuburg Austria
| | - Christian Kunkel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany
| | - Bingqing Cheng
- Institute of Science and Technology Am Campus 1 3400 Klosterneuburg Austria
| | - Karsten Reuter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München Lichtenbergstraße 4 D-85747 Garching Germany
| | - Johannes T Margraf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany
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215
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Fraccia TP, Martin N. Non-enzymatic oligonucleotide ligation in coacervate protocells sustains compartment-content coupling. Nat Commun 2023; 14:2606. [PMID: 37160869 PMCID: PMC10169843 DOI: 10.1038/s41467-023-38163-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/18/2023] [Indexed: 05/11/2023] Open
Abstract
Modern cells are complex chemical compartments tightly regulated by an underlying DNA-encoded program. Achieving a form of coupling between molecular content, chemical reactions, and chassis in synthetic compartments represents a key step to the assembly of evolvable protocells but remains challenging. Here, we design coacervate droplets that promote non-enzymatic oligonucleotide polymerization and that restructure as a result of the reaction dynamics. More specifically, we rationally exploit complexation between end-reactive oligonucleotides able to stack into long physical polymers and a cationic azobenzene photoswitch to produce three different phases-soft solids, liquid crystalline or isotropic coacervates droplets-each of them having a different impact on the reaction efficiency. Dynamical modulation of coacervate assembly and dissolution via trans-cis azobenzene photo-isomerization is used to demonstrate cycles of light-actuated oligonucleotide ligation. Remarkably, changes in the population of polynucleotides during polymerization induce phase transitions due to length-based DNA self-sorting to produce multiphase coacervates. Overall, by combining a tight reaction-structure coupling and environmental responsiveness, our reactive coacervates provide a general route to the non-enzymatic synthesis of polynucleotides and pave the way to the emergence of a primitive compartment-content coupling in membrane-free protocells.
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Affiliation(s)
- Tommaso P Fraccia
- Institut Pierre-Gilles de Gennes, Chimie Biologie et Innovation, UMR 8231, ESPCI Paris, PSL University, CNRS, 6 rue Jean Calvin, 75005, Paris, France.
- Department of Pharmacological and Biomolecular Sciences, University of Milano, 20133, Milano, Italy.
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France.
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216
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Kim HE, Choi JH, Chung WJ. Fluorine-Assisted Rearrangement of Geminal Azidofluorides to Imidoyl Fluorides. J Org Chem 2023. [PMID: 37130141 DOI: 10.1021/acs.joc.3c00183] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Organoazide rearrangement constitutes versatile synthetic strategies but typically requires an extremely strong acid and/or a high reaction temperature. Our group recently discovered the remarkable accelerating effect of the geminal fluorine substituent that enables the facile rearrangement of azides into imidoyl fluorides without the aid of acid under much milder reaction conditions. The role of geminal fluorine was elucidated by both experimental and computational investigations. This new reactivity led to the development of a practical one-step tandem preparative method for potentially useful and bench-stable imidoyl fluorides from a wide range of structurally diverse geminal chlorofluorides. Our additional efforts to expand the reaction scope regarding the migrating group, halogen, and carbonyl function are described, and the synthetic utility of the imidoyl fluoride products was demonstrated in hopes of promoting the use of this under-appreciated functional group in the synthetic organic community.
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Affiliation(s)
- Ha Eun Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Won-Jin Chung
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
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217
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Kobayashi K, Ise JI, Aoki R, Kinoshita M, Naito K, Udo T, Kunwar B, Takahashi JI, Shibata H, Mita H, Fukuda H, Oguri Y, Kawamura K, Kebukawa Y, Airapetian VS. Formation of Amino Acids and Carboxylic Acids in Weakly Reducing Planetary Atmospheres by Solar Energetic Particles from the Young Sun. Life (Basel) 2023; 13:1103. [PMID: 37240748 PMCID: PMC10221653 DOI: 10.3390/life13051103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Life most likely started during the Hadean Eon; however, the environmental conditions which contributed to the complexity of its chemistry are poorly known. A better understanding of various environmental conditions, including global (heliospheric) and local (atmospheric, surface, and oceanic), along with the internal dynamic conditions of the early Earth, are required to understand the onset of abiogenesis. Herein, we examine the contributions of galactic cosmic rays (GCRs) and solar energetic particles (SEPs) associated with superflares from the young Sun to the formation of amino acids and carboxylic acids in weakly reduced gas mixtures representing the early Earth's atmosphere. We also compare the products with those introduced by lightning events and solar ultraviolet light (UV). In a series of laboratory experiments, we detected and characterized the formation of amino acids and carboxylic acids via proton irradiation of a mixture of carbon dioxide, methane, nitrogen, and water in various mixing ratios. These experiments show the detection of amino acids after acid hydrolysis when 0.5% (v/v) of initial methane was introduced to the gas mixture. In the set of experiments with spark discharges (simulation of lightning flashes) performed for the same gas mixture, we found that at least 15% methane was required to detect the formation of amino acids, and no amino acids were detected in experiments via UV irradiation, even when 50% methane was used. Carboxylic acids were formed in non-reducing gas mixtures (0% methane) by proton irradiation and spark discharges. Hence, we suggest that GCRs and SEP events from the young Sun represent the most effective energy sources for the prebiotic formation of biologically important organic compounds from weakly reducing atmospheres. Since the energy flux of space weather, which generated frequent SEPs from the young Sun in the first 600 million years after the birth of the solar system, was expected to be much greater than that of GCRs, we conclude that SEP-driven energetic protons are the most promising energy sources for the prebiotic production of bioorganic compounds in the atmosphere of the Hadean Earth.
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Affiliation(s)
- Kensei Kobayashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Jun-ichi Ise
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Ryohei Aoki
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Miei Kinoshita
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Koki Naito
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Takumi Udo
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Bhagawati Kunwar
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Jun-ichi Takahashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Hiromi Shibata
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki 567-0047, Japan
| | - Hajime Mita
- Department of Life, Environment and Applied Chemistry, Faculty of Engineering, Fukuoka Institute of Technology, Fukuoka 811-0295, Japan
| | - Hitoshi Fukuda
- Open Facility Center, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yoshiyuki Oguri
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kimitaka Kawamura
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Yoko Kebukawa
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Vladimir S. Airapetian
- NASA Goddard Space Flight Center/Sellers Exoplanetary Environments Collaboration, Greenbelt, MD 20771, USA
- Department of Physics, American University, Washington, DC 20016, USA
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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218
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Chen J, Bai Q, Li Y, Liu Z, Li Y, Liang D. Coacervates Forming Coexisting Phases on a Mineral Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5814-5824. [PMID: 37053474 DOI: 10.1021/acs.langmuir.3c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Minerals played a crucial role in the chemical evolution of small molecules into biopolymers. Yet, it is still not clear how the minerals are related to the formation and the evolution of protocells on early Earth. In this work, using the coacervate formed by quaternized dextran (Q-dextran) and single-stranded oligonucleotides (ss-oligo) as the protocell model, we systematically studied the phase separation of Q-dextran and ss-oligo on the muscovite surface. Serving as rigid and 2D polyelectrolytes, the muscovite surface can be treated by Q-dextran to become negatively charged, neutral, or positively charged. We observed that Q-dextran and ss-oligo form uniform coacervates on naked and neutral muscovite surfaces, while they form biphasic coacervates containing Q-dextran-rich phases and ss-oligo-rich phases on positively or negatively charged muscovite surfaces that were pretreated by Q-dextran. The evolution of the phases is caused by the redistribution of the components as the coacervate touches the surface. Our study indicates that the mineral surface could be a potential driving force for the formation of protocells with hierarchical structures and desirable functions on prebiotic Earth.
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Affiliation(s)
- Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yanzhang Li
- Beijing Key Laboratory of Mineral Environmental Function, and the Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing 100871, China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yan Li
- Beijing Key Laboratory of Mineral Environmental Function, and the Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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219
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Sharko A, Spitzbarth B, Hermans TM, Eelkema R. Redox-Controlled Shunts in a Synthetic Chemical Reaction Cycle. J Am Chem Soc 2023; 145:9672-9678. [PMID: 37092741 PMCID: PMC10161229 DOI: 10.1021/jacs.3c00985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Shunts, alternative pathways in chemical reaction networks (CRNs), are ubiquitous in nature, enabling adaptability to external and internal stimuli. We introduce a CRN in which the recovery of Michael-accepting species is driven by oxidation chemistry. Using weak oxidants can enable access to two shunts within this CRN with different kinetics and a reduced number of side reactions compared to the main cycle that is driven by strong oxidants. Furthermore, we introduce a strategy to recycle one of the main products under flow conditions to partially reverse the CRN and control product speciation throughout time. These findings introduce new levels of control over artificial CRNs, driven by redox chemistry, narrowing the gap between synthetic and natural systems.
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Affiliation(s)
| | - Benjamin Spitzbarth
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Thomas M Hermans
- University of Strasbourg & CNRS, UMR7140, 67083 Strasbourg, France
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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220
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Matsuura U, Tahara S, Kajimoto S, Nakabayashi T. Label-free autofluorescence lifetime reveals the structural dynamics of ataxin-3 inside droplets formed via liquid-liquid phase separation. Sci Rep 2023; 13:6389. [PMID: 37076520 PMCID: PMC10113985 DOI: 10.1038/s41598-023-33268-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
Liquid-liquid phase separation is a phenomenon that features the formation of liquid droplets containing concentrated solutes. The droplets of neurodegeneration-associated proteins are prone to generate aggregates and cause diseases. To uncover the aggregation process from the droplets, it is necessary to analyze the protein structure with keeping the droplet state in a label-free manner, but there was no suitable method. In this study, we observed the structural changes of ataxin-3, a protein associated with Machado-Joseph disease, inside the droplets, using autofluorescence lifetime microscopy. Each droplet showed autofluorescence due to tryptophan (Trp) residues, and its lifetime increased with time, reflecting structural changes toward aggregation. We used Trp mutants to reveal the structural changes around each Trp and showed that the structural change consists of several steps on different timescales. We demonstrated that the present method visualizes the protein dynamics inside a droplet in a label-free manner. Further investigations revealed that the aggregate structure formed in the droplets differs from that formed in dispersed solutions and that a polyglutamine repeat extension in ataxin-3 hardly modulates the aggregation dynamics in the droplets. These findings highlight that the droplet environment facilitates unique protein dynamics different from those in solutions.
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Affiliation(s)
- Uchu Matsuura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Shinya Tahara
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan.
| | - Shinji Kajimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
- JST PRESTO, Kawaguchi, Saitama, 332-0012, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan.
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221
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Kassem S, McPhee SA, Berisha N, Ulijn RV. Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems. J Am Chem Soc 2023; 145:9800-9807. [PMID: 37075194 DOI: 10.1021/jacs.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.
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Affiliation(s)
- Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Scott A McPhee
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Naxhije Berisha
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
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222
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de Herrera AG, Markert T, Trixler F. Temporal nanofluid environments induce prebiotic condensation in water. Commun Chem 2023; 6:69. [PMID: 37059805 PMCID: PMC10104841 DOI: 10.1038/s42004-023-00872-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Water is a problem in understanding chemical evolution towards life's origins on Earth. Although all known life is being based on water key prebiotic reactions are inhibited by it. The prebiotic plausibility of current strategies to circumvent this paradox is questionable regarding the principle that evolution builds on existing pathways. Here, we report a straightforward way to overcome the water paradox in line with evolutionary conservatism. By utilising a molecular deposition method as a physicochemical probe, we uncovered a synergy between biomolecule assembly and temporal nanofluid conditions that emerge within transient nanoconfinements of water between suspended particles. Results from fluorometry, quantitative PCR, melting curve analysis, gel electrophoresis and computational modelling reveal that such conditions induce nonenzymatic polymerisation of nucleotides and promote basic cooperation between nucleotides and amino acids for RNA formation. Aqueous particle suspensions are a geochemical ubiquitous and thus prebiotic highly plausible setting. Harnessing nanofluid conditions in this setting for prebiotic syntheses is consistent with evolutionary conservatism, as living cells also work with temporal nanoconfined water for biosynthesis. Our findings add key insights required to understand the transition from geochemistry to biochemistry and open up systematic pathways to water-based green chemistry approaches in materials science and nanotechnology.
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Affiliation(s)
- Andrea Greiner de Herrera
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Theresienstraße 41, 80333, Munich, Germany
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- School of Education, Technical University of Munich and Deutsches Museum, Museumsinsel 1, 80538, Munich, Germany
| | - Thomas Markert
- Institute of Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank Trixler
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Theresienstraße 41, 80333, Munich, Germany.
- School of Education, Technical University of Munich and Deutsches Museum, Museumsinsel 1, 80538, Munich, Germany.
- Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Schellingtr. 4, 80799, Munich, Germany.
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223
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Archer RJ, Hamada S, Shimizu R, Nomura SIM. Scalable Synthesis of Planar Macroscopic Lipid-Based Multi-Compartment Structures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4863-4871. [PMID: 36973945 PMCID: PMC10100540 DOI: 10.1021/acs.langmuir.2c02859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/28/2023] [Indexed: 06/18/2023]
Abstract
As life evolved, the path from simple single cell organisms to multicellular enabled increasingly complex functionalities. The spatial separation of reactions at the micron scale achieved by cellular structures allowed diverse and scalable implementation in biomolecular systems. Mimicking such spatially separated domains in a scalable approach could open a route to creating synthetic cell-like structured systems. Here, we report a facile and scalable method to create multicellular-like, multi-compartment (MC) structures. Aqueous droplet-based compartments ranging from 50 to 400 μm were stabilized and connected together by hydrophobic layers composed of phospholipids and an emulsifier. Planar centimeter-scale MC structures were formed by droplet deposition on a water interface. Further, the resulting macroscopic shapes were shown to be achieved by spatially controlled deposition. To demonstrate configurability and potential versatility, MC assemblies of both homogeneous and mixed compartment types were shown. Notably, magnetically heterogeneous systems were achieved by the inclusion of magnetic nanoparticles in defined sections. Such structures demonstrated actuated motion with structurally imparted directionality. These novel and functionalized structures exemplify a route toward future applications including compartmentally assembled "multicellular" molecular robots.
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224
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Huang Y, Huang J, Yin W, Xie F, Coleman B, Cao Y, Aya S, Zhu W, Yang Z, Jiang L. Encoding Coacervate Droplets with Paramagnetism for Dynamical Reconfigurability and Spatial Addressability. ACS NANO 2023; 17:6234-6246. [PMID: 36951305 DOI: 10.1021/acsnano.2c09617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
It is an ongoing endeavor in chemistry and materials science to regulate coacervate droplets on a physiologically relevant spatiotemporal scale to ultimately match or even surpass living cells' precision, complexity, and functionality. Herein, we develop a magnetic strategy orthogonal to the thermal, pH, light, or chemical counterparts that are commonly employed by biotic or artificial systems; its successful implementation thus adds a missing piece to the current arsenal of manipulative methodologies. Specifically, we paramagnetize the otherwise diamagnetic coacervate droplets by cooperatively combining paramagnetic ingredients (including organic radicals, metal ions, and Fe3O4 nanoparticles) and coacervate ingredients to obtain "MagCoa" droplets. A simple model is derived theoretically to account for migration and division of MagCoa droplets in an uneven magnetic field. Experimentally, we produce an array of compartmentalized and monodispersed droplets using microfluidics and magnetically steer them with uniformity and synchronicity. We design and fabricate spatial magnetic modulators to engineer the landscape of a magnetic field that, in turn, directs the MagCoa droplets into predesigned patterns in a reconfigurable fashion. These programmable liquid patterns can be potentially extended to dynamic assembly and information encryption. We envision that the toolbox established here is of generality and multitudes to serve as a practical guide to control droplets magnetically.
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Affiliation(s)
- Yangkun Huang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
| | - Jinpeng Huang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Wenxiang Yin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Fei Xie
- Institute of Information Technology, Handan University, Handan 056005, China
| | - Benjamin Coleman
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005-1892, United States
| | - Yaoyu Cao
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 511443, China
| | - Satoshi Aya
- College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zhijie Yang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Lingxiang Jiang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
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225
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Kürsteiner R, Ritter M, Sologubenko A, Stricker L, Panzarasa G. Time-domain Tollens reaction: synthesising silver nanoparticles with the formaldehyde clock. NANOSCALE ADVANCES 2023; 5:2175-2179. [PMID: 37056627 PMCID: PMC10089108 DOI: 10.1039/d3na00121k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
The addition of silver(i) ions to the methylene glycol-sulphite (MGS) clock reaction results in the sudden formation of metallic silver nanoparticles. Stable suspensions are obtained in the presence of poly(vinylpyrrolidone). The time delay before the appearance of the particles, as well as their size, decreases with the initial methylene glycol concentration while their monodispersity increases.
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Affiliation(s)
- Ronny Kürsteiner
- Institute for Building Materials, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich Laura-Hezner-Weg 7 8093 Zürich Switzerland
| | - Maximilian Ritter
- Institute for Building Materials, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich Laura-Hezner-Weg 7 8093 Zürich Switzerland
| | - Alla Sologubenko
- Scientific Center for Light and Electron Microscopy (ScopeM), ETH Zürich Otto-Stern-Weg 3 8093 Zürich Switzerland
| | - Laura Stricker
- Institute for Building Materials, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich Laura-Hezner-Weg 7 8093 Zürich Switzerland
| | - Guido Panzarasa
- Institute for Building Materials, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich Laura-Hezner-Weg 7 8093 Zürich Switzerland
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226
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Zahorán R, Kumar P, Deák Á, Lantos E, Horváth D, Tóth Á. From Balloon to Crystalline Structure in the Calcium Phosphate Flow-Driven Chemical Garden. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5078-5083. [PMID: 36972336 PMCID: PMC10100542 DOI: 10.1021/acs.langmuir.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/02/2023] [Indexed: 06/18/2023]
Abstract
We have studied the calcium phosphate precipitation reaction by producing chemical gardens in a controlled manner using a three-dimensional flow-driven technique. The injection of the phosphate containing solution into the calcium ion reservoir has resulted in structures varying from membranes to crystals. Dynamical phase diagrams are constructed by varying chemical composition and flow rates from which three different growth mechanisms have been revealed. The microstructural analysis by scanning electron microscopy and powder X-ray diffraction confirmed the morphological transition from membrane tubes to crystalline branches upon decreasing pH.
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Affiliation(s)
- Réka Zahorán
- Department
of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Pawan Kumar
- Department
of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Ágota Deák
- Department
of Physical Chemistry and Materials Science, Interdisciplinary Excellence
Centre, University of Szeged, Aradi sq. 1, Szeged 6720, Hungary
| | - Emese Lantos
- Department
of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Dezső Horváth
- Department
of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Ágota Tóth
- Department
of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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227
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Zhang Z, Jiang H, Ju P, Pan L, Rouillard J, Zhou G, Huang F, Hao J. Evaluating the abiotic synthesis potential and the stability of building blocks of life beneath an impact-induced steam atmosphere. Front Microbiol 2023; 14:1032073. [PMID: 37089554 PMCID: PMC10116804 DOI: 10.3389/fmicb.2023.1032073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
A prerequisite for prebiotic chemistry is the accumulation of critical building blocks of life. Some studies argue that more frequent impact events on the primitive Earth could have induced a more reducing steam atmosphere and thus favor widespread and more efficient synthesis of life building blocks. However, elevated temperature is also proposed to threaten the stability of organics and whether life building blocks could accumulate to appreciable levels in the reducing yet hot surface seawater beneath the steam atmosphere is still poorly examined. Here, we used a thermodynamic tool to examine the synthesis affinity of various life building blocks using inorganic gasses as reactants at elevated temperatures and corresponding steam pressures relevant with the steam-seawater interface. Our calculations show that although the synthesis affinity of all life building blocks decreases when temperature increases, many organics, including methane, methanol, and carboxylic acids, have positive synthesis affinity over a wide range of temperatures, implying that these species were favorable to form (>10-6 molal) in the surface seawater. However, cyanide and formaldehyde have overall negative affinities, suggesting that these critical compounds would tend to undergo hydrolysis in the surface seawaters. Most of the 18 investigated amino acids have positive affinities at temperature <220°C and their synthesis affinity increases under more alkaline conditions. Sugars, ribose, and nucleobases have overall negative synthesis affinities at the investigated range of temperatures. Synthesis affinities are shown to be sensitive to the hydrogen fugacity. Higher hydrogen fugacity (in equilibrium with FQI or IW) favors the synthesis and accumulation of nearly all the investigated compounds, except for HCN and its derivate products. In summary, our results suggest that reducing conditions induced by primitive impacts could indeed favor the synthesis/accumulation of some life building blocks, but some critical species, particularly HCN and nucleosides, were still unfavorable to accumulate to appreciable levels. Our results can provide helpful guidance for future efforts to search for or understand the stability of biomolecules on other planets like Mars and icy moons. We advocate examining craters formed by more reducing impactors to look for the preservation of prebiotic materials.
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Affiliation(s)
- Zongbin Zhang
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Haofan Jiang
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Pengcheng Ju
- State Key Laboratory of Continental Dynamics, Northwest University, Xi’an, China
- Shaanxi Key Laboratory of Early Life and Environment, Department of Geology, Northwest University, Xi’an, China
| | - Lu Pan
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- Centre for Star and Planet Formation, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joti Rouillard
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Comparative Planetology, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Gentao Zhou
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Fang Huang
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
| | - Jihua Hao
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Comparative Planetology, University of Science and Technology of China (USTC), Hefei, Anhui, China
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228
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Wang X, Huang Y, Ren Y, Wang S, Li J, Lin Y, Chen H, Wang L, Huang X. Biotic communities inspired proteinosome-based aggregation for enhancing utilization rate of enzyme. J Colloid Interface Sci 2023; 635:456-465. [PMID: 36599243 DOI: 10.1016/j.jcis.2022.12.132] [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: 10/13/2022] [Revised: 12/12/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
Compared with the individuals, the collective behavior of biotic communities could show certain superior characteristics. Inspired by this idea and based on the conjugation between phenylboronic acid-grafted mesoporous silica nanoparticles and the polysaccharide functionalized membrane of proteinosomes, a type of proteinosomes-based aggregations was constructed. We demonstrated the emergent characteristics of proteinosomes aggregations including accelerated settling velocity and population surviving by sacrificing outside members for the inside. Moreover, this kind of "hand in hand" architecture provided the proteinosomes aggregations with the characteristic of resistance to the negative pressure phagocytosis of micropipette, as well as enhancing utilization rate of the encapsulated enzymes. Overall, it is anticipated that the construction and application of proteinosomes aggregations could contribute to advance the functionality of life-like assembled biomaterial in another way.
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Affiliation(s)
- Xiaoliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yan Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yu Ren
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Shengliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Junbo Li
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Youping Lin
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Haixu Chen
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Lei Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China.
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229
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Cook A, Novosedlik S, van Hest JCM. Complex Coacervate Materials as Artificial Cells. ACCOUNTS OF MATERIALS RESEARCH 2023; 4:287-298. [PMID: 37009061 PMCID: PMC10043873 DOI: 10.1021/accountsmr.2c00239] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/07/2023] [Indexed: 05/19/2023]
Abstract
Cells have evolved to be self-sustaining compartmentalized systems that consist of many thousands of biomolecules and metabolites interacting in complex cycles and reaction networks. Numerous subtle intricacies of these self-assembled structures are still largely unknown. The importance of liquid-liquid phase separation (both membraneless and membrane bound) is, however, recognized as playing an important role in achieving biological function that is controlled in time and space. Reconstituting biochemical reactions in vitro has been a success of the last decades, for example, establishment of the minimal set of enzymes and nutrients able to replicate cellular activities like the in vitro transcription translation of genes to proteins. Further than this though, artificial cell research has the aim of combining synthetic materials and nonliving macromolecules into ordered assemblies with the ability to carry out more complex and ambitious cell-like functions. These activities can provide insights into fundamental cell processes in simplified and idealized systems but could also have an applied impact in synthetic biology and biotechnology in the future. To date, strategies for the bottom-up fabrication of micrometer scale life-like artificial cells have included stabilized water-in-oil droplets, giant unilamellar vesicles (GUV's), hydrogels, and complex coacervates. Water-in-oil droplets are a valuable and easy to produce model system for studying cell-like processes; however, the lack of a crowded interior can limit these artificial cells in mimicking life more closely. Similarly membrane stabilized vesicles, such as GUV's, have the additional membrane feature of cells but still lack a macromolecularly crowded cytoplasm. Hydrogel-based artificial cells have a macromolecularly dense interior (although cross-linked) that better mimics cells, in addition to mechanical properties more similar to the viscoelasticity seen in cells but could be seen as being not dynamic in nature and limiting to the diffusion of biomolecules. On the other hand, liquid-liquid phase separated complex coacervates are an ideal platform for artificial cells as they can most accurately mimic the crowded, viscous, highly charged nature of the eukaryotic cytoplasm. Other important key features that researchers in the field target include stabilizing semipermeable membranes, compartmentalization, information transfer/communication, motility, and metabolism/growth. In this Account, we will briefly cover aspects of coacervation theory and then outline key cases of synthetic coacervate materials used as artificial cells (ranging from polypeptides, modified polysaccharides, polyacrylates, and polymethacrylates, and allyl polymers), finishing with envisioned opportunities and potential applications for coacervate artificial cells moving forward.
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Affiliation(s)
- Alexander
B. Cook
- Bio-Organic
Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sebastian Novosedlik
- Bio-Organic
Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Bio-Organic
Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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230
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Stano P, Damiano L. Synthetic cell research: Is technical progress leaving theoretical and epistemological investigations one step behind? Front Robot AI 2023; 10:1143196. [PMID: 37033673 PMCID: PMC10076886 DOI: 10.3389/frobt.2023.1143196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Advancements in the research on so-called "synthetic (artificial) cells" have been mainly characterized by an important acceleration in all sorts of experimental approaches, providing a growing amount of knowledge and techniques that will shape future successful developments. Synthetic cell technology, indeed, shows potential in driving a revolution in science and technology. On the other hand, theoretical and epistemological investigations related to what synthetic cells "are," how they behave, and what their role is in generating knowledge have not received sufficient attention. Open questions about these less explored subjects range from the analysis of the organizational theories applied to synthetic cells to the study of the "relevance" of synthetic cells as scientific tools to investigate life and cognition; and from the recognition and the cultural reappraisal of cybernetic inheritance in synthetic biology to the need for developing concepts on synthetic cells and to the exploration, in a novel perspective, of information theories, complexity, and artificial intelligence applied in this novel field. In these contributions, we will briefly sketch some crucial aspects related to the aforementioned issues, based on our ongoing studies. An important take-home message will result: together with their impactful experimental results and potential applications, synthetic cells can play a major role in the exploration of theoretical questions as well.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Luisa Damiano
- RG-ESA (Research Group on the Epistemology of the Sciences of the Artificial), Libera Università di Lingue e Comunicazione (IULM), Milan, Italy
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231
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Cardellini A, Crippa M, Lionello C, Afrose SP, Das D, Pavan GM. Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles. J Phys Chem B 2023; 127:2595-2608. [PMID: 36891625 PMCID: PMC10041528 DOI: 10.1021/acs.jpcb.2c08726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The reshuffling mobility of molecular building blocks in self-assembled micelles is a key determinant of many their interesting properties, from emerging morphologies and surface compartmentalization, to dynamic reconfigurability and stimuli-responsiveness. However, the microscopic details of such complex structural dynamics are typically nontrivial to elucidate, especially in multicomponent assemblies. Here we show a machine-learning approach that allows us to reconstruct the structural and dynamic complexity of mono- and bicomponent surfactant micelles from high-dimensional data extracted from equilibrium molecular dynamics simulations. Unsupervised clustering of smooth overlap of atomic position (SOAP) data enables us to identify, in a set of multicomponent surfactant micelles, the dominant local molecular environments that emerge within them and to retrace their dynamics, in terms of exchange probabilities and transition pathways of the constituent building blocks. Tested on a variety of micelles differing in size and in the chemical nature of the constitutive self-assembling units, this approach effectively recognizes the molecular motifs populating them in an exquisitely agnostic and unsupervised way, and allows correlating them to their composition in terms of constitutive surfactant species.
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Affiliation(s)
- Annalisa Cardellini
- 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
| | - Martina Crippa
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Chiara Lionello
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - 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
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - 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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232
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Zhao Q, Garimella SS, Savoie BM. Thermally Accessible Prebiotic Pathways for Forming Ribonucleic Acid and Protein Precursors from Aqueous Hydrogen Cyanide. J Am Chem Soc 2023; 145:6135-6143. [PMID: 36883252 DOI: 10.1021/jacs.2c11857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The search for prebiotic chemical pathways to biologically relevant molecules is a long-standing puzzle that has generated a menagerie of competing hypotheses with limited experimental prospects for falsification. However, the advent of computational network exploration methodologies has created the opportunity to compare the kinetic plausibility of various channels and even propose new pathways. Here, the space of organic molecules that can be formed within four polar or pericyclic reactions from water and hydrogen cyanide (HCN), two established prebiotic candidates for generating biological precursors, was comprehensively explored with a state-of-the-art exploration algorithm. A surprisingly diverse reactivity landscape was revealed within just a few steps of these simple molecules. Reaction pathways to several biologically relevant molecules were discovered involving lower activation energies and fewer reaction steps compared with recently proposed alternatives. Accounting for water-catalyzed reactions qualitatively affects the interpretation of the network kinetics. The case-study also highlights omissions of simpler and lower barrier reaction pathways to certain products by other algorithms that qualitatively affect the interpretation of HCN reactivity.
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Affiliation(s)
- Qiyuan Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Sanjay S Garimella
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Brett M Savoie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
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233
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Salditt A, Karr L, Salibi E, Le Vay K, Braun D, Mutschler H. Ribozyme-mediated RNA synthesis and replication in a model Hadean microenvironment. Nat Commun 2023; 14:1495. [PMID: 36932102 PMCID: PMC10023712 DOI: 10.1038/s41467-023-37206-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Enzyme-catalyzed replication of nucleic acid sequences is a prerequisite for the survival and evolution of biological entities. Before the advent of protein synthesis, genetic information was most likely stored in and replicated by RNA. However, experimental systems for sustained RNA-dependent RNA-replication are difficult to realise, in part due to the high thermodynamic stability of duplex products and the low chemical stability of catalytic RNAs. Using a derivative of a group I intron as a model for an RNA replicase, we show that heated air-water interfaces that are exposed to a plausible CO2-rich atmosphere enable sense and antisense RNA replication as well as template-dependent synthesis and catalysis of a functional ribozyme in a one-pot reaction. Both reactions are driven by autonomous oscillations in salt concentrations and pH, resulting from precipitation of acidified dew droplets, which transiently destabilise RNA duplexes. Our results suggest that an abundant Hadean microenvironment may have promoted both replication and synthesis of functional RNAs.
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Affiliation(s)
- Annalena Salditt
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig Maximilian University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Leonie Karr
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig Maximilian University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Elia Salibi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Kristian Le Vay
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig Maximilian University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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234
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Chen X, Stasi M, Rodon-Fores J, Großmann PF, Bergmann AM, Dai K, Tena-Solsona M, Rieger B, Boekhoven J. A Carbodiimide-Fueled Reaction Cycle That Forms Transient 5(4 H)-Oxazolones. J Am Chem Soc 2023; 145:6880-6887. [PMID: 36931284 PMCID: PMC10064336 DOI: 10.1021/jacs.3c00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
In life, molecular architectures, like the cytoskeletal proteins or the nucleolus, catalyze the conversion of chemical fuels to perform their functions. For example, tubulin catalyzes the hydrolysis of GTP to form a dynamic cytoskeletal network. In contrast, myosin uses the energy obtained by catalyzing the hydrolysis of ATP to exert forces. Artificial examples of such beautiful architectures are scarce partly because synthetic chemically fueled reaction cycles are relatively rare. Here, we introduce a new chemical reaction cycle driven by the hydration of a carbodiimide. Unlike other carbodiimide-fueled reaction cycles, the proposed cycle forms a transient 5(4H)-oxazolone. The reaction cycle is efficient in forming the transient product and is robust to operate under a wide range of fuel inputs, pH, and temperatures. The versatility of the precursors is vast, and we demonstrate several molecular designs that yield chemically fueled droplets, fibers, and crystals. We anticipate that the reaction cycle can offer a range of other assemblies and, due to its versatility, can also be incorporated into molecular motors and machines.
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Affiliation(s)
- Xiaoyao Chen
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michele Stasi
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Jennifer Rodon-Fores
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Paula F Großmann
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Alexander M Bergmann
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Kun Dai
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Marta Tena-Solsona
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Bernhard Rieger
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Job Boekhoven
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
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235
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Fan X, Liu S, Jia Z, Koh JJ, Yeo JCC, Wang CG, Surat'man NE, Loh XJ, Le Bideau J, He C, Li Z, Loh TP. Ionogels: recent advances in design, material properties and emerging biomedical applications. Chem Soc Rev 2023; 52:2497-2527. [PMID: 36928878 DOI: 10.1039/d2cs00652a] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Ionic liquid (IL)-based gels (ionogels) have received considerable attention due to their unique advantages in ionic conductivity and their biphasic liquid-solid phase property. In ionogels, the negligibly volatile ionic liquid is retained in the interconnected 3D pore structure. On the basis of these physical features as well as the chemical properties of well-chosen ILs, there is emerging interest in the anti-bacterial and biocompatibility aspects. In this review, the recent achievements of ionogels for biomedical applications are summarized and discussed. Following a brief introduction of the various types of ILs and their key physicochemical and biological properties, the design strategies and fabrication methods of ionogels are presented by means of different confining networks. These sophisticated ionogels with diverse functions, aimed at biomedical applications, are further classified into several active domains, including wearable strain sensors, therapeutic delivery systems, wound healing and biochemical detections. Finally, the challenges and possible strategies for the design of future ionogels by integrating materials science with a biological interface are proposed.
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Affiliation(s)
- Xiaotong Fan
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore.
| | - Siqi Liu
- Department of Materials Science & Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore.
| | - Zhenhua Jia
- College of Advanced Interdisciplinary Science and Technology, Henan University of Technology, Zhengzhou, 450001, P. R. China. .,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - J Justin Koh
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634, Singapore
| | - Jayven Chee Chuan Yeo
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634, Singapore
| | - Chen-Gang Wang
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore.
| | - Nayli Erdeanna Surat'man
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore.
| | - Xian Jun Loh
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore. .,Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634, Singapore
| | - Jean Le Bideau
- Nantes Université, CNRS, Institut des Matériaux de Nantes Jean Rouxel, IMN, F-44000 Nantes, France.
| | - Chaobin He
- Department of Materials Science & Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore. .,Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634, Singapore
| | - Zibiao Li
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore. .,Department of Materials Science & Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore. .,Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634, Singapore
| | - Teck-Peng Loh
- College of Advanced Interdisciplinary Science and Technology, Henan University of Technology, Zhengzhou, 450001, P. R. China. .,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
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236
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Fielden SDP, Derry MJ, Miller A, Topham PD, O’Reilly RK. Triggered Polymersome Fusion. J Am Chem Soc 2023; 145:5824-5833. [PMID: 36877655 PMCID: PMC10021019 DOI: 10.1021/jacs.2c13049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 03/07/2023]
Abstract
The contents of biological cells are retained within compartments formed of phospholipid membranes. The movement of material within and between cells is often mediated by the fusion of phospholipid membranes, which allows mixing of contents or excretion of material into the surrounding environment. Biological membrane fusion is a highly regulated process that is catalyzed by proteins and often triggered by cellular signaling. In contrast, the controlled fusion of polymer-based membranes is largely unexplored, despite the potential application of this process in nanomedicine, smart materials, and reagent trafficking. Here, we demonstrate triggered polymersome fusion. Out-of-equilibrium polymersomes were formed by ring-opening metathesis polymerization-induced self-assembly and persist until a specific chemical signal (pH change) triggers their fusion. Characterization of polymersomes was performed by a variety of techniques, including dynamic light scattering, dry-state/cryogenic-transmission electron microscopy, and small-angle X-ray scattering (SAXS). The fusion process was followed by time-resolved SAXS analysis. Developing elementary methods of communication between polymersomes, such as fusion, will prove essential for emulating life-like behaviors in synthetic nanotechnology.
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Affiliation(s)
| | - Matthew J. Derry
- Aston
Advanced Materials Research Centre, Aston
University, Birmingham B4 7ET, UK
| | - Alisha
J. Miller
- School
of Chemistry, University of Birmingham,
Edgbaston, Birmingham B15 2TT, UK
| | - Paul D. Topham
- Aston
Advanced Materials Research Centre, Aston
University, Birmingham B4 7ET, UK
| | - Rachel K. O’Reilly
- School
of Chemistry, University of Birmingham,
Edgbaston, Birmingham B15 2TT, UK
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237
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Del Giudice D, Di Stefano S. Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids. Acc Chem Res 2023; 56:889-899. [PMID: 36916734 PMCID: PMC10077594 DOI: 10.1021/acs.accounts.3c00047] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
ConspectusThe achievement of artificial systems capable of being maintained in out-of-equilibrium states featuring functional properties is a main goal of current chemical research. Absorption of electromagnetic radiation or consumption of a chemical species (a "chemical fuel") are the two strategies typically employed to reach such out-of-equilibrium states, which have to persist as long as one of the above stimuli is present. For this reason such systems are often referred to as "dissipative systems". In the simplest scheme, the dissipative system is initially found in a resting, equilibrium state. The addition of a chemical fuel causes the system to shift to an out-of-equilibrium state. When the fuel is exhausted, the system reverts to the initial, equilibrium state. Thus, from a mechanistic standpoint, the dissipative system turns out to be a catalyst for the fuel consumption. It has to be noted that, although very simple, this scheme implies the chance to temporally control the dissipative system. In principle, modulating the nature and/or the amount of the chemical fuel added, one can have full control of the time spent by the system in the out-of-equilibrium state.In 2016, we found that 2-cyano-2-phenylpropanoic acid (1a), whose decarboxylation proceeds smoothly under mild basic conditions, could be used as a chemical fuel to drive the back and forth motion of a catenane-based molecular switch. The acid donates a proton to the catenane that passes from the neutral state A to the transient protonated state B. Decarboxylation of the resulting carboxylate (1acb), generates a carbanion, which, being a strong base, retakes the proton from the protonated catenane that, consequently, returns to the initial state A. The larger the amount of the added fuel, the longer the time spent by the catenane in the transient, out-of-equilibrium state. Since then, acid 1a and other activated carboxylic acids (ACAs) have been used to drive the operation of a large number of dissipative systems based on the acid-base reaction, from molecular machines to host-guest systems, from catalysts to smart materials, and so on. This Account illustrates such systems with the purpose to show the wide applicability of ACAs as chemical fuels. This generality is due to the simplicity of the idea underlying the operation principle of ACAs, which always translates into simple experimental requirements.
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Affiliation(s)
- Daniele Del Giudice
- Dipartimento di Chimica and ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione, Università degli Studi di Roma "La Sapienza", P.le A. Moro 5, 00185 Rome, Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica and ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione, Università degli Studi di Roma "La Sapienza", P.le A. Moro 5, 00185 Rome, Italy
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238
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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239
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Shandilya E, Maiti S. Self-Regulatory Micro- and Macroscale Patterning of ATP-Mediated Nanobioconjugate. ACS NANO 2023; 17:5108-5120. [PMID: 36827433 DOI: 10.1021/acsnano.3c00431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Directional interactions and the assembly of a nanobioconjugate in clusters at a specific location are important for patterning and microarrays in biomedical research. Herein, we report that self-assembly and spatial control in surface patterning of the surfactant-functionalized nanoparticles can be governed in micro- and macroscale environments by two factors, synergistic enzyme-substrate-nanoparticle affinity and the phoretic effect. First, we show that aggregation of cationic gold nanoparticles (GNP) can be modulated by multivalent anionic nanoparticle binding of an adenosine-based nucleotide and enzyme, alkaline phosphatase. We further demonstrate two different types of their autonomous aggregation pattern: (i) by introducing an enzyme gradient that modulates the synergistic nonequilibrium interactivity of the nanoparticle, nucleotide, and enzyme both in microfluidic conditions and at the macroscale; and (ii) the surface deposition pattern from evaporating droplets via the coffee ring effect. Here, temporal control over the width and site of the patterning area inside the microfluidic channel under catalytic and noncatalytic conditions has also been demonstrated. Finally, we show a change in capillary phoresis parameters responsible for the coffee ring due to introduction of ATP-loaded GNP in the blood serum, showing applicability in low-cost disease diagnostics. Overall, an enzyme-actuated surface nanobiopatterning method has been demonstrated that has potential application in controlled micro- and macroscale area patterning with a diverse cascade catalytic surface and spatiotemporal multisensory-based application.
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Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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240
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.531990. [PMID: 36993592 PMCID: PMC10054940 DOI: 10.1101/2023.03.12.531990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory Random Coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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241
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Nikfarjam S, Gibbons R, Burni F, Raghavan SR, Anisimov MA, Woehl TJ. Chemically Fueled Dissipative Cross-Linking of Protein Hydrogels Mediated by Protein Unfolding. Biomacromolecules 2023; 24:1131-1140. [PMID: 36795055 DOI: 10.1021/acs.biomac.2c01186] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Cells assemble dynamic protein-based nanostructures far from equilibrium, such as microtubules, in a process referred to as dissipative assembly. Synthetic analogues have utilized chemical fuels and reaction networks to form transient hydrogels and molecular assemblies from small molecule or synthetic polymer building blocks. Here, we demonstrate dissipative cross-linking of transient protein hydrogels using a redox cycle, which exhibit protein unfolding-dependent lifetimes and mechanical properties. Fast oxidation of cysteine groups on bovine serum albumin by hydrogen peroxide, the chemical fuel, formed transient hydrogels with disulfide bond cross-links that degraded over hours by a slow reductive back reaction. Interestingly, despite increased cross-linking, the hydrogel lifetime decreased as a function of increasing denaturant concentration. Experiments showed that the solvent-accessible cysteine concentration increased with increasing denaturant concentration due to unfolding of secondary structures. The increased cysteine concentration consumed more fuel, which led to less direction oxidation of the reducing agent and affected a shorter hydrogel lifetime. Increased hydrogel stiffness, disulfide cross-linking density, and decreased oxidation of redox-sensitive fluorescent probes at a high denaturant concentration provided evidence supporting the unveiling of additional cysteine cross-linking sites and more rapid consumption of hydrogen peroxide at higher denaturant concentrations. Taken together, the results indicate that the protein secondary structure mediated the transient hydrogel lifetime and mechanical properties by mediating the redox reactions, a feature unique to biomacromolecules that exhibit a higher order structure. While prior works have focused on the effects of the fuel concentration on dissipative assembly of non-biological molecules, this work demonstrates that the protein structure, even in nearly fully denatured proteins, can exert similar control over reaction kinetics, lifetime, and resulting mechanical properties of transient hydrogels.
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Affiliation(s)
- Shakiba Nikfarjam
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, United States
| | - Rebecca Gibbons
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, United States
| | - Faraz Burni
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, United States
| | - Srinivasa R Raghavan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, United States
| | - Mikhail A Anisimov
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, United States
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20740, United States
| | - Taylor J Woehl
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, United States
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242
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Ji J, Hossain MS, Krueger EN, Zhang Z, Nangia S, Carpentier B, Martel M, Nangia S, Mozhdehi D. Lipidation Alters the Structure and Hydration of Myristoylated Intrinsically Disordered Proteins. Biomacromolecules 2023; 24:1244-1257. [PMID: 36757021 PMCID: PMC10017028 DOI: 10.1021/acs.biomac.2c01309] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/25/2023] [Indexed: 02/10/2023]
Abstract
Lipidated proteins are an emerging class of hybrid biomaterials that can integrate the functional capabilities of proteins into precisely engineered nano-biomaterials with potential applications in biotechnology, nanoscience, and biomedical engineering. For instance, fatty-acid-modified elastin-like polypeptides (FAMEs) combine the hierarchical assembly of lipids with the thermoresponsive character of elastin-like polypeptides (ELPs) to form nanocarriers with emergent temperature-dependent structural (shape or size) characteristics. Here, we report the biophysical underpinnings of thermoresponsive behavior of FAMEs using computational nanoscopy, spectroscopy, scattering, and microscopy. This integrated approach revealed that temperature and molecular syntax alter the structure, contact, and hydration of lipid, lipidation site, and protein, aligning with the changes in the nanomorphology of FAMEs. These findings enable a better understanding of the biophysical consequence of lipidation in biology and the rational design of the biomaterials and therapeutics that rival the exquisite hierarchy and capabilities of biological systems.
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Affiliation(s)
- Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Md Shahadat Hossain
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Emily N. Krueger
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Zhe Zhang
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shivangi Nangia
- Department
of Chemistry, University of Hartford, West Hartford, Connecticut 06117, United States
| | - Britnie Carpentier
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Mae Martel
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
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243
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Rajawasam CWH, Tran C, Weeks M, McCoy KS, Ross-Shannon R, Dodo OJ, Sparks JL, Hartley CS, Konkolewicz D. Chemically Fueled Reinforcement of Polymer Hydrogels. J Am Chem Soc 2023; 145:5553-5560. [PMID: 36848549 DOI: 10.1021/jacs.3c00668] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Carbodiimide-fueled anhydride bond formation has been used to enhance the mechanical properties of permanently crosslinked polymer networks, giving materials that exhibit transitions from soft gels to covalently reinforced gels, eventually returning to the original soft gels. Temporary changes in mechanical properties result from a transient network of anhydride crosslinks, which eventually dissipate by hydrolysis. Over an order of magnitude increase in the storage modulus is possible through carbodiimide fueling. The time-dependent mechanical properties can be modulated by the concentration of carbodiimide, temperature, and primary chain architecture. Because the materials remain rheological solids, new material functions such as temporally controlled adhesion and rewritable spatial patterns of mechanical properties have been realized.
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Affiliation(s)
- Chamoni W H Rajawasam
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Corvo Tran
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael Weeks
- Instrumentation Laboratory, Miami University, Oxford, Ohio 45056, United States
| | - Kathleen S McCoy
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Robert Ross-Shannon
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Obed J Dodo
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Jessica L Sparks
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - C Scott Hartley
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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244
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Singh H, Pragya P, Mittal A, Haridas V. Pseudopeptosomes: non-lipidated vesicular assemblies from bispidine-appended pseudopeptides. Org Biomol Chem 2023; 21:3557-3566. [PMID: 36883655 DOI: 10.1039/d3ob00201b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
We report a novel molecular topology-based approach for creating reproducible vesicular assemblies in different solvent environments (including aqueous) using specifically designed pseudopeptides. Deviating from the classical "polar head group and hydrophobic tail" model of amphiphiles, we showed (reversible) self-assembly of synthesized pseudopeptides into vesicles. Naming these new type/class of vesicles "pseudopetosomes", we characterized them by high-resolution microscopy (scanning electron, transmission electron, atomic force, epifluorescence and confocal) along with dynamic light scattering. While accounting for hydropathy index of the constituent amino acids (side chains) of pseudopeptides, we probed molecular interactions, resulting in assembly of pseudopeptosomes by spectroscopy (fourier-transform infrared and fluorescence). Molecular characterization by X-ray crystallography and circular dichroism revealed "tryptophan (Trp)-Zip" arrangements and/or hydrogen-bonded one-dimensional assembly depending on specific pseudopeptides and solvent environments. Our data indicated that pseudopeptosomes are formed in solutions by self-assembly of bispidine pseudopeptides (of Trp, leucine and alanine amino-acid constituents) into sheets that transform into vesicular structures. Thus, we showed that assembly of pseudopeptosomes utilizes the full spectrum of all four weak interactions essential in biological systems. Our findings have direct implications in chemical and synthetic biology, but may also provide a new avenue of investigations on origins of life via pseudopeptosome-like assemblies. We also showed that these designer peptides can act as carriers for cellular transport.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Pragya Pragya
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Aditya Mittal
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. .,Supercomputing Facility for Bioinformatics, and Computational Biology (SCFBio), IIT Delhi, Hauz Khas, New Delhi 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
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245
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Su B, Chi T, Ye Z, Xiang Y, Dong P, Liu D, Addonizio CJ, Webber MJ. Transient and Dissipative Host-Guest Hydrogels Regulated by Consumption of a Reactive Chemical Fuel. Angew Chem Int Ed Engl 2023; 62:e202216537. [PMID: 36598411 DOI: 10.1002/anie.202216537] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/05/2023]
Abstract
The transient self-assembly of molecules under the direction of a consumable fuel source is fundamental to biological processes such as cellular organization and motility. Such biomolecular assemblies exist in an out-of-equilibrium state, requiring continuous consumption of high energy molecules. At the same time, the creation of bioinspired supramolecular hydrogels has traditionally focused on associations occurring at the thermodynamic equilibrium state. Here, hydrogels are prepared from cucurbit[7]uril host-guest supramolecular interactions through transient physical crosslinking driven by the consumption of a reactive chemical fuel. Upon action from this fuel, the affinity and dynamics of CB[7]-guest recognition are altered. In this way, the lifetime of transient hydrogel formation and the dynamic modulus obtained are governed by fuel consumption, rather than being directed by equilibrium complex formation.
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Affiliation(s)
- Bo Su
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
| | - Teng Chi
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
| | - Zhou Ye
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
| | - Yuanhui Xiang
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
| | - Ping Dong
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
| | - Dongping Liu
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
| | - Christopher J Addonizio
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
| | - Matthew J Webber
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA
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246
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Yamashita K, Numata M. Automated Supramolecular Polymerization in a Microflow: A Versatile Platform for Multistep Supramolecular Reactions. Chempluschem 2023; 88:e202200254. [PMID: 36328773 DOI: 10.1002/cplu.202200254] [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: 07/29/2022] [Revised: 10/04/2022] [Indexed: 11/10/2022]
Abstract
This work reports a basic microflow system capable of performing multistep supramolecular polymerization. In this system, injection of the monomer, directional supramolecular copolymerization, removal of the unreacted monomer, and purification of the product supramolecular diblock copolymers are realized along a three-stream flow. When injecting a supramolecular polymer into the central stream of the three-stream flow, the supramolecular polymerization always occurs in the central flow, with the two lateral flows serving as supply and removal lines for the monomer. Employing two kinds of perylene bisimide derivatives as monomers, we confirmed that the reaction occurred selectively at the forward-facing terminus of the supramolecular polymer, along with recovery of the unreacted monomer, ultimately leading to a high-purity supramolecular diblock copolymer. Diblock copolymers are basic units for preparing multicomponent supramolecular block copolymers. Thus, connecting the present system in series would, in principle, result in a "microplant" capable of producing supramolecular polymers having desired inner complexity.
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Affiliation(s)
- Kae Yamashita
- Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Munenori Numata
- Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan
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247
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Karan C, Chaudhuri D. Cooperation and competition in the collective drive by motor proteins: mean active force, fluctuations, and self-load. SOFT MATTER 2023; 19:1834-1843. [PMID: 36789956 DOI: 10.1039/d2sm01183b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We consider the dynamics of a bio-filament under the collective drive of motor proteins. They are attached irreversibly to a substrate and undergo stochastic attachment-detachment with the filament to produce a directed force on it. We establish the dependence of the mean directed force and force correlations on the parameters describing the individual motor proteins using analytical theory and direct numerical simulations. The effective Langevin description for the filament motion gives mean-squared displacement, asymptotic diffusion constant, and mobility leading to an effective temperature. Finally, we show how competition between motor protein extensions generates a self-load, describable in terms of the effective temperature, affecting the filament motion.
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Affiliation(s)
- Chitrak Karan
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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248
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DEAD-box ATPases as regulators of biomolecular condensates and membrane-less organelles. Trends Biochem Sci 2023; 48:244-258. [PMID: 36344372 DOI: 10.1016/j.tibs.2022.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
RNA-dependent DEAD-box ATPases (DDXs) are emerging as major regulators of RNA-containing membrane-less organelles (MLOs). On the one hand, oligomerizing DDXs can promote condensate formation 'in cis', often using RNA as a scaffold. On the other hand, DDXs can disrupt RNA-RNA and RNA-protein interactions and thereby 'in trans' remodel the multivalent interactions underlying MLO formation. In this review, we discuss the best studied examples of DDXs modulating MLOs in cis and in trans. Further, we illustrate how this contributes to the dynamic assembly and turnover of MLOs which might help cells to modulate RNA sequestration and processing in a temporal and spatial manner.
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249
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Saud KT, Solomon MJ. Microdynamics of active particles in defect-rich colloidal crystals. J Colloid Interface Sci 2023; 641:950-960. [PMID: 36989821 DOI: 10.1016/j.jcis.2023.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/04/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]
Abstract
HYPOTHESIS Because they are self-propulsive, active colloidal particles can interact with their environment in ways that differ from passive, Brownian particles. Here, we explore how interactions in different microstructural regions may contribute to colloidal crystal annealing. EXPERIMENTS We investigate active particles propagating in a quasi-2D colloidal crystal monolayer produced by alternating current electric fields (active-to-passive particle ratio ∼ 1:720). The active particle is a platinum Janus sphere propelled by asymmetric decomposition of hydrogen peroxide. Crystals are characterized for changes in void properties. The mean-squared-displacement of Janus particles are measured to determine how active microdynamics depend on the local microstructure, which is comprised of void regions, void-adjacent regions (defined as within three particle diameters of a void), and interstitial regions. FINDINGS At active particle energy EA = 2.55 kBT, the average void size increases as much as three times and the average void anisotropy increases about 40% relative to the passive case. The average microdynamical enhancement, <δ(t)>, of Janus particles in the crystal relative to an equivalent passive Janus particle is reduced compared to that of a free, active particle (<δ(t) > is 1.88 ± 0.04 and 2.66 ± 0.08, respectively). The concentration of active particles is enriched in void and void-adjacent regions. Active particles exhibit the greatest change in dynamics relative to the passive control in void-adjacent regions (<δ(t)> = 2.58 ± 0.06). The results support the conjecture that active particle microdynamical enhancement in crystal lattices is affected by local defect structure.
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Affiliation(s)
- Keara T Saud
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, United States; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States
| | - Michael J Solomon
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States.
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250
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Katke C, Pedrueza-Villalmanzo E, Spustova K, Ryskulov R, Kaplan CN, Gözen I. Colony-like Protocell Superstructures. ACS NANO 2023; 17:3368-3382. [PMID: 36795609 PMCID: PMC9979656 DOI: 10.1021/acsnano.2c08093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
We report the formation, growth, and dynamics of model protocell superstructures on solid surfaces, resembling single cell colonies. These structures, consisting of several layers of lipidic compartments enveloped in a dome-shaped outer lipid bilayer, emerged as a result of spontaneous shape transformation of lipid agglomerates deposited on thin film aluminum surfaces. Collective protocell structures were observed to be mechanically more stable compared to isolated spherical compartments. We show that the model colonies encapsulate DNA and accommodate nonenzymatic, strand displacement DNA reactions. The membrane envelope is able to disassemble and expose individual daughter protocells, which can migrate and attach via nanotethers to distant surface locations, while maintaining their encapsulated contents. Some colonies feature "exocompartments", which spontaneously extend out of the enveloping bilayer, internalize DNA, and merge again with the superstructure. A continuum elastohydrodynamic theory that we developed suggests that a plausible driving force behind subcompartment formation is attractive van der Waals (vdW) interactions between the membrane and surface. The balance between membrane bending and vdW interactions yields a critical length scale of 236 nm, above which the membrane invaginations can form subcompartments. The findings support our hypotheses that in extension of the "lipid world hypothesis", protocells may have existed in the form of colonies, potentially benefiting from the increased mechanical stability provided by a superstructure.
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Affiliation(s)
- Chinmay Katke
- Department
of Physics, Virginia Polytechnic Institute
and State University, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Esteban Pedrueza-Villalmanzo
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Göteborg SE-412 96, Sweden
- Department
of Physics, University of Gothenburg, Universitetsplatsen 1, Gothenburg 405 30, Sweden
| | - Karolina Spustova
- Centre
for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
| | - Ruslan Ryskulov
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Göteborg SE-412 96, Sweden
| | - C. Nadir Kaplan
- Department
of Physics, Virginia Polytechnic Institute
and State University, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Irep Gözen
- Centre
for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
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