ChemSystemsChem最新文献

{"title":"Nonequilibrium Membrane Dynamics Induced by Active Protein Interactions and Chemical Reactions: A Review","authors":"Prof. Hiroshi Noguchi","doi":"10.1002/syst.202400042","DOIUrl":"10.1002/syst.202400042","url":null,"abstract":"<p>Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns and fluctuations of membranes under nonequilibrium conditions. In particular, we focus on theoretical analyses and simulations. Protein active forces enhance or suppress the membrane fluctuations; the membrane height spectra are deviated from the thermal spectra. Protein binding or unbinding to the membrane is activated or inhibited by other proteins and chemical reactions, such as ATP hydrolysis. Such active binding processes can induce traveling waves, Turing patterns, and membrane morphological changes. They can be represented by the continuum reaction-diffusion equations and discrete lattice/particle models with state flips. The effects of structural changes in amphiphilic molecules on the molecular-assembly structures are also discussed.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"7 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202400042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141815102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Information Processing in a Chemical Reaction Network Using Surface-Mediated Polyelectrolyte Complexation","authors":"A. Hazal Koyuncu,&nbsp;Giulia Allegri,&nbsp;Dr. Taghi Moazzenzade,&nbsp;Prof. Dr. Jurriaan Huskens,&nbsp;Dr. Saskia Lindhoud,&nbsp;Dr. Albert S. Y. Wong","doi":"10.1002/syst.202400050","DOIUrl":"10.1002/syst.202400050","url":null,"abstract":"<p>Biochemical communication is ubiquitous in life. Biology uses chemical reaction networks to regulate concentrations of myriad signaling molecules. Recent advances in supramolecular and systems chemistry demonstrate that feedback mechanisms of such networks can be rationally designed but strategies to transmit and process information encoded in molecules are still in their infancy. Here, we designed a polyelectrolyte reaction network maintained under out-of-equilibrium conditions using pH gradients in flow. The network comprises two weak polyelectrolytes (polyallylamine, PAH, and polyacrylic acid, PAA) in solution and one immobilized on the surface (poly-l-lysine, PLL). We chose PAH and PAA as their complexation process is known to be history-dependent (<i>i. e</i>., the preceding state of the system can determine the next state). Surprisingly, we found that the hysteresis diminished as the PLL-coated surface supported rather than perturbed the formation of the complex. PLL-coated surfaces are further exploited to establish that reversible switching between the assembled and disassembled state of polyelectrolytes can process signals encoded in the frequency and duration of pH pulses. We envision that the strategy employed to modulate information in this polyelectrolyte reaction network could open novel routes to transmit and process molecular information in biologically relevant processes.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 6","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202400050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141818800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Front Cover: Artificial Molecular Systems for Complex Functions Based on DNA Nanotechnology and Cell-Sized Lipid Vesicles (ChemSystemsChem 4/2024)","authors":"Prof. Dr. Yusuke Sato","doi":"10.1002/syst.202480401","DOIUrl":"https://doi.org/10.1002/syst.202480401","url":null,"abstract":"<p><b>The front cover</b> illustrates cell-like functional molecular systems based on DNA nanotechnology and lipid vesicles. The base-specific interactions of DNA enable the construction of various functional components that can be integrated into lipid vesicles, aiming to create artificial molecular systems comparable to, or even surpassing, natural molecular systems, such as living cells. The Review by Y. Sato describes the latest achievements in functions realized through the combination of DNA nanotechnology and lipid vesicles.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202480401","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141624528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Life in Lab: Chemically Fueled Systems Chemistry for Emergent Properties","authors":"Sudeep Koppayithodi,&nbsp;Prerna Ranasingh,&nbsp;Dr. Nishant Singh","doi":"10.1002/syst.202400028","DOIUrl":"10.1002/syst.202400028","url":null,"abstract":"<p>Understanding the emergence of complex properties in dissipative non-equilibrium systems is crucial for unraveling the mysteries of life processes. The review focuses on the documented research on chemically fueled autonomous systems, self-sorting towards compartmentalization, self-replication via autocatalysis, and rhythmic chemical oscillators. In addition to that, the review also discusses newly introduced reactions and dynamic combinatorial libraries in dissipative systems.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 6","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202400028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141663063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Chemical Mechanism for the Bistable-to-Oscillatory Transition in Colloidal Aggregates of Silver Phosphate","authors":"María Antonieta Sánchez-Farrán,&nbsp;Ali Borhan,&nbsp;Ayusman Sen,&nbsp;Vincent H. Crespi","doi":"10.1002/syst.202400024","DOIUrl":"https://doi.org/10.1002/syst.202400024","url":null,"abstract":"<p>We previously reported collective behavior in colloidal aggregates of silver phosphate in H₂O₂ and under UV light. Diffusiophoretic interactions between aggregates lead to non-linear behavior such as oscillations and synchronization, in which oscillation frequencies increase with H₂O₂ concentration. The aggregates transition between schooling and dispersed behaviors with incipient spatiotemporal correlations. We identified a kinetic model that maps the chemical species that are thought to underlie non-linear phenomena in the colloidal aggregates, i. e. adsorbed oxygen species *OOH⁻ and *O. We investigate the emergent dynamics for the simplest case, the coupling of two otherwise bistable clusters. Two coupling schemes are proposed and we find that – depending on whether the coupling is excitatory or inhibitory – the clusters may oscillate with zero or <i>π</i> phase shift.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202400024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Photostimuli Reach a Selective Intermediate in a Microflow: One-Shot Transformation from a Supramolecular Co-Polymer to a Micro-Disk Structure","authors":"Akira Kaneyoshi,&nbsp;Shota Nomura,&nbsp;Takato Maeda,&nbsp;Dr. Takahiro Kusukawa,&nbsp;Dr. Yoshihiro Kikkawa,&nbsp;Dr. Munenori Numata","doi":"10.1002/syst.202400031","DOIUrl":"10.1002/syst.202400031","url":null,"abstract":"<p>In supramolecular chemistry, photostimulants are generally combined with a static solution under thermodynamic equilibrium with no time progression. After reaching the thermodynamic state, self-assembly events contain various species–a mixture of component molecules, intermediate species, and completed assemblies–which light reaches uniformly. In this study, snapshot control of supramolecular polymerization was first combined with pinpoint photoirradiation using a microflow system. Employing the azobenzene derivative <i>trans-</i>C3NO as a monomer, a snapshot moment of supramolecular polymerization along a microflow channel was selectively irradiated with UV light at 365 nm in a space-resolved manner, so that the monomers, intermediates (oligomers), or extended supramolecular polymers were selectively exposed to light stimuli. We found that a pinpoint photostimulus to each snapshot moment had a pronounced effect on the kinetic pathway by tuning the timing at which the snapshot moment of <i>cis-</i>C3NO was generated. Upon irradiation in the upstream region, in the very early stages before initiating polymerization, supramolecular polymerization was suppressed by generating a less reactive <i>cis-</i>C3NO monomer. However, photoirradiation does not affect the supramolecular polymers in the downstream region because of their stiff nature. Remarkably, when irradiating the middle stream region involving a soft-natured intermediate species, supramolecular copolymerization occurred through in situ conversion from <i>trans-</i> and <i>cis-</i>C3NO inside the primitive supramolecular polymer. Loose monomer stacking in the primitive aggregate endows it with mechanoresponsiveness. Under the influence of shear force in a Hagen–Poiseuille flow, the resultant supramolecular copolymers containing geometrically different <i>cis-</i>isomers were rolled up and transformed into a micrometer-sized disk-like structure. During the in situ supramolecular copolymerization and transformation to the disk structure, a liquid–liquid interface generated in the laminar flow acted as a template to fix the orientation of the monomers and supramolecular polymers, leading to the uniform disk formation. Furthermore, monomers’ orientation in the aligned supramolecular polymers are fixed on the interface, on which light is always irradiated in an anisotropic manner. This results in both complexity at the molecular level and long-range structural order such as regular rolling up at the micrometer range over the molecular scale. By incorporating the photostimulus system, microflow extends its potential for supramolecular chemistry.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 6","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141365643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Many-Chemicals Problem of Systems Chemistry","authors":"Dr. Oliver R. Maguire","doi":"10.1002/syst.202400027","DOIUrl":"10.1002/syst.202400027","url":null,"abstract":"<p>An <i>E. coli</i> cell contains ~2500 different chemicals which combine into an ordered biochemical reaction network out of which emerges a living system. A chemist taking 2500 different chemicals from a laboratory chemical cabinet and combining them together will likely cause an explosive disaster and produce an intractable chemical sludge. Systems Chemistry aspires to construct systems whose complexity rivals that of life. However, to do this we will need to learn how to combine hundreds or thousands of different chemicals together to form a functional system without descending into a disordered chemical sludge. This is the Many-Chemicals Problem of Systems Chemistry. I explore a key strategy life employs to overcome this challenge. Namely, the combination of kinetically stable and thermodynamically activated molecules (e. g. ATP) with enzyme catalysts (e. g. histidine kinases). I suggest how the strategy could have begun at the origin of life. Finally, I assess the implications of this strategy for Systems Chemistry and how it will enable systems chemists to construct systems whose complexity rivals that of life.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141108586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Slow Freeze-Thaw Cycles Enhanced Hybridization of Kilobase DNA with Long Complementary Sticky Ends","authors":"Dr. Natsumi Noda,&nbsp;Kohei Nomura,&nbsp;Naho Takahashi,&nbsp;Dr. Fumitaka Hashiya,&nbsp;Prof. Dr. Hiroshi Abe,&nbsp;Prof. Dr. Tomoaki Matsuura","doi":"10.1002/syst.202400025","DOIUrl":"10.1002/syst.202400025","url":null,"abstract":"<p>The creation of large information molecules may have played an essential role in the origins of life. In this study, we conducted slow freeze-thaw (F/T) experiments to test the possibility of enhanced hybridization between the complementary sticky ends attached to kilobase-sized DNA fragments at sub-nanomolar concentrations. DNA fragments of 2- and 3-kilobase pairs (kbp) with 50-base complementary sticky ends that can form 5 kbp-sized hybridization products were mixed. While simple incubation provided little hybridization product, significantly effective hybridization was observed after freezing and thawing at a controlled time rate (&lt;0.3 K min⁻¹), even with small DNA concentrations (&lt;1 nM). Furthermore, slow thawing had a more effect on hybridization than slow freezing. The reaction efficiency was reduced by rapid thawing instead of slow thawing, suggesting that the eutectic phase concentration played an important role in hybridization. A slow F/T cycle was effective even for the hybridization reaction between two 10 kbp DNA fragments, which yielded a 20 kbp product at sub-nanomolar concentrations. Repeating the slow F/T cycle significantly improved the reaction efficiency. The possible role of the F/T cycles in early Earth environments is discussed here.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202400025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140979943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autonomous Development of Compositional Diversity in Self-Spreading Flat Protocells","authors":"Dr. İrep Gözen,&nbsp;Prof. Stephen Mann,&nbsp;Prof. Aldo Jesorka","doi":"10.1002/syst.202400029","DOIUrl":"10.1002/syst.202400029","url":null,"abstract":"<p>An experimental pathway to the spontaneous generation of compositionally diverse synthetic protocells is presented. The pathway is initiated by flat giant unilamellar vesicles (FGUVs) that originate from compositionally different multilamellar lipid reservoirs and undergo spontaneous spreading across solid surfaces. On contact, the spreading FGUVs merge to produce a concentration gradient in membrane lipids across the fusion interface. Subsequent reconstruction through a series of shape transformations produces a network of nanotube-connected lipid vesicles that inherit different ratios of the membrane constituents derived from the bilayers of the parent FGUVs. The fusion process leads to the engulfment of small FGUVs by larger FGUVs, mimicking predator-prey behavior in which the observable characteristics of the prey are lost but the constituents are carried by the predator FGUV to the next generation of lipid vesicles. We speculate that our results could provide a feasible pathway to autonomous protocell diversification in origin of life theories and highlight the possible role of solid surfaces in the development of diversity and rudimentary speciation of natural protocells on the early Earth.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 6","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202400029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140987127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Artificial Molecular Systems for Complex Functions Based on DNA Nanotechnology and Cell-Sized Lipid Vesicles","authors":"Prof. Dr. Yusuke Sato","doi":"10.1002/syst.202400021","DOIUrl":"10.1002/syst.202400021","url":null,"abstract":"<p>Cells are highly functional and complex molecular systems. Artificially creating such systems remains a challenge, which has been extensively studied in various research fields, including synthetic biology and molecular robotics. DNA nanotechnology is a powerful tool for bottom-up engineering for constructing functional nanostructures or chemical reaction networks which can be utilized as components for artificial molecular systems. Encapsulation of these components into a giant unilamellar vesicle (GUV) composed of a lipid bilayer, the base structure of the cellular membrane, results in a functional cell-sized structure that partially mimics some cellular functions. This review discusses the studies contributing to the construction of GUV-based artificial molecular systems based on DNA nanotechnology. Molecular transport and signal transduction through lipid membranes are essential to uptake molecules from the environment and respond to stimuli. Membrane shaping relates to various functions, including motility and signaling. A chemical reaction network is required to autonomously regulate the system‘s functions. This review describes the functions realized using DNA nanostructures and DNA reaction networks. Given the designability and programmability of DNA nanotechnology, it may be possible that the functionality of artificial molecular systems could be comparable to or even surpass that of natural molecular systems.</p>","PeriodicalId":72566,"journal":{"name":"ChemSystemsChem","volume":"6 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/syst.202400021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140991172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}