Pub Date : 2025-04-28DOI: 10.1038/s41428-025-01040-w
Michelle Gracia Lay, Nur Alia Oktaviani, Ali D. Malay, Keiji Numata
Silk fibers have been used by humans for millennia to create textiles and have recently gained the attention of scientists due to their unsurpassed mechanical properties. These properties arise from a sophisticated process by which the starting material, a liquid feedstock consisting of high-molecular-weight silk proteins, is rapidly converted within silk glands into solid fibers with a multi-scale hierarchical structure that is responsible for the material’s incredible robustness. Recently, liquid-liquid phase separation (LLPS) has emerged as a powerful framework for understanding the self-assembly behavior of silk proteins. Interestingly, LLPS-associated proteins typically exhibit disordered or dynamic conformations and have sequences rich in low-complexity multivalent repeats, reminiscent of silk protein sequences. In this review, we explore the evidence indicating that LLPS is a major aspect of silk fiber storage and assembly in both lepidopteran and spider systems. We discuss insights derived from comparative analyses of amino acid sequences, specific chemical triggers, and potential chemical interactions and contextualize the results from recent empirical investigations based on native and recombinant silk materials. We also discuss how LLPS mechanisms might be applied to the sustainable production of silk-like materials that replicate native hierarchical structures. Finally, we outline important areas for future investigations and speculate on how findings from the field of silk research may help illuminate the more general field of biomolecular condensates. The production of silk in spiders and silkworms involves the transformation of concentrated liquid protein feedstock into hierarchically organized solid fibers through a highly controlled mechanism facilitated by their respective glandular spinning apparatus. Recent insights suggest that liquid–liquid phase separation (LLPS) plays a central role in organizing the initially disordered silk protein chains into dense yet dynamic condensates, which is a key step towards rapid fiber formation. This hierarchical assembly process underlies the remarkable mechanical properties of silk fibers.
{"title":"Exploring the self-assembly of silk proteins through liquid-liquid phase separation","authors":"Michelle Gracia Lay, Nur Alia Oktaviani, Ali D. Malay, Keiji Numata","doi":"10.1038/s41428-025-01040-w","DOIUrl":"10.1038/s41428-025-01040-w","url":null,"abstract":"Silk fibers have been used by humans for millennia to create textiles and have recently gained the attention of scientists due to their unsurpassed mechanical properties. These properties arise from a sophisticated process by which the starting material, a liquid feedstock consisting of high-molecular-weight silk proteins, is rapidly converted within silk glands into solid fibers with a multi-scale hierarchical structure that is responsible for the material’s incredible robustness. Recently, liquid-liquid phase separation (LLPS) has emerged as a powerful framework for understanding the self-assembly behavior of silk proteins. Interestingly, LLPS-associated proteins typically exhibit disordered or dynamic conformations and have sequences rich in low-complexity multivalent repeats, reminiscent of silk protein sequences. In this review, we explore the evidence indicating that LLPS is a major aspect of silk fiber storage and assembly in both lepidopteran and spider systems. We discuss insights derived from comparative analyses of amino acid sequences, specific chemical triggers, and potential chemical interactions and contextualize the results from recent empirical investigations based on native and recombinant silk materials. We also discuss how LLPS mechanisms might be applied to the sustainable production of silk-like materials that replicate native hierarchical structures. Finally, we outline important areas for future investigations and speculate on how findings from the field of silk research may help illuminate the more general field of biomolecular condensates. The production of silk in spiders and silkworms involves the transformation of concentrated liquid protein feedstock into hierarchically organized solid fibers through a highly controlled mechanism facilitated by their respective glandular spinning apparatus. Recent insights suggest that liquid–liquid phase separation (LLPS) plays a central role in organizing the initially disordered silk protein chains into dense yet dynamic condensates, which is a key step towards rapid fiber formation. This hierarchical assembly process underlies the remarkable mechanical properties of silk fibers.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 8","pages":"799-814"},"PeriodicalIF":2.7,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41428-025-01040-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Protein aggregation and liquid‒liquid phase separation (LLPS), as key physicochemical processes, orchestrate protein behavior and function, and engineering a protein surface charge offers a robust approach to modulate protein‒protein interactions and, consequently, aggregation and phase separation. Among protein surface engineering methods, supercharging leads to a drastic increase in the protein net charge by replacing surface residues with charged amino acid residues. Previous studies have reported that some physicochemical properties of proteins are improved by supercharging, and changing the surface charge is considered to affect intermolecular interactions. In this study, we designed a new supercharged antigen-binding fragment (Fab) antibody mutant and investigated its aggregation behavior. Upon examination of the physicochemical properties of the designed supercharged antibody, the thermal stability, structure, and ligand binding affinity of the antibody were retained despite having the same charge pairing of both the antibody and the antigen. Furthermore, we revealed that the antibody exhibited reversible ligand- and salt concentration-dependent aggregation. Our study demonstrated how supercharging can potentially modulate protein aggregation and LLPS. It is expected that this approach can be extended to other proteins, through which its applicability in various biological and biotechnological fields can be explored. Protein aggregation and liquid‒liquid phase separation (LLPS) orchestrate protein behavior and function. Engineering protein surface charge offers a robust approach to modulating these phenomena, and supercharging, which replaces surface residues with charged ones, leads to a drastic change in the protein net charge. In this study, we designed a new supercharged antigen-binding fragment antibody mutant and investigated its aggregation behavior. We revealed that the antibody exhibited reversible ligand- and salt concentration-dependent aggregation while retaining the physicochemical properties. Our study demonstrated how supercharging can potentially modulate protein aggregation and LLPS.
{"title":"Supercharging design of an anti-lysozyme Fab antibody to regulate ligand-dependent reversible aggregation","authors":"Keisuke Kasahara, Makoto Nakakido, Daisuke Kuroda, Satoru Nagatoishi, Kouhei Tsumoto","doi":"10.1038/s41428-025-01046-4","DOIUrl":"10.1038/s41428-025-01046-4","url":null,"abstract":"Protein aggregation and liquid‒liquid phase separation (LLPS), as key physicochemical processes, orchestrate protein behavior and function, and engineering a protein surface charge offers a robust approach to modulate protein‒protein interactions and, consequently, aggregation and phase separation. Among protein surface engineering methods, supercharging leads to a drastic increase in the protein net charge by replacing surface residues with charged amino acid residues. Previous studies have reported that some physicochemical properties of proteins are improved by supercharging, and changing the surface charge is considered to affect intermolecular interactions. In this study, we designed a new supercharged antigen-binding fragment (Fab) antibody mutant and investigated its aggregation behavior. Upon examination of the physicochemical properties of the designed supercharged antibody, the thermal stability, structure, and ligand binding affinity of the antibody were retained despite having the same charge pairing of both the antibody and the antigen. Furthermore, we revealed that the antibody exhibited reversible ligand- and salt concentration-dependent aggregation. Our study demonstrated how supercharging can potentially modulate protein aggregation and LLPS. It is expected that this approach can be extended to other proteins, through which its applicability in various biological and biotechnological fields can be explored. Protein aggregation and liquid‒liquid phase separation (LLPS) orchestrate protein behavior and function. Engineering protein surface charge offers a robust approach to modulating these phenomena, and supercharging, which replaces surface residues with charged ones, leads to a drastic change in the protein net charge. In this study, we designed a new supercharged antigen-binding fragment antibody mutant and investigated its aggregation behavior. We revealed that the antibody exhibited reversible ligand- and salt concentration-dependent aggregation while retaining the physicochemical properties. Our study demonstrated how supercharging can potentially modulate protein aggregation and LLPS.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 8","pages":"923-930"},"PeriodicalIF":2.7,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41428-025-01046-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Enzyme condensates are powerful tools for controlling enzymatic reactions in living cells. Recent advances in polymer science have enabled the design of artificial enzyme condensates in vitro, providing a promising approach to enhance enzymatic activity and stability for various biotechnological applications. In this review, we describe a systematic approach to engineering enzyme condensates through polymer-based strategies. First, we consider the design principles for tailoring the state of the enzyme condensates using charged polymers, including approaches that utilize enzymes as scaffolds or clients, and compare these condensates with other enzyme activation methods, highlighting the advantages and potential limitations of enzyme condensates. Second, we review the major factors that affect enzyme performance within the condensates, including size-dependent effects and local environmental changes. These data are supported by recent mechanistic studies using various enzyme systems, including oxidoreductases. Finally, we focus on possible applications and outline the key challenges in expanding the utility of enzyme condensates from single-enzyme to multienzyme systems and from solution-based to surface-bound architectures. Our comprehensive overview of enzyme condensate engineering provides a new perspective to bridge cellular organization principles and innovations in enzyme catalysis. This review highlights recent advances in engineering artificial enzyme condensates in vitro using charged polymers. Based on our recent findings, we describe strategies for designing condensates through interactions between polymers and enzymes or coenzymes. We then summarize enzyme activation mechanisms triggered by enzyme condensates, including size-dependent effects and conformational changes in enzymes. We also discuss potential applications and future directions, including multienzyme systems, integration with solid surfaces, and combination with rational enzyme design.
{"title":"Polymer-engineered condensates for enzyme activation","authors":"Tomoto Ura, Toya Yoshida, Tsutomu Mikawa, Kentaro Shiraki","doi":"10.1038/s41428-025-01042-8","DOIUrl":"10.1038/s41428-025-01042-8","url":null,"abstract":"Enzyme condensates are powerful tools for controlling enzymatic reactions in living cells. Recent advances in polymer science have enabled the design of artificial enzyme condensates in vitro, providing a promising approach to enhance enzymatic activity and stability for various biotechnological applications. In this review, we describe a systematic approach to engineering enzyme condensates through polymer-based strategies. First, we consider the design principles for tailoring the state of the enzyme condensates using charged polymers, including approaches that utilize enzymes as scaffolds or clients, and compare these condensates with other enzyme activation methods, highlighting the advantages and potential limitations of enzyme condensates. Second, we review the major factors that affect enzyme performance within the condensates, including size-dependent effects and local environmental changes. These data are supported by recent mechanistic studies using various enzyme systems, including oxidoreductases. Finally, we focus on possible applications and outline the key challenges in expanding the utility of enzyme condensates from single-enzyme to multienzyme systems and from solution-based to surface-bound architectures. Our comprehensive overview of enzyme condensate engineering provides a new perspective to bridge cellular organization principles and innovations in enzyme catalysis. This review highlights recent advances in engineering artificial enzyme condensates in vitro using charged polymers. Based on our recent findings, we describe strategies for designing condensates through interactions between polymers and enzymes or coenzymes. We then summarize enzyme activation mechanisms triggered by enzyme condensates, including size-dependent effects and conformational changes in enzymes. We also discuss potential applications and future directions, including multienzyme systems, integration with solid surfaces, and combination with rational enzyme design.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 8","pages":"885-896"},"PeriodicalIF":2.7,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41428-025-01042-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-25DOI: 10.1038/s41428-025-01038-4
Ryutaro Fujimoto, Sayuri L. Higashi, Yuki Shintani, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Masato Ikeda
Herein, we describe the construction of coacervates composed of an oligo(ethylene glycol) derivative bearing benzyl sulfide groups. The obtained liquid-like coacervates (droplets) can undergo oxidation-responsive disassembly through the conversion of the sulfide groups to the sulfoxide groups. Moreover, the coacervates selectively encapsulate hydrophobic molecules; therefore, oxidation-responsive disassembly can lead to the controlled release of the encapsulated molecules. The construction of coacervates composed of an oligo(ethylene glycol) derivative bearing benzyl sulfide groups is presented. The obtained liquid-like coacervates (droplets) can undergo oxidation-responsive disassembly through the conversion of the sulfide groups to the sulfoxide groups. Moreover, the coacervates selectively encapsulate hydrophobic molecules; therefore, oxidation-responsive disassembly can lead to the controlled release of the encapsulated molecules.
{"title":"Oxidation-responsive coacervates composed of oligo(ethylene glycol) bearing benzyl sulfide groups","authors":"Ryutaro Fujimoto, Sayuri L. Higashi, Yuki Shintani, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Masato Ikeda","doi":"10.1038/s41428-025-01038-4","DOIUrl":"10.1038/s41428-025-01038-4","url":null,"abstract":"Herein, we describe the construction of coacervates composed of an oligo(ethylene glycol) derivative bearing benzyl sulfide groups. The obtained liquid-like coacervates (droplets) can undergo oxidation-responsive disassembly through the conversion of the sulfide groups to the sulfoxide groups. Moreover, the coacervates selectively encapsulate hydrophobic molecules; therefore, oxidation-responsive disassembly can lead to the controlled release of the encapsulated molecules. The construction of coacervates composed of an oligo(ethylene glycol) derivative bearing benzyl sulfide groups is presented. The obtained liquid-like coacervates (droplets) can undergo oxidation-responsive disassembly through the conversion of the sulfide groups to the sulfoxide groups. Moreover, the coacervates selectively encapsulate hydrophobic molecules; therefore, oxidation-responsive disassembly can lead to the controlled release of the encapsulated molecules.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 8","pages":"941-947"},"PeriodicalIF":2.7,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41428-025-01038-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The development of environmentally sustainable preparation methods is crucial for developing coatings that combine high mechanical strength with superior antifouling properties. Herein, a dual-repellent coating (PKF-SiO2) was fabricated through an epoxy ring-opening reaction in an aqueous environment using γ-glycidoxypropyltrimethoxysilane (KH560), nanosilica (SiO2), and 1H,1H,2H,2H-perfluorodecyltrimethoxysilane (PFAS) as raw materials. The resulting PKF-SiO2 coating exhibited exceptional mechanical robustness and antifouling properties. Remarkably, liquids such as n-hexadecane, soybean oil, and glycerin showed no adhesion to the coating surface even after being subjected to 1000 cycles of friction or bending tests. Anti-icing evaluations further demonstrated that the ice adhesion pressure on the PKF-SiO2 coating was reduced to 17 kPa, whereas the freezing time of the water droplets was extended to 1167 s, representing a 9-min delay compared with that of the bare substrate. These findings underscore the promising potential of the PKF-SiO2 coating for enhancing antifouling and self-cleaning protection in diverse fields, such as textiles and construction. γ-glycidoxypropyltrimethoxysilane was used as a bridge between hydrophobic particles and polyurethane to prepare dual-repellent coating in aqueous environment. This coating demonstrates superior mechanical strength, antifouling properties, and self-cleaning capabilities. In comparison to the uncoated substrate, the amphiphobic coating exhibited a 9-minute delay in freezing time and a reduced adhesion strength of 17 kPa. These results highlight the promising potential of the PKF-SiO2 coating for enhancing antifouling and self-cleaning functionalities in various applications, including textiles and construction
{"title":"Durable dual-repellent coatings with anti-fouling and anti-icing performance","authors":"Shuyang Xing, Xin Wang, Wei Kuang, Xinyu Wang, Huilin Tian, Jianhan Huang, Ruiyi Luo","doi":"10.1038/s41428-025-01034-8","DOIUrl":"10.1038/s41428-025-01034-8","url":null,"abstract":"The development of environmentally sustainable preparation methods is crucial for developing coatings that combine high mechanical strength with superior antifouling properties. Herein, a dual-repellent coating (PKF-SiO2) was fabricated through an epoxy ring-opening reaction in an aqueous environment using γ-glycidoxypropyltrimethoxysilane (KH560), nanosilica (SiO2), and 1H,1H,2H,2H-perfluorodecyltrimethoxysilane (PFAS) as raw materials. The resulting PKF-SiO2 coating exhibited exceptional mechanical robustness and antifouling properties. Remarkably, liquids such as n-hexadecane, soybean oil, and glycerin showed no adhesion to the coating surface even after being subjected to 1000 cycles of friction or bending tests. Anti-icing evaluations further demonstrated that the ice adhesion pressure on the PKF-SiO2 coating was reduced to 17 kPa, whereas the freezing time of the water droplets was extended to 1167 s, representing a 9-min delay compared with that of the bare substrate. These findings underscore the promising potential of the PKF-SiO2 coating for enhancing antifouling and self-cleaning protection in diverse fields, such as textiles and construction. γ-glycidoxypropyltrimethoxysilane was used as a bridge between hydrophobic particles and polyurethane to prepare dual-repellent coating in aqueous environment. This coating demonstrates superior mechanical strength, antifouling properties, and self-cleaning capabilities. In comparison to the uncoated substrate, the amphiphobic coating exhibited a 9-minute delay in freezing time and a reduced adhesion strength of 17 kPa. These results highlight the promising potential of the PKF-SiO2 coating for enhancing antifouling and self-cleaning functionalities in various applications, including textiles and construction","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 9","pages":"1003-1013"},"PeriodicalIF":2.7,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144990813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-24DOI: 10.1038/s41428-025-01039-3
Lisa Zeußel, Hendrik Bargel, Gregory P. Holland, Thomas Scheibel
Liquid‒liquid phase separation (LLPS) is a phenomenon relevant in the multicomponent settings of many biological processes, including compartmentation, pathological conditions such as Alzheimer’s disease, and protein assembly. LLPS also plays a key role in spider silk fiber formation. Many spider silk fibers display properties such as elasticity in combination with high mechanical strength, which result in an outstanding toughness exceeding that of steel or Kevlar. A thorough understanding of the natural silk spinning process is thus vital for translation to artificial spinning techniques to achieve biomimetic fibers with properties superior to those of other fibrous materials. This focus review summarizes the milestones of research on spider silk assembly, starting from two initial theories, i.e., the liquid crystal theory and the micelle theory, followed by evidence for the importance of LLPS in this process. Ex vivo studies and experiments utilizing recombinant spider silk proteins have highlighted the importance of LLPS during spider silk assembly. Here, we provide a consolidated view of the previously separate theories as a concerted, transitional concept, and describe practical implications showcasing the importance of this unifying concept for technical silk spinning. The process of spider silk assembly is a concerted, transitional process that combines liquid‒liquid phase separation (LLPS), liquid‒crystal (LC) and liquid‒solid phase separation (LSP), yielding fibers with outstanding mechanical properties. Spider silk proteins form micelle-like assemblies that undergo LLPS to form larger droplets, which are highly relevant for preorientation and permit intra- and intermolecular interactions, leading to a dimerized protein network and a nematic crystal phase of β-sheet-rich nanofibrils. The final solid fiber is drawn via LSP.
{"title":"Liquid‒liquid phase separation of spider silk proteins","authors":"Lisa Zeußel, Hendrik Bargel, Gregory P. Holland, Thomas Scheibel","doi":"10.1038/s41428-025-01039-3","DOIUrl":"10.1038/s41428-025-01039-3","url":null,"abstract":"Liquid‒liquid phase separation (LLPS) is a phenomenon relevant in the multicomponent settings of many biological processes, including compartmentation, pathological conditions such as Alzheimer’s disease, and protein assembly. LLPS also plays a key role in spider silk fiber formation. Many spider silk fibers display properties such as elasticity in combination with high mechanical strength, which result in an outstanding toughness exceeding that of steel or Kevlar. A thorough understanding of the natural silk spinning process is thus vital for translation to artificial spinning techniques to achieve biomimetic fibers with properties superior to those of other fibrous materials. This focus review summarizes the milestones of research on spider silk assembly, starting from two initial theories, i.e., the liquid crystal theory and the micelle theory, followed by evidence for the importance of LLPS in this process. Ex vivo studies and experiments utilizing recombinant spider silk proteins have highlighted the importance of LLPS during spider silk assembly. Here, we provide a consolidated view of the previously separate theories as a concerted, transitional concept, and describe practical implications showcasing the importance of this unifying concept for technical silk spinning. The process of spider silk assembly is a concerted, transitional process that combines liquid‒liquid phase separation (LLPS), liquid‒crystal (LC) and liquid‒solid phase separation (LSP), yielding fibers with outstanding mechanical properties. Spider silk proteins form micelle-like assemblies that undergo LLPS to form larger droplets, which are highly relevant for preorientation and permit intra- and intermolecular interactions, leading to a dimerized protein network and a nematic crystal phase of β-sheet-rich nanofibrils. The final solid fiber is drawn via LSP.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 8","pages":"831-843"},"PeriodicalIF":2.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41428-025-01039-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this study, we developed two types of lattice-type β-cyclodextrin (β-CyD)-containing spherical hydrogels to immobilize phenol (PhOH)-degrading bacteria. One type, ENTG-mix-βCyD/HDI, consists of mixed-type spherical hydrogels containing β-CyD ring-bearing polymer microparticles embedded within the gel matrix. The other type, ENTG-co-PSβCyD, consists of copolymerized spherical hydrogels in which β-CyD-substituted monomers are copolymerized and crosslinked. The former features an aggregated distribution of β-CyD rings, whereas the latter exhibits a uniform distribution. Continuous PhOH degradation experiments revealed that both of the β-CyD-containing spherical hydrogel catalysts exhibited catalytic activity exceeding that of the ENTG spherical catalyst without β-CyD. Immobilized bacteria were distributed both on the surface and within the structure of the copolymerized carrier, whereas in the mixed carrier, many bacteria were dispersed throughout. Analysis of the PhOH-degrading flora revealed that Pseudomonas putida formed a niche in the copolymerized hydrogels, whereas Sphingomonas sp. formed a niche in the mixed hydrogels. Batch experiments using p-xylene instead of PhOH demonstrated that the degradation rates of the copolymerized and mixed gels were 2.4 times and 1.6 times greater than that of the ENTG gel, respectively. The copolymerized gel exhibited a faster p-xylene degradation rate due to the reactivity of P. putida. Continuous phenol (PhOH) decomposition experiments were carried out with PhOH-degrading bacteria immobilized in a copolymerized spherical hydrogel (ENTG-co-PSβCyD) and a mixed spherical hydrogel (ENTG-mix-βCyD/HDI). Similar to the results obtained from the batch PhOH degradation experiments, both β-CyD-containing spherical hydrogels, which feature cylindrical hydrophobic intramolecular spaces, exhibited higher activity than the ENTG spherical hydrogels lacking β-CyD. The bacterial cells were extensively distributed on the surface and inside the copolymerized carrier and throughout the entire mixed carrier, while only a small amount of bacteria were found on the surface of the ENTG carrier. Furthermore, the PhOH-degrading bacterial flora (microflora) in the copolymerized and mixed spherical gel matrices were identified. Pseudomonas putida formed a niche in the copolymerized spherical hydrogel, and Sphingomonas sp. formed a niche in the mixed hydrogel. In the continuous PhOH degradation experiment, the performance of both hydrogels was almost identical because the ability of both strains to degrade PhOH is similar. However, in the batch removal experiment using p-xylene as the substrate instead of PhOH, the rates of substrate removal by the copolymerized gel and mixed gel 2.4 times and 1.6 times greater than that of the ENTG gel, respectively. This occurred because the bacterial species in the mixed gel was Sphingomonas sp. instead of P. putida, and the high substrate removal by the copolymerized gel was a result of the high r
{"title":"Effects of β-Cyclodextrin Introduced by Different Methods on the Immobilized Phenol-Degrading Bacteria in Photocrosslinked Spherical Hydrogels","authors":"Hirohito Yamasaki, Yasu-yuki Nagasawa, Narumi Uchida, Taiji Ito, Kimitoshi Fukunaga","doi":"10.1038/s41428-025-01032-w","DOIUrl":"10.1038/s41428-025-01032-w","url":null,"abstract":"In this study, we developed two types of lattice-type β-cyclodextrin (β-CyD)-containing spherical hydrogels to immobilize phenol (PhOH)-degrading bacteria. One type, ENTG-mix-βCyD/HDI, consists of mixed-type spherical hydrogels containing β-CyD ring-bearing polymer microparticles embedded within the gel matrix. The other type, ENTG-co-PSβCyD, consists of copolymerized spherical hydrogels in which β-CyD-substituted monomers are copolymerized and crosslinked. The former features an aggregated distribution of β-CyD rings, whereas the latter exhibits a uniform distribution. Continuous PhOH degradation experiments revealed that both of the β-CyD-containing spherical hydrogel catalysts exhibited catalytic activity exceeding that of the ENTG spherical catalyst without β-CyD. Immobilized bacteria were distributed both on the surface and within the structure of the copolymerized carrier, whereas in the mixed carrier, many bacteria were dispersed throughout. Analysis of the PhOH-degrading flora revealed that Pseudomonas putida formed a niche in the copolymerized hydrogels, whereas Sphingomonas sp. formed a niche in the mixed hydrogels. Batch experiments using p-xylene instead of PhOH demonstrated that the degradation rates of the copolymerized and mixed gels were 2.4 times and 1.6 times greater than that of the ENTG gel, respectively. The copolymerized gel exhibited a faster p-xylene degradation rate due to the reactivity of P. putida. Continuous phenol (PhOH) decomposition experiments were carried out with PhOH-degrading bacteria immobilized in a copolymerized spherical hydrogel (ENTG-co-PSβCyD) and a mixed spherical hydrogel (ENTG-mix-βCyD/HDI). Similar to the results obtained from the batch PhOH degradation experiments, both β-CyD-containing spherical hydrogels, which feature cylindrical hydrophobic intramolecular spaces, exhibited higher activity than the ENTG spherical hydrogels lacking β-CyD. The bacterial cells were extensively distributed on the surface and inside the copolymerized carrier and throughout the entire mixed carrier, while only a small amount of bacteria were found on the surface of the ENTG carrier. Furthermore, the PhOH-degrading bacterial flora (microflora) in the copolymerized and mixed spherical gel matrices were identified. Pseudomonas putida formed a niche in the copolymerized spherical hydrogel, and Sphingomonas sp. formed a niche in the mixed hydrogel. In the continuous PhOH degradation experiment, the performance of both hydrogels was almost identical because the ability of both strains to degrade PhOH is similar. However, in the batch removal experiment using p-xylene as the substrate instead of PhOH, the rates of substrate removal by the copolymerized gel and mixed gel 2.4 times and 1.6 times greater than that of the ENTG gel, respectively. This occurred because the bacterial species in the mixed gel was Sphingomonas sp. instead of P. putida, and the high substrate removal by the copolymerized gel was a result of the high r","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 9","pages":"949-958"},"PeriodicalIF":2.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144990844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-23DOI: 10.1038/s41428-025-01035-7
Yuichi Shichino, Shintaro Iwasaki
Ribonucleoprotein (RNP) granules—membraneless organelles formed through the condensation of RNA and proteins—play pivotal roles in diverse biological processes and diseases, opening new directions in molecular biology. Identifying the RNA composition of these granules is crucial for understanding their formation and functions. However, conventional approaches based on the simple immunoprecipitation of specific granule markers struggle to capture the precise nature of RNP granules. This review summarizes recent advances in granule transcriptome analysis, including the use of purification strategies, such as centrifugation and fluorescence-activated particle sorting, as well as proximity labeling techniques, which may help to increase the understanding of RNP granule biology. Ribonucleoprotein (RNP) granules are membraneless organelles formed through the condensation of RNA and proteins, which serve critical functions in diverse biological processes and disease contexts. Identifying their RNA composition is vital for understanding their molecular functions and mechanisms of formation, yet conventional approaches often fail to fully capture the complexity of these granules. This review highlights recent advances in transcriptome profiling of RNP granules using biochemical purification and proximity labeling, offering new insights into their molecular roles.
{"title":"Expanding toolkit for RNP granule transcriptomics","authors":"Yuichi Shichino, Shintaro Iwasaki","doi":"10.1038/s41428-025-01035-7","DOIUrl":"10.1038/s41428-025-01035-7","url":null,"abstract":"Ribonucleoprotein (RNP) granules—membraneless organelles formed through the condensation of RNA and proteins—play pivotal roles in diverse biological processes and diseases, opening new directions in molecular biology. Identifying the RNA composition of these granules is crucial for understanding their formation and functions. However, conventional approaches based on the simple immunoprecipitation of specific granule markers struggle to capture the precise nature of RNP granules. This review summarizes recent advances in granule transcriptome analysis, including the use of purification strategies, such as centrifugation and fluorescence-activated particle sorting, as well as proximity labeling techniques, which may help to increase the understanding of RNP granule biology. Ribonucleoprotein (RNP) granules are membraneless organelles formed through the condensation of RNA and proteins, which serve critical functions in diverse biological processes and disease contexts. Identifying their RNA composition is vital for understanding their molecular functions and mechanisms of formation, yet conventional approaches often fail to fully capture the complexity of these granules. This review highlights recent advances in transcriptome profiling of RNP granules using biochemical purification and proximity labeling, offering new insights into their molecular roles.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 8","pages":"873-883"},"PeriodicalIF":2.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41428-025-01035-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-23DOI: 10.1038/s41428-025-01036-6
Sefan Asamitsu, Yuka W. Iwasaki
Liquid‒liquid phase separation (LLPS) is a fundamental physical phenomenon in which a homogenous liquid spontaneously demixes into distinct liquid phases. A mounting body of evidence has shown that biomolecular LLPS is an essential biological event. In particular, highly condensed environments such as the nucleus are inevitably influenced by biomolecular LLPS, in which extremely long biopolymers, including genomic DNA and associated proteins/RNAs, are present. Given that almost half of the human genome is composed of repetitive elements and that various proteins interact with these sequences in diverse biological contexts, these regions clearly play substantial roles in regulating biomolecular LLPS. In this review, we summarize examples of biomolecular LLPS occurring in repetitive genomic elements. We also discuss how these intrinsic biophysical properties reflect cellular phenotypes by describing intermediate pathways and biomolecular complexes. Biomolecular liquid‒liquid phase separation (LLPS) is a critical process shaping cellular organization, particularly within the densely packed environment of the nucleus. Repetitive genomic elements, constituting nearly half of the human genome, play a pivotal role in regulating LLPS through interactions with associated proteins and RNAs. These sequences act as dynamic platforms for phase separation, influencing nuclear architecture and cellular phenotypes. This review highlights instances of LLPS formation within repetitive elements and explores their contributions to intermediate pathways and biomolecular complexes.
{"title":"Biomolecular liquid‒liquid phase separation associated with repetitive genomic elements","authors":"Sefan Asamitsu, Yuka W. Iwasaki","doi":"10.1038/s41428-025-01036-6","DOIUrl":"10.1038/s41428-025-01036-6","url":null,"abstract":"Liquid‒liquid phase separation (LLPS) is a fundamental physical phenomenon in which a homogenous liquid spontaneously demixes into distinct liquid phases. A mounting body of evidence has shown that biomolecular LLPS is an essential biological event. In particular, highly condensed environments such as the nucleus are inevitably influenced by biomolecular LLPS, in which extremely long biopolymers, including genomic DNA and associated proteins/RNAs, are present. Given that almost half of the human genome is composed of repetitive elements and that various proteins interact with these sequences in diverse biological contexts, these regions clearly play substantial roles in regulating biomolecular LLPS. In this review, we summarize examples of biomolecular LLPS occurring in repetitive genomic elements. We also discuss how these intrinsic biophysical properties reflect cellular phenotypes by describing intermediate pathways and biomolecular complexes. Biomolecular liquid‒liquid phase separation (LLPS) is a critical process shaping cellular organization, particularly within the densely packed environment of the nucleus. Repetitive genomic elements, constituting nearly half of the human genome, play a pivotal role in regulating LLPS through interactions with associated proteins and RNAs. These sequences act as dynamic platforms for phase separation, influencing nuclear architecture and cellular phenotypes. This review highlights instances of LLPS formation within repetitive elements and explores their contributions to intermediate pathways and biomolecular complexes.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 8","pages":"785-797"},"PeriodicalIF":2.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41428-025-01036-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this study, the crystallization kinetics of 1-butene (B-PE) and 1-hexene (H-PE) polyethylene copolymers with varying comonomer contents are investigated, and an in-depth understanding of how chain branching impacts the crystal growth and nucleation is provided. By performing differential scanning calorimetry (DSC), we discern a distinctly slower crystallization rate for B-PEs than for H-PEs at equivalent comonomer contents. In-situ isothermal crystallization with wide-angle X-ray diffraction (WAXD) measurements demonstrates the delayed emergence of the (200) crystallite plane () in the B-PEs, indicating slower lamellar width expansion. Small-angle light scattering (SALS) analysis of the spherulite formation during isothermal crystallization confirms that B-PEs exhibit both a lower spherulite growth rate and nucleation density. These results are likely attributed to the preferential inclusion of 1-butene in the PE crystal, thereby amplifying the crystallization disturbance in the B-PEs. Furthermore, to elucidate these observations, we experimentally determine the thermodynamic parameters. Remarkably, the values of the free energy of the lamellar folded surface (σf) for B-PEs are significantly greater than those of H-PEs. This discrepancy potentially stems from the higher surface entropy because of the denser excluded 1-hexene comonomers on the lamellar folded surface. The lower σf value causes a reduction in the free energy barrier for critical nucleus formation; thus, this facilitates the preferential nucleation and accelerated lamellar development in H-PEs than in B-PEs. Crystallization kinetics of high-density polyethylene copolymers containing 1-butene and 1-hexene were investigated using differential scanning calorimetry (DSC), in-situ wide-angle X-ray diffraction (WAXD), and in-situ small-angle light scattering (SALS). Compared to 1-hexene copolymers, 1-butene copolymers exhibit slower isothermal crystallization, reduced spherulite growth, and higher lamellar surface free energy (σf), highlighting the pronounced impact of comonomer type on nucleation thermodynamics and lamellar development.
{"title":"Influences of the comonomer type on the crystallization kinetics of high-density polyethylene","authors":"Wonchalerm Rungswang, Chatchai Jarumaneeroj, Bharanabha Makkaroon, Manutsavin Charernsuk, Rossarin Duekunthod, Nattapinya Nakawong, Siriwat Soontaranon, Supagorn Rugmai","doi":"10.1038/s41428-025-01033-9","DOIUrl":"10.1038/s41428-025-01033-9","url":null,"abstract":"In this study, the crystallization kinetics of 1-butene (B-PE) and 1-hexene (H-PE) polyethylene copolymers with varying comonomer contents are investigated, and an in-depth understanding of how chain branching impacts the crystal growth and nucleation is provided. By performing differential scanning calorimetry (DSC), we discern a distinctly slower crystallization rate for B-PEs than for H-PEs at equivalent comonomer contents. In-situ isothermal crystallization with wide-angle X-ray diffraction (WAXD) measurements demonstrates the delayed emergence of the (200) crystallite plane () in the B-PEs, indicating slower lamellar width expansion. Small-angle light scattering (SALS) analysis of the spherulite formation during isothermal crystallization confirms that B-PEs exhibit both a lower spherulite growth rate and nucleation density. These results are likely attributed to the preferential inclusion of 1-butene in the PE crystal, thereby amplifying the crystallization disturbance in the B-PEs. Furthermore, to elucidate these observations, we experimentally determine the thermodynamic parameters. Remarkably, the values of the free energy of the lamellar folded surface (σf) for B-PEs are significantly greater than those of H-PEs. This discrepancy potentially stems from the higher surface entropy because of the denser excluded 1-hexene comonomers on the lamellar folded surface. The lower σf value causes a reduction in the free energy barrier for critical nucleus formation; thus, this facilitates the preferential nucleation and accelerated lamellar development in H-PEs than in B-PEs. Crystallization kinetics of high-density polyethylene copolymers containing 1-butene and 1-hexene were investigated using differential scanning calorimetry (DSC), in-situ wide-angle X-ray diffraction (WAXD), and in-situ small-angle light scattering (SALS). Compared to 1-hexene copolymers, 1-butene copolymers exhibit slower isothermal crystallization, reduced spherulite growth, and higher lamellar surface free energy (σf), highlighting the pronounced impact of comonomer type on nucleation thermodynamics and lamellar development.","PeriodicalId":20302,"journal":{"name":"Polymer Journal","volume":"57 7","pages":"711-722"},"PeriodicalIF":2.3,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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