Biomacromolecules最新文献

{"title":"Accelerated Missense Mutation Identification in Intrinsically Disordered Proteins Using Deep Learning.","authors":"Swarnadeep Seth, Aniket Bhattacharya","doi":"10.1021/acs.biomac.4c01124","DOIUrl":"https://doi.org/10.1021/acs.biomac.4c01124","url":null,"abstract":"<p><p>We use a combination of Brownian dynamics (BD) simulation results and deep learning (DL) strategies for the rapid identification of large structural changes caused by missense mutations in intrinsically disordered proteins (IDPs). We used ∼6500 IDP sequences from MobiDB database of length 20-300 to obtain gyration radii from BD simulation on a coarse-grained single-bead amino acid model (HPS2 model) used by us and others [Dignon, G. L. <i>PLoS Comput. Biol.</i> 2018, 14, e1005941,Tesei, G. <i>Proc. Natl. Acad. Sci. U.S.A.</i> 2021, 118, e2111696118,Seth, S. <i>J. Chem. Phys.</i> 2024, 160, 014902] to generate the training sets for the DL algorithm. Using the gyration radii ⟨<i>R</i>_g⟩ of the simulated IDPs as the training set, we develop a multilayer perceptron neural net (NN) architecture that predicts the gyration radii of 33 IDPs previously studied by using BD simulation with 97% accuracy from the sequence and the corresponding parameters from the HPS model. We now utilize this NN to predict gyration radii of every permutation of missense mutations in IDPs. Our approach successfully identifies mutation-prone regions that induce significant alterations in the radius of gyration when compared to the wild-type IDP sequence. We further validate the prediction by running BD simulations on the subset of identified mutants. The neural network yields a (10⁴-10⁶)-fold faster computation in the search space for potentially harmful mutations. Our findings have substantial implications for rapid identification and understanding of diseases related to missense mutations in IDPs and for the development of potential therapeutic interventions. The method can be extended to accurate predictions of other mutation effects in disordered proteins.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accelerated Missense Mutation Identification in Intrinsically Disordered Proteins Using Deep Learning","authors":"Swarnadeep Seth,&nbsp; and ,&nbsp;Aniket Bhattacharya*,&nbsp;","doi":"10.1021/acs.biomac.4c0112410.1021/acs.biomac.4c01124","DOIUrl":"https://doi.org/10.1021/acs.biomac.4c01124https://doi.org/10.1021/acs.biomac.4c01124","url":null,"abstract":"<p >We use a combination of Brownian dynamics (BD) simulation results and deep learning (DL) strategies for the rapid identification of large structural changes caused by missense mutations in intrinsically disordered proteins (IDPs). We used ∼6500 IDP sequences from MobiDB database of length 20–300 to obtain gyration radii from BD simulation on a coarse-grained single-bead amino acid model (HPS2 model) used by us and others [<contrib-group><span>Dignon, G. L.</span></contrib-group> <cite><i>PLoS Comput. Biol.</i></cite> <span>2018</span>, <em>14</em>, <elocation-id>e1005941</elocation-id>,<contrib-group><span>Tesei, G.</span></contrib-group> <cite><i>Proc. Natl. Acad. Sci. U.S.A.</i></cite> <span>2021</span>, <em>118</em>, <elocation-id>e2111696118</elocation-id>,<contrib-group><span>Seth, S.</span></contrib-group> <cite><i>J. Chem. Phys.</i></cite> <span>2024</span>, <em>160</em>, <elocation-id>014902</elocation-id>] to generate the training sets for the DL algorithm. Using the gyration radii ⟨<i>R</i>_g⟩ of the simulated IDPs as the training set, we develop a multilayer perceptron neural net (NN) architecture that predicts the gyration radii of 33 IDPs previously studied by using BD simulation with 97% accuracy from the sequence and the corresponding parameters from the HPS model. We now utilize this NN to predict gyration radii of every permutation of missense mutations in IDPs. Our approach successfully identifies mutation-prone regions that induce significant alterations in the radius of gyration when compared to the wild-type IDP sequence. We further validate the prediction by running BD simulations on the subset of identified mutants. The neural network yields a (10⁴–10⁶)-fold faster computation in the search space for potentially harmful mutations. Our findings have substantial implications for rapid identification and understanding of diseases related to missense mutations in IDPs and for the development of potential therapeutic interventions. The method can be extended to accurate predictions of other mutation effects in disordered proteins.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":"26 4","pages":"2106–2115 2106–2115"},"PeriodicalIF":5.5,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143825142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fabrication of pH- and Ultrasound-Responsive Polymeric Micelles: The Effect of Amphiphilic Block Copolymers with Different Hydrophilic/Hydrophobic Block Ratios for Self-Assembly and Controlled Drug Release","authors":"Hong-Xiang Wei,&nbsp;Ming-Hsin Liu,&nbsp;Tzu-Ying Wang,&nbsp;Meng-Hsiu Shih,&nbsp;Jiashing Yu* and Yi-Cheun Yeh*,&nbsp;","doi":"10.1021/acs.biomac.4c0120210.1021/acs.biomac.4c01202","DOIUrl":"https://doi.org/10.1021/acs.biomac.4c01202https://doi.org/10.1021/acs.biomac.4c01202","url":null,"abstract":"<p >Stimuli-responsive polymeric vehicles can change their physical or chemical properties when exposed to internal or external triggers, enabling precise spatiotemporal control of drug release. Nevertheless, systematic research is lacking in preparing dual stimuli-responsive amphiphilic block copolymers with different hydrophilic/hydrophobic block ratios in forming self-assembled structures. Here, we synthesized two types of block copolymers consisting of the hydrophobic segments (i.e., pH-responsive 2-(diethylamino)ethyl methacrylate (DEA) and ultrasound-responsive 2-methoxyethyl methacrylate (MEMA)) and hydrophilic poly(ethylene glycol) methyl ether (mPEG) segments, forming mPEG_X-<i>b</i>-P(DEA_Y-<i>co</i>-MEMA_Z). These amphiphilic block copolymers can self-assemble to form polymeric micelles, and their structures (e.g., size) and properties (e.g., critical vesicle concentration, stability, stimuli-responsiveness to pH and ultrasound, drug loading efficiency, and controlled drug release performance) were thoroughly investigated. <i>In vitro</i> cell studies further demonstrate that ultrasound can efficiently trigger drug release from polymeric micelles, emphasizing their potential for controlled drug delivery in therapeutic applications.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":"26 4","pages":"2116–2130 2116–2130"},"PeriodicalIF":5.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.biomac.4c01202","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143825139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fabrication of pH- and Ultrasound-Responsive Polymeric Micelles: The Effect of Amphiphilic Block Copolymers with Different Hydrophilic/Hydrophobic Block Ratios for Self-Assembly and Controlled Drug Release.","authors":"Hong-Xiang Wei, Ming-Hsin Liu, Tzu-Ying Wang, Meng-Hsiu Shih, Jiashing Yu, Yi-Cheun Yeh","doi":"10.1021/acs.biomac.4c01202","DOIUrl":"https://doi.org/10.1021/acs.biomac.4c01202","url":null,"abstract":"<p><p>Stimuli-responsive polymeric vehicles can change their physical or chemical properties when exposed to internal or external triggers, enabling precise spatiotemporal control of drug release. Nevertheless, systematic research is lacking in preparing dual stimuli-responsive amphiphilic block copolymers with different hydrophilic/hydrophobic block ratios in forming self-assembled structures. Here, we synthesized two types of block copolymers consisting of the hydrophobic segments (i.e., pH-responsive 2-(diethylamino)ethyl methacrylate (DEA) and ultrasound-responsive 2-methoxyethyl methacrylate (MEMA)) and hydrophilic poly(ethylene glycol) methyl ether (mPEG) segments, forming mPEG_X-<i>b</i>-P(DEA_Y-<i>co</i>-MEMA_Z). These amphiphilic block copolymers can self-assemble to form polymeric micelles, and their structures (e.g., size) and properties (e.g., critical vesicle concentration, stability, stimuli-responsiveness to pH and ultrasound, drug loading efficiency, and controlled drug release performance) were thoroughly investigated. <i>In vitro</i> cell studies further demonstrate that ultrasound can efficiently trigger drug release from polymeric micelles, emphasizing their potential for controlled drug delivery in therapeutic applications.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface-Vinylated Cellulose Nanocrystals as Cross-Linkers for Hydrogel Composites","authors":"Marcel Kröger,&nbsp;Timo Pääkkönen,&nbsp;Lukas Fliri,&nbsp;Anna F. Lehrhofer,&nbsp;Irina Sulaeva,&nbsp;Antje Potthast and Eero Kontturi*,&nbsp;","doi":"10.1021/acs.biomac.4c0161910.1021/acs.biomac.4c01619","DOIUrl":"https://doi.org/10.1021/acs.biomac.4c01619https://doi.org/10.1021/acs.biomac.4c01619","url":null,"abstract":"<p >Cellulose nanocrystal (CNC) fillers have been shown to significantly improve the performance of polymer composites and hydrogels, elevating both strength and toughness. Polymer grafting from the surface of the nanocrystals has been employed to enhance matrix–filler interactions and keep the fillers dispersed within the matrix. However, such approaches often rely on multistep syntheses and diligent process control. Here, we propose modifying the nanocrystal surface to carry vinyl moieties, turning the particles into cross-linking comonomers. Using allyl glycidyl ether in an aqueous modification route, we were able to decorate the CNCs with varying amounts of vinyl moieties. Subsequent dispersion in 2-hydroxy methacrylate and thermally initiated free radical polymerization yielded composite materials that showed superior mechanical performance compared to those obtained from monomeric cross-linkers and unmodified CNCs. The large discrepancies in the observed glass transition temperatures of the obtained materials suggest, however, that the impact of the fillers on the polymerization kinetics is significant and less easily explained.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":"26 4","pages":"2282–2292 2282–2292"},"PeriodicalIF":5.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.biomac.4c01619","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143825136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface-Vinylated Cellulose Nanocrystals as Cross-Linkers for Hydrogel Composites.","authors":"Marcel Kröger, Timo Pääkkönen, Lukas Fliri, Anna F Lehrhofer, Irina Sulaeva, Antje Potthast, Eero Kontturi","doi":"10.1021/acs.biomac.4c01619","DOIUrl":"https://doi.org/10.1021/acs.biomac.4c01619","url":null,"abstract":"<p><p>Cellulose nanocrystal (CNC) fillers have been shown to significantly improve the performance of polymer composites and hydrogels, elevating both strength and toughness. Polymer grafting from the surface of the nanocrystals has been employed to enhance matrix-filler interactions and keep the fillers dispersed within the matrix. However, such approaches often rely on multistep syntheses and diligent process control. Here, we propose modifying the nanocrystal surface to carry vinyl moieties, turning the particles into cross-linking comonomers. Using allyl glycidyl ether in an aqueous modification route, we were able to decorate the CNCs with varying amounts of vinyl moieties. Subsequent dispersion in 2-hydroxy methacrylate and thermally initiated free radical polymerization yielded composite materials that showed superior mechanical performance compared to those obtained from monomeric cross-linkers and unmodified CNCs. The large discrepancies in the observed glass transition temperatures of the obtained materials suggest, however, that the impact of the fillers on the polymerization kinetics is significant and less easily explained.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-Molecule Imaging of Wood Xylans on Surfaces and Their Interaction with GH11 Xylanase.","authors":"Jana B Schaubeder, Christian Ganser, Chonnipa Palasingh, Manuel Eibinger, Tiina Nypelö, Takayuki Uchihashi, Stefan Spirk","doi":"10.1021/acs.biomac.4c01446","DOIUrl":"10.1021/acs.biomac.4c01446","url":null,"abstract":"<p><p>The knowledge of the molecular properties and arrangements of biopolymers in both solid and solution state are essential in the design of sustainable materials and biomedicine as they are decisive for mechanical strength, flexibility, and biodegradability. However, the structure of most biopolymers at charged interfaces can vary considerably, and their time-dependent visualization in liquid-state still remains challenging. In this work, we employed high-speed atomic force microscopy (HS-AFM) to visualize single xylan macromolecules from alkali-extracted birch and beechwood. On negatively charged mica surfaces, they appeared as individual macromolecules but assembled into aggregates on 3-aminopropyltriethoxysilane (APTES) surfaces (AP-mica). Hence, we further investigated the susceptibility to enzymatic degradation using an endoxylanase, which showed that the individual xylan macromolecules remained intact, while larger assemblies on AP-mica degraded over time. We demonstrate that HS-AFM is a powerful tool for understanding the molecular properties and degradation mechanisms of biopolymers. Moreover, by identifying alignment-dependent binding sites, strategies can be developed to ensure the biodegradability of composite materials by intelligent interface design.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":"1639-1646"},"PeriodicalIF":5.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation Study of the Water Ordering Effect of the β-(1,3)-Glucan Callose Biopolymer.","authors":"Robinson Cortes-Huerto, Nancy C Forero-Martinez, Pietro Ballone","doi":"10.1021/acs.biomac.4c01524","DOIUrl":"10.1021/acs.biomac.4c01524","url":null,"abstract":"<p><p>Callose, a polysaccharide closely related to cellulose, plays a crucial role in plant development and resistance to environmental stress. These functions are often attributed to the enhancement by callose of the mechanical properties of semiordered assemblies of cellulose nanofibers. A recent study, however, suggested that the enhancement of mechanical properties by callose might be due to its ability to order neighboring water molecules, resulting in the formation, up to room temperature, of solid-like water-callose domains. This hypothesis is tested by atomistic molecular dynamics simulations using <i>ad hoc</i> models consisting of callose and cellulose hydrogels. The simulation results, however, do not show significant crystallinity in the callose/water samples. Moreover, the computation of the Young's modulus gives nearly the same result in callose/water and in cellulose/water samples, leaving callose's ability to link cellulose nanofibers into networks as the most likely mechanism underlying the strengthening of the plant cell wall.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":"1748-1760"},"PeriodicalIF":5.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Poly(2-alkyl-2-oxazoline) Hydrogels as Synthetic Matrices for Multicellular Spheroid and Intestinal Organoid Cultures.","authors":"Robin Vanhoeijen, Irina A Okkelman, Nette Rogier, Tomáš Sedlačík, Daniel D Stöbener, Bert Devriendt, Ruslan I Dmitriev, Richard Hoogenboom","doi":"10.1021/acs.biomac.4c01627","DOIUrl":"10.1021/acs.biomac.4c01627","url":null,"abstract":"<p><p>The extracellular matrix (ECM) plays a crucial role in organoid cultures by supporting cell proliferation and differentiation. A key feature of the ECM is its mechanical influence on the surrounding cells, directly affecting their behavior. Matrigel, the most commonly used ECM, is limited by its animal-derived origin, batch variability, and uncontrollable mechanical properties, restricting its use in 3D cell-model-based mechanobiological studies. Poly(2-alkyl-2-oxazoline) (PAOx) synthetic hydrogels represent an appealing alternative because of their reproducibility and versatile chemistry, enabling tuning of hydrogel stiffness and functionalization. Here, we studied PAOx hydrogels with differing compressive moduli for their potential to support 3D cell growth. PAOx hydrogels support spheroid and organoid growth over several days without the addition of ECM components. Furthermore, we discovered intestinal organoid epithelial polarity reversion in PAOx hydrogels and demonstrate how the tunable mechanical properties of PAOx can be used to study effects on the morphology and oxygenation of live multicellular spheroids.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":"1860-1872"},"PeriodicalIF":5.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coral-Inspired Zinc Acrylate Polymer Utilizing Coumarin as the Fluorescent Unit for Marine Antifouling.","authors":"Jianwei Hou, Guobo Chen, Xinghai Hao, Jiali Xu, Geoffrey I N Waterhouse, Zhiming Zhang, Liangmin Yu","doi":"10.1021/acs.biomac.4c01574","DOIUrl":"10.1021/acs.biomac.4c01574","url":null,"abstract":"<p><p>The need for low-cost and effective antifouling solutions drives innovation in the fields of chemistry, materials science, and biology. In this work, guided by the antifouling strategies used by fluorescent corals, a series of fluorescent zinc acrylate polymer coatings containing coumarin units (ZAR-coumarin) was successfully prepared. The ZAR-coumarin coatings demonstrated excellent antifouling properties due to the synergistic action of multiple antifouling mechanisms, including fluorescent antifouling, natural bactericidal activity, and self-polishing surface renewal (due to ester group (-COO-Zn-OOC-) cleavage). Compared with zinc acrylate coatings without coumarin units (ZAR), the introduction of coumarin units significantly improved the inhibition efficiency for both bacteria and algae. In marine environment tests, the ZAR-AMCO-1, ZAR-ADMCO-1, and ZAR-CAMCO-1 coatings containing optimized amounts of different types of coumarin units maintained good antifouling properties over a 160-day field test period. This research presents an innovative approach to creating marine antifouling coatings.</p>","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":"1799-1815"},"PeriodicalIF":5.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}