Cell Reports Physical Science最新文献_第10页

A variational graph-partitioning approach to modeling protein liquid-liquid phase separation. 蛋白质液-液相分离模型的变分图划分方法。

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-20 DOI: 10.1016/j.xcrp.2024.102292

Gaoyuan Wang, Jonathan Warrell, Suchen Zheng, Mark Gerstein

{"title":"A variational graph-partitioning approach to modeling protein liquid-liquid phase separation.","authors":"Gaoyuan Wang, Jonathan Warrell, Suchen Zheng, Mark Gerstein","doi":"10.1016/j.xcrp.2024.102292","DOIUrl":"10.1016/j.xcrp.2024.102292","url":null,"abstract":"Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes from specific subgraphs. In this work, we introduce a GNN-based framework (graph-partitioned GNN [GP-GNN]) to partition the GNN graph to focus on the most relevant subgraphs. Our approach jointly learns task-dependent graph partitions and node representations, making it particularly effective when critical features reside within initially unidentified subgraphs. Protein liquid-liquid phase separation (LLPS) is a problem especially well-suited to GP-GNNs because intrinsically disordered regions (IDRs) are known to function as protein subdomains in it, playing a key role in the phase separation process. In this study, we demonstrate how GP-GNN accurately predicts LLPS by partitioning protein graphs into task-relevant subgraphs consistent with known IDRs. Our model achieves state-of-the-art accuracy in predicting LLPS and offers biological insights valuable for downstream investigation.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 11","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sequence-dependent conformational preferences of disordered single-stranded RNA. 无序单链RNA的序列依赖构象偏好。

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-20 Epub Date: 2024-10-29 DOI: 10.1016/j.xcrp.2024.102264

Tong Wang, Weiwei He, Suzette A Pabit, Lois Pollack, Serdal Kirmizialtin

{"title":"Sequence-dependent conformational preferences of disordered single-stranded RNA.","authors":"Tong Wang, Weiwei He, Suzette A Pabit, Lois Pollack, Serdal Kirmizialtin","doi":"10.1016/j.xcrp.2024.102264","DOIUrl":"10.1016/j.xcrp.2024.102264","url":null,"abstract":"Disordered single-stranded RNA (ssRNA) molecules, like their well-folded counterparts, have crucial functions that depend on their structures. However, since native ssRNAs constitute a highly heterogeneous conformer population, their structural characterization poses challenges. One important question regards the role of sequence in influencing ssRNA structure. Here, we adopt an integrated approach that combines solution-based measurements, including small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET), with experimentally guided all-atom molecular dynamics (MD) simulations, to construct structural ensembles of a 30-nucleotide RNA homopolymer (rU30) and a 30-nucleotide RNA heteropolymer with an A-/C-rich sequence. We compare the size, shape, and flexibility of the two different ssRNAs. While the average properties align with polymer-physics descriptions of flexible polymers, we discern distinct, sequence-dependent conformations at the molecular level that demand a more detailed representation than provided by polymer models. These findings emphasize the role of sequence in shaping the overall properties of ssRNA.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 11","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11671127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142892393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lignin as a bioderived modular surfactant and intercalant for Ti₃C₂T_x MXene stabilization and tunable functions. 木质素作为一种生物来源的模块化表面活性剂和插层剂，用于 Ti3C2Tx MXene 的稳定和可调功能。

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-20 DOI: 10.1016/j.xcrp.2024.102259

Pan Jiang, Xiaodan Hong, Jin Zhang, Jiali Sheng, Jiahui Kang, Olli Ikkala, Fuxiang Chu, Bo Peng, Yanming Han, Zhong-Peng Lv

{"title":"Lignin as a bioderived modular surfactant and intercalant for Ti3C2Tx MXene stabilization and tunable functions.","authors":"Pan Jiang, Xiaodan Hong, Jin Zhang, Jiali Sheng, Jiahui Kang, Olli Ikkala, Fuxiang Chu, Bo Peng, Yanming Han, Zhong-Peng Lv","doi":"10.1016/j.xcrp.2024.102259","DOIUrl":"10.1016/j.xcrp.2024.102259","url":null,"abstract":"Controlled tailoring of atomically thin MXene interlayer spacings by surfactant/intercalants (e.g., polymers, ligands, small molecules) is important to maximize their potential for application. However, challenges persist in achieving precise spacing tunability in a well-defined stacking, combining long-term stability and dispersibility in various solvents. Here, we discovered that lignin can be used as surfactants/intercalants of Ti3C2Tx MXenes. The resulting MXene@lignin complexes exhibit superior colloidal stability and oxidation resistance in both water and different organic solvents. More important, we reveal a dynamic interaction between MXene and lignin that enables a wide-range fine interlayer distance tuning at a sub-nanometer scale. Such dynamic interaction is sparse in the reported organic surfactants/intercalants containing single types of functional groups. We also demonstrate the tunability of electrical conductivity, infrared emissivity, and electromagnetic interference shielding effectiveness. Our approach offers a starting point to explore the potential of MXene-biomacromolecule composites for electronics and photonics applications.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 11","pages":"102259"},"PeriodicalIF":7.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Raising enzymatic stability during biocatalysis with hierarchically hollow two-dimensional MOF nanocapsules 用分层中空二维MOF纳米胶囊提高生物催化过程中的酶稳定性

2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-01 DOI: 10.1016/j.xcrp.2024.102285

Mengfan Mao, S.B. Liu, Xiaolong Zhong, Yue Lin, Cuiying Lin, Guoqing Hu, Kang Liang, Chuanhui Huang, Zhenyu Lin

引用次数: 6

Efficient mild depolymerization of polyester plastics accomplished by engineered PETase via directed evolution of flexible loops 通过柔性环的定向进化，工程PETase完成了聚酯塑料的高效温和解聚

2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-01 DOI: 10.1016/j.xcrp.2024.102295

Yidi Liu, Huanliu Lin, Zhisheng Wei, S. J. Bai, Sheng Chen, Jing Wu, Zhanzhi Liu

{"title":"Efficient mild depolymerization of polyester plastics accomplished by engineered PETase via directed evolution of flexible loops","authors":"Yidi Liu, Huanliu Lin, Zhisheng Wei, S. J. Bai, Sheng Chen, Jing Wu, Zhanzhi Liu","doi":"10.1016/j.xcrp.2024.102295","DOIUrl":"https://doi.org/10.1016/j.xcrp.2024.102295","url":null,"abstract":"<h2>Summary</h2> Due to inadequate disposal and recycling of polyethylene terephthalate (PET) plastic products, there has been growing concern about the severe environmental consequences. Biocatalytic degradation of PET has emerged as a promising solution. The PET hydrolase IsPETase from Ideonella sakaiensis exhibits distinctive substrate activity at mild temperatures, but its practical application is limited by restricted catalytic efficiency. In this study, the highly flexible loops of IsPETase are targeted for engineering after a detailed structural analysis. A customized dual-fluorescence high-throughput assay is then developed to facilitate the directed evolution of these selected loops in order to enhance IsPETase's catalytic performance, specifically at mild temperatures. Through implementation of this system, the evolved IsPETase mutant M4-Q demonstrates exceptional PET biodegradation activity at mild temperatures and advantages in degrading various aliphatic-aromatic copolyesters. These findings offer innovative insights into the enzymatic degradation of PET and other polyester plastic waste.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 11","pages":"102295-102295"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147898686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Thermostimulated shrinking and adhesive hydrogel dressing for treating chronic diabetic wounds 热刺激收缩和黏附水凝胶敷料治疗慢性糖尿病创面

2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-01 DOI: 10.1016/j.xcrp.2024.102289

Zhongwu Bei, Lin Ye, Qi Tong, Ming Yang, Tingyu Yang, Yuzhou Zhu, Linghong Zhang, Xicheng Li, Hanzhi Deng, Jie Liu, Wen Chen, Bingyang Chu, Zhiyong Qian

{"title":"Thermostimulated shrinking and adhesive hydrogel dressing for treating chronic diabetic wounds","authors":"Zhongwu Bei, Lin Ye, Qi Tong, Ming Yang, Tingyu Yang, Yuzhou Zhu, Linghong Zhang, Xicheng Li, Hanzhi Deng, Jie Liu, Wen Chen, Bingyang Chu, Zhiyong Qian","doi":"10.1016/j.xcrp.2024.102289","DOIUrl":"https://doi.org/10.1016/j.xcrp.2024.102289","url":null,"abstract":"<h2>Summary</h2> Localized hyperglycemia, chronic inflammation, and recurrent infections severely impair wound healing in diabetes. Traditional wound dressings that passively promote healing maintain wound moisture with only limited efficacy, while microbial infections further complicate the healing process. Herein, we develop a thermostimulated shrinking and adhesive hydrogel dressing for chronic wound healing composed of N-isopropylacrylamide (NIPAM), polyacrylic acid grafted with N-hydroxysuccinimide ester, dopamine-modified gelatin (GelDA), and silver-coated clay-tannic acid nanoparticles (Ag@Clay-TA), integrating properties such as tissue adhesion and antibacterial and antioxidant functions. Notably, it adheres to skin wounds, actively contracts the wound in response to skin temperature, and releases antibacterial nanoparticles. In vivo analyses confirm that this hydrogel effectively eliminates bacteria at the wound site, reduces inflammation and oxidative stress, and promotes rapid wound closure and healing. This hydrogel dressing shows promising potential in alleviating inflammation and accelerating wound closure in chronic wounds infected with methicillin-resistant Staphylococcus aureus (MRSA).","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 11","pages":"102289-102289"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147900528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 27

Harness-inspired and fully implantable electronic system for real-time urine volume monitoring 用于实时尿量监测的全植入式电子系统

2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-01 DOI: 10.1016/j.xcrp.2024.102281

Xinyu Shen, Yihua Zhong, Jie Han, Jing Wei, Bowen Yang, Jihan Wang, Yuxuan Zhang, Ruiran Li, Chunlin Li, Lixue Tang, Xu Zhang

引用次数: 4

A robust, storable, and controllable cold-set protein adhesive enabled by Pickering emulsion-templated microcapsules 一种坚固的，可储存的，可控的冷凝蛋白粘合剂，由皮克林乳液模板微胶囊实现

2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-11-01 DOI: 10.1016/j.xcrp.2024.102266

Zhiqiang Zhu, Menghan Li, Youhui Huang, Jiayi Zhang, Nairong Chen, Li Feng

{"title":"A robust, storable, and controllable cold-set protein adhesive enabled by Pickering emulsion-templated microcapsules","authors":"Zhiqiang Zhu, Menghan Li, Youhui Huang, Jiayi Zhang, Nairong Chen, Li Feng","doi":"10.1016/j.xcrp.2024.102266","DOIUrl":"https://doi.org/10.1016/j.xcrp.2024.102266","url":null,"abstract":"<h2>Summary</h2> Cold-set protein adhesives (CPAs) show great advantages in sustainability, eco-friendliness, and cost effectiveness but suffer from weak adhesion and poor storability as imposed by the difficulty in controlling molecular crosslinks. Here, we develop a robust, storable, and controllable CPA enabled by Pickering emulsion-templated microcapsules (PETMs). The PETMs are synthesized by leveraging highly reactive isocyanates as the core phase for cold-set adhesion, and cellulose nanofibers are densified by polyurea as a shell phase to present a responsive, adjustable, and stable nature. Also, inorganic magnesium oxide (MgO) binders are introduced to further strengthen CPA via MgO-protein complexation. Our design not only enables superior cold-set adhesion (0.98 MPa to wood) induced by pressure but also imparts the adhesive with much-improved storability (high-strength maintenance at inferior conditions). This strategy resolves the conflict between high reactivity and long storability in cold-set adhesion, offering a promising direction for the development of high-performance bio-based adhesives satisfying practical demands.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 11","pages":"102266-102266"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.cell.com/article/S266638642400571X/pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147889092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Flexible low dielectric permittivity paper as a disposable substrate for centimeter wave patch antennas 挠性低介电常数纸作为毫米波贴片天线的一次性衬底

2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-10-22 DOI: 10.1016/j.xcrp.2024.102253

Fukun Niu, Rong Yu, Yibo Zhang, Ru Song, Zhiwei Ye, Peifeng Zou, Chuanxi Xiong, Zhuqun Shi, Quanling Yang

{"title":"Flexible low dielectric permittivity paper as a disposable substrate for centimeter wave patch antennas","authors":"Fukun Niu, Rong Yu, Yibo Zhang, Ru Song, Zhiwei Ye, Peifeng Zou, Chuanxi Xiong, Zhuqun Shi, Quanling Yang","doi":"10.1016/j.xcrp.2024.102253","DOIUrl":"https://doi.org/10.1016/j.xcrp.2024.102253","url":null,"abstract":"<h2>Summary</h2> For mid-to-low-end and disposable wireless transmission devices, paper-based low dielectric substrates are cost-effective and environmentally friendly compared to traditional petroleum-based plastics such as polyimides. In this work, we introduce (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO)-mediated oxidation technology into commercial copy paper to achieve in situ growth of zeolitic imidazolate framework (ZIF-67) while increasing porosity. Through impregnation technology, ethyl cellulose and h-BN are combined to improve the water resistance (water contact angle: 122°), thermal conductivity (in-plane thermal conductivity: 13.55 W m−1 K−1), and antibacterial properties of the paper. The dielectric permittivity of modified paper is about 3, which exhibits excellent potential as a substrate for centimeter wave patch antennas. After verification, our developed paper oxidation technology is reliable and effective for various cellulose-based papers. This paper provides a low-cost and low-energy approach for the construction of cellulose-based porous structures, which promote the development and application of green materials and alleviate the serious global problem of electronic waste pollution.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 11","pages":"102253-102253"},"PeriodicalIF":0.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147905064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Amino acid-dependent phase equilibrium and material properties of tetrapeptide condensates. 四肽缩合物的氨基酸相平衡和材料特性。

IF 6.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-10-16 Epub Date: 2024-09-23 DOI: 10.1016/j.xcrp.2024.102218

Yi Zhang, Ramesh Prasad, Siyuan Su, Daesung Lee, Huan-Xiang Zhou

引用次数: 0