Cell Reports Physical Science最新文献

Chemiosmotic ATP synthesis by minimal protocells.

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2025-03-19 DOI: 10.1016/j.xcrp.2025.102461

Fanchen Yu, Jinbo Fei, Yi Jia, Tonghui Wang, William F Martin, Junbai Li

{"title":"Chemiosmotic ATP synthesis by minimal protocells.","authors":"Fanchen Yu, Jinbo Fei, Yi Jia, Tonghui Wang, William F Martin, Junbai Li","doi":"10.1016/j.xcrp.2025.102461","DOIUrl":"10.1016/j.xcrp.2025.102461","url":null,"abstract":"Energy conservation is crucial to life's origin and evolution. The common ancestor of all cells used ATP synthase to convert proton gradients into ATP. However, pumps generating proton gradients and lipids maintaining proton gradients are not universally conserved across all lineages. A solution to this paradox is that ancestral ATP synthase could harness naturally formed geochemical ion gradients with simpler environmentally provided precursors preceding both proton pumps and biogenic membranes. This runs counter to traditional views that phospholipid bilayers are required to maintain proton gradients. Here, we show that fatty acid membranes can maintain sufficient proton gradients to synthesize ATP by ATP synthase under the steep pH and temperature gradients observed in hydrothermal vent systems. These findings shed substantial light on early membrane bioenergetics, uncovering a functional intermediate in the evolution of chemiosmotic ATP synthesis during protocellular stages postdating the ATP synthase's origin but preceding the advent of enzymatically synthesized cell membranes.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 3","pages":"102461"},"PeriodicalIF":7.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11922820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691277","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

Transporter excess and clustering facilitate adaptor protein shuttling for bacterial efflux.

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2025-02-19 Epub Date: 2025-02-12 DOI: 10.1016/j.xcrp.2025.102441

Wenyao Zhang, Christine E Harper, Junsung Lee, Bing Fu, Malissa Ramsukh, Christopher J Hernandez, Peng Chen

{"title":"Transporter excess and clustering facilitate adaptor protein shuttling for bacterial efflux.","authors":"Wenyao Zhang, Christine E Harper, Junsung Lee, Bing Fu, Malissa Ramsukh, Christopher J Hernandez, Peng Chen","doi":"10.1016/j.xcrp.2025.102441","DOIUrl":"10.1016/j.xcrp.2025.102441","url":null,"abstract":"Multidrug efflux pumps confer not only antibiotic resistance to bacteria but also cell proliferation. In gram-negative bacteria, the ATP-binding cassette (ABC)-family transporter MacB, the adaptor protein MacA, and the outer membrane protein TolC form the MacA6:MacB2:TolC3 assembly to extrude antibiotics and virulence factors. Here, using quantitative single-molecule single-cell imaging, we uncover that, in E. coli cells, there is a large excess of MacB (and TolC) driving the limiting adaptor protein MacA mostly into the MacAB-TolC assembly. Moreover, the excess MacB transporters can dynamically cluster around the assembly, and MacA can dynamically disassemble from the MacAB-TolC assembly, leading to an adaptor protein shuttling mechanism for efficient substrate sequestration from the periplasm toward efflux. We further show that both MacB clustering and MacAB-TolC assembly can be perturbed chemically or physically via microfluidics-based extrusion loading for compromised antibiotic tolerance. These insights may provide opportunities for countering the activities of multidrug efflux systems for antimicrobial treatments.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 2","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623726","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

Membrane-assisted Aβ40 aggregation pathways.

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2025-02-19 Epub Date: 2025-02-11 DOI: 10.1016/j.xcrp.2025.102436

Fidha Nazreen Kunnath Muhammedkutty, Huan-Xiang Zhou

{"title":"Membrane-assisted Aβ40 aggregation pathways.","authors":"Fidha Nazreen Kunnath Muhammedkutty, Huan-Xiang Zhou","doi":"10.1016/j.xcrp.2025.102436","DOIUrl":"10.1016/j.xcrp.2025.102436","url":null,"abstract":"Alzheimer's disease (AD) is caused by the assembly of amyloid-beta (Aβ) peptides into oligomers and fibrils. Endogenous Aβ aggregation may be assisted by cell membranes, which can accelerate the nucleation step enormously, but knowledge of membrane-assisted aggregation is still very limited. Here, we used extensive molecular dynamics (MD) simulations to structurally and energetically characterize key intermediates along the membrane-assisted aggregation pathways of Aβ40. Reinforcing experimental observations, the simulations reveal unique roles of GM1 ganglioside and cholesterol in stabilizing membrane-embedded β sheets and of Y10 and K28 in the ordered release of a small oligomeric seed into solution. The same seed leads to either an open-shaped or R-shaped fibril, with significant stabilization provided by inter- or intra-subunit interfaces between a straight β sheet (residues Q15-D23) and a bent β sheet (residues A30-V36). This work presents a comprehensive picture of membrane-assisted aggregation of Aβ40, with broad implications for developing AD therapies and rationalizing disease-specific polymorphisms of amyloidogenic proteins.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 2","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623724","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

Leveraging large language models for peptide antibiotic design.

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2025-01-15 Epub Date: 2024-12-31 DOI: 10.1016/j.xcrp.2024.102359

Changge Guan, Fabiano C Fernandes, Octavio L Franco, Cesar de la Fuente-Nunez

引用次数: 0

Ultrafast synthesis of zirconium-porphyrin framework nanocrystals from alkoxide precursors. 醇盐前驱体超快合成锆-卟啉骨架纳米晶。

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-12-18 DOI: 10.1016/j.xcrp.2024.102318

Manuel Ceballos, Giulia Zampini, Oleg Semyonov, Samuel Funes-Hernando, José Manuel Vila-Fungueiriño, Sonia Martínez-Giménez, Sergio Tatay, Carlos Martí-Gastaldo, Thomas Devic, Beatriz Pelaz, Pablo Del Pino

{"title":"Ultrafast synthesis of zirconium-porphyrin framework nanocrystals from alkoxide precursors.","authors":"Manuel Ceballos, Giulia Zampini, Oleg Semyonov, Samuel Funes-Hernando, José Manuel Vila-Fungueiriño, Sonia Martínez-Giménez, Sergio Tatay, Carlos Martí-Gastaldo, Thomas Devic, Beatriz Pelaz, Pablo Del Pino","doi":"10.1016/j.xcrp.2024.102318","DOIUrl":"10.1016/j.xcrp.2024.102318","url":null,"abstract":"Porphyrinic metal-organic frameworks (MOFs) offer high surface areas and tunable catalytic and optoelectronic properties, making them versatile candidates for applications in phototherapy, drug delivery, photocatalysis, electronics, and energy storage. However, a key challenge for industrial integration is the rapid, cost-effective production of suitable sizes. This study introduces Zr(IV) alkoxides as metal precursors, achieving ultrafast (∼minutes) and high-yield (>90%) synthesis of three well-known Zr-based porphyrinic MOF nanocrystals: MOF-525, PCN-224, and PCN-222, each with distinct topologies. By adjusting linker-to-metal and modulator-to-metal ratios, we attain precise control over single-phase formation. Demonstrating alkoxides' potential, we synthesized nanosized PCN-224 at room temperature within seconds using a continuous multifluidic method. This advancement greatly simplifies porphyrinic MOF production, enabling broader industrial and scientific applications.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 12","pages":"102318"},"PeriodicalIF":7.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876220","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

De novo design of a mechano-pharmaceutical screening platform against formation of individual beta-amyloid oligomers. 从头设计抗单个β-淀粉样蛋白寡聚体形成的机械药物筛选平台。

IF 7.9 2区综合性期刊

Cell Reports Physical Science Pub Date : 2024-12-18 DOI: 10.1016/j.xcrp.2024.102336

Shankar Pandey, Mathias Bogetoft Danielsen, Yuan Xiang, Zhilei Zhang, Grinsun Sharma, Byeong Tak Jeon, Shixi Song, Yitong Hao, Gunan Zhang, Niels Johan Christensen, Kasper Kildegaard Sørensen, Pernille Harris, Pravin Pokhrel, Richard Cunningham, Min-Ho Kim, Yongsheng Leng, Chenguang Lou, Hanbin Mao

{"title":"De novo design of a mechano-pharmaceutical screening platform against formation of individual beta-amyloid oligomers.","authors":"Shankar Pandey, Mathias Bogetoft Danielsen, Yuan Xiang, Zhilei Zhang, Grinsun Sharma, Byeong Tak Jeon, Shixi Song, Yitong Hao, Gunan Zhang, Niels Johan Christensen, Kasper Kildegaard Sørensen, Pernille Harris, Pravin Pokhrel, Richard Cunningham, Min-Ho Kim, Yongsheng Leng, Chenguang Lou, Hanbin Mao","doi":"10.1016/j.xcrp.2024.102336","DOIUrl":"10.1016/j.xcrp.2024.102336","url":null,"abstract":"Small molecules that can reduce the neurotoxic beta-amyloid (Aβ) aggregates in the brain provide a potential treatment for Alzheimer disease (AD). Most screening methods for small-molecule hits focus on the overall Aβ aggregations without a specific target, such as the very first association step (i.e., nucleation) en route to the Aβ oligomers. Located in the middle of a full-length Aβ peptide, Aβ19-20 (diphenylalanine or FF) nucleates the neurotoxic Aβ oligomer formation. Here, we innovate a single-molecule screen method in optical tweezers by targeting the nucleation process in Aβ aggregation, namely FF-dimerization. With a 121-compound National Institutes of Health (NIH) library, we identify 12 inhibitors and 8 stimulants that can inhibit/promote Aβ19-20 dimerization significantly. The representative hits are subjected to the thioflavin T and cell toxicity assays to confirm their inhibiting or stimulating activities. By replacing FF with longer Aβ sequences, our single-molecule platform may identify more specific and potent small molecules to fight AD.","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"5 12","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623722","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

A variational graph-partitioning approach to modeling protein liquid-liquid phase separation.

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

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 7.9 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