化学•材料最新文献

{"title":"ssDNA and ssRNA Promote Phase Condensation of SAMHD1.","authors":"Brandon E Smith, Ankita Pohnerkar, Benjamin Orris, Shridhar Bhat, Matthew Egleston, James T Stivers","doi":"10.1021/acs.biochem.5c00422","DOIUrl":"https://doi.org/10.1021/acs.biochem.5c00422","url":null,"abstract":"<p><p>SAMHD1 (SAM domain and HD domain-containing protein 1) is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) with functions in viral restriction, R-loop resolution, DNA repair, telomere maintenance, ssRNA homeostasis, and regulation of self-nucleic acids. As a dNTPase, SAMHD1 functions as an allosterically activated tetramer, where binding of GTP to the A1 activator site of each monomer initiates dNTP-dependent tetramerization. cEM structures reveal that the nucleic-acid-related functions of SAMHD1 involve binding of guanine residues to the A1 site, leading to oligomeric forms that appear as beads-on-a-string on single-stranded RNA and DNA. SAMHD1's cellular activities and known protein interactions involve liquid-liquid phase separation (LLPS), although there are no reports that SAMHD1 itself exhibits phase separation properties. The protein phase separation prediction algorithm MolPhase indicated an overall phase separation probability score of 0.65 and suggested that the amino terminal SAM domain and the disordered carboxyl terminus (CT) may promote phase separation. Although no phase separation behavior was observed in physiological buffer, in the presence of 9% PEG 2000 and ssDNA or ssRNA, SAMHD1 condensed into liquid-like droplets. These droplets were disrupted by deletion of the SAM or CT domains, showed fusion behavior, and were rapidly disrupted by the addition of A1 site ligands GTP, dGTP, and small-molecule inhibitors. We also observed that SAMHD1-ssDNA condensates within the nuclei of human cells in microinjection experiments, supporting a biological relevance for such complexes. LLPS by SAMHD1 could serve a regulatory role in cells and provide a new therapeutic target for the treatment of cancer and viral infections.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microplastic Diversity as a Potential Driver of Soil Denitrification Shifts.","authors":"Tian-Gui Cai,Da Lin,Bang Ni,Tian-Lun Zhang,Yi-Fei Wang,Dong Zhu","doi":"10.1021/acs.est.5c04981","DOIUrl":"https://doi.org/10.1021/acs.est.5c04981","url":null,"abstract":"Microplastics (MPs) are raising significant global concerns due to their environmental impacts. While most studies have focused on the effects of individual MP types, MPs in natural environments typically coexist as multiple types, and their combined effects remain poorly understood. In this study, we conducted a microcosm experiment with four levels of MP diversity (0, 1, 3, and 5 types) to investigate the effects of MP diversity on soil ecosystem functions using metagenomic sequencing. Our results revealed that increasing MP diversity significantly raised soil pH and organic carbon content while reducing available nitrogen. Notably, bacterial alpha diversity (Shannon and Invsimpson indices) increased significantly with higher MP diversity. Moreover, increasing MP diversity markedly shifted bacterial life-history strategies to adapt to the altered environment. Importantly, the abundance of nitrogen-related functional genes also increased with MP diversity. In particular, the abundance of denitrifying genes, predominantly driven by Rhodocyclaceae, was notably enhanced, resulting in a reduction of soil available nitrogen. Collectively, these findings offer valuable insights into the impact of MP diversity on soil function─especially within the nitrogen cycle─and have important implications for soil management strategies under MP stress.","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":"25 1","pages":""},"PeriodicalIF":9.028,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145003218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strong Metal-Support Interactions in Catalytic Oxidation of VOCs: Mechanistic Insights, Support Engineering Strategies, and Emerging Catalyst Design Paradigms.","authors":"Ziyue Jiang,Yongtao Li,Ziyu Tang,Dingkun Yuan,Fawei Lin","doi":"10.1021/acs.est.5c09511","DOIUrl":"https://doi.org/10.1021/acs.est.5c09511","url":null,"abstract":"Volatile organic compounds (VOCs) significantly impact air quality as photochemical smog precursors and health hazards. Catalytic oxidation is a leading VOC abatement method but suffers from catalyst deactivation due to metal sintering and competitive adsorption in complex mixtures. Strong metal-support interactions (SMSIs) provide atomic level control of interfacial electronic and geometric structures. SMSI enables bidirectional charge transfer, d band center modulation, oxygen vacancy generation, and tunable encapsulation that together promote O2 activation, lower barriers, and impart thermal and chemical robustness. This review synthesizes mechanistic insights and recent progress in SMSI-enabled VOC oxidation, integrating in situ and operando probes with kinetics. Reactivity and selectivity across aromatics, alkanes, oxygenates, and chlorinated species are rationalized by SMSI-mediated tuning of adsorption and intermediate evolution. Practical levers include control of particle size and dispersion, core-shell architectures, metal loading, and support acidity or basicity. Emerging directions include single atom catalysts, high entropy alloys, and nonmetal supports. Key challenges concern the dynamic evolution of SMSI under realistic feeds and the scalable, reproducible synthesis of interfaces. Future developments combining in situ characterization with data-driven catalyst design hold promise for achieving durable, high-performance VOC abatement with reduced precious metal usage.","PeriodicalId":36,"journal":{"name":"环境科学与技术","volume":"16 1","pages":""},"PeriodicalIF":9.028,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145003217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanistic and Kinetic Insights into Nitrogen Chemistry: NH₂-Mediated H-Abstraction and HCN Addition Pathways in NH₃/Ethanol Combustion.","authors":"Tong Yan, Pan Wang, Jianmin Liu, Jinsheng Zhang, Lidong Zhang","doi":"10.1021/acs.jpca.5c03451","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c03451","url":null,"abstract":"<p><p>To elucidate possible mechanisms of nitrogen chemistry between ammonia (NH₃) and ethanol, the potential pathways of ethanol radicals (Wa, Wb, and Wc) following H-abstraction by NH₂ radicals were primarily investigated including HCN addition, H-transfer, and dissociation reactions by quantum chemical calculations. The rate constants were solved in the master equation based on RRKM and TST theory and fitted to the Arrhenius equation. The results demonstrate that H-abstraction from C₂H₅OH by NH₂ at the b-site is the most competitive, facilitating subsequent HCN addition. The HCN addition-entranced channel exhibits a negative temperature coefficient (NTC) behavior at 0.01 atm, and the onset of this effect is progressively delayed with pressure. The low-temperature reaction path of ethanol radicals with HCN is dominated by the initial adduct (WaHCN, WbHCN, and WcHCN) formation and subsequent isomerization. The multiple dissociation product channels become more competitive with temperature, especially the HCNH elimination. Findings from this study identify new growth pathways for NPAHs and OPAHs in the reaction of straight-chain molecules with HCN and provide comprehensive kinetic insights.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008039","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":"Recyclable Cu-Catalyzed N-Methylation and C5-Methylthiomethylation of Isatins with DMSO.","authors":"Yi Xiao,Xiya Zhang,Junyu Zhou,Fei Yuan,Lei Wu,Zheng Liu,Xiaojuan Wang,Jingxian Yu,Shiqing Li","doi":"10.1021/acs.joc.5c01815","DOIUrl":"https://doi.org/10.1021/acs.joc.5c01815","url":null,"abstract":"An unprecedented recyclable system of copper-catalyzed C-C/N coupling of isatins and DMSO without any oxidant and acidic/basic additive has been unlocked. The NH-isatins occur tandem N-methylation and C5-methylthiomethylation in order, while N-substituted isatins proceed C5-methylthiomethylation only. DMSO serves as Me and MeSCH2 sources as well as the solvent. DCE is essential for providing a radical initiator and halogen cation pool. In this protocol, two vital ionic liquids (ILs), reactive methyl(methylene)-sulfonium and inert trimethylsulfonium, are generated in situ to promote homogeneous-to-heterogeneous phase transition. The ILs accumulate in the lower layer to drag the copper catalyst but push the product, enabling separating the catalyst and product through simple decantation. The lower layer can be recycled as a catalyst for at least six cycles. The systematic and comprehensive control experiments, ESI-MS, and DFT calculations indicate that site selectivity is controlled by atomic charge distribution and steric factors; and the interaction between ILs and Cu salts can reduce the reaction energy barrier.","PeriodicalId":57,"journal":{"name":"Journal of Organic Chemistry","volume":"40 1","pages":""},"PeriodicalIF":4.354,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145003254","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":"Recent advances in bismuth oxyhalides BiOX (X = Cl, Br and I) based photocatalyst: Synthesis, properties, applications and looking beyond","authors":"Linlin Zhang ,&nbsp;Xiaonan Sun ,&nbsp;Rongrong Chen ,&nbsp;Jun Wang","doi":"10.1016/j.rser.2025.116249","DOIUrl":"10.1016/j.rser.2025.116249","url":null,"abstract":"<div><div>To solve the problems of global energy shortage and environmental pollution, in recent years, semiconductor photocatalysis technology that converts solar energy into chemical energy has been extensively studied. In terms of semiconductor photocatalysts, BiOX has received extensive attention due to its adjustable band structure and the characteristics of exposing different high-energy surfaces. A large number of studies have shown that BiOX-based photocatalysts have excellent photocatalytic performance in energy and environmental purification. This article reviews the latest developments in the design and synthesis of various BiOX and BiOX-based photocatalysts. The basic physical and chemical properties of BiOX and its growth mechanism are summarized. In addition, the application of BiOX-based photocatalysts in photocatalytic hydrogen production, CO₂ reduction to hydrocarbon fuels, and pollutant degradation are also discussed. Finally, a brief outlook on the development prospects and challenges of BiOX and BiOX-based photocatalysts is given.</div></div>","PeriodicalId":418,"journal":{"name":"Renewable and Sustainable Energy Reviews","volume":"226 ","pages":"Article 116249"},"PeriodicalIF":16.3,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Barrier-Free Zinc Dimer Rotor on a Borozene-like BSi₅^3- Stator: The Smallest Molecular Compass with Planar Pentacoordinate Boron.","authors":"Bo Jin, Miao Yan, Lin-Yan Feng, Zai-Ran Wang, Chang-Qing Miao, Ying-Jin Wang","doi":"10.1021/acs.jpca.5c04721","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04721","url":null,"abstract":"<p><p>This work introduces the novel anionic cluster BSi₅Zn₂^- as the smallest molecular \"compass\", featuring a unique two-layered architecture with a planar pentacoordinate boron (ppB) center. The cluster comprises a quasi-planar BSi₅^3- stator─a silicon-based analogue of borozene with σ/π double aromaticity (6π + 10σ delocalized electrons)─and a Zn₂ rotor dimer. High-level calculations (CCSD(T)//PBE0-D3) reveal an ultralow rotational barrier of 0.02 kcal mol^-1 for the Zn₂ dimer, enabling barrier-free 360° rotation on the stator surface, as confirmed by Born-Oppenheimer molecular dynamics (BOMD) simulations at 298-800 K. Bonding analysis attributes this exceptional fluxionality to a hybrid ionic-covalent interaction best described as [Zn₂⁺][BSi₅^2-], where charge transfer (Zn₂ → BSi₅) ensures electrostatic stability, while the delocalized electron cloud of the aromatic stator minimizes rotational resistance. This design successfully extends to BGe₅Zn₂^- but fails for BSn₅Zn₂^- due to size mismatch, highlighting the synergy of electronic delocalization and geometric constraints. The study pioneers the extension of nanorotor design from pure boron clusters to group 14 element-based platforms with benzene-like σ/π delocalization, establishing the smallest molecular compass based on a minimal stator (6-atom BSi₅^3-) and establishing a new paradigm for dynamic molecular machines.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005646","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":"Molecular Dynamics Simulation of the Interaction of Lipidated Structurally Nano Engineered Antimicrobial Peptide Polymers with Bacterial Cell Membrane.","authors":"Amal Jayawardena, Andrew Hung, Greg Qiao, Elnaz Hajizadeh","doi":"10.1021/acs.jpcb.5c02067","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02067","url":null,"abstract":"<p><p>The rapid emergence of multidrug-resistant (MDR) bacteria demands development of novel and effective antimicrobial agents. Structurally nanoengineered antimicrobial peptide polymers (SNAPPs), characterized by their unique star-shaped architecture and potent multivalent interactions, represent a promising solution. This study leverages molecular dynamics simulations to investigate the impact of lipidation on SNAPPs' structural stability, membrane interactions, and antibacterial efficacy. We show that lipidation with hexanoic acid (C6), lauric acid (C12), and stearic acid (C18) enhances the α-helical stability of SNAPP arms, facilitating deeper insertion into the hydrophobic core of bacterial membranes. Among the variants, C12-SNAPP exhibits the most significant bilayer disruption, followed by C6-SNAPP, whereas the excessive hydrophobicity of C18-SNAPP leads to pronounced arm back-folding toward the core, reducing its effective interaction with the bilayer and limiting its bactericidal performance. Additionally, potential of mean force (PMF) analysis reveals that lipidation reduces the free energy barrier for translocation through the bilipid membrane compared to nonlipidated SNAPPs. These findings underscore the critical role of lipidation in optimizing SNAPPs for combating MDR pathogens. By fine-tuning lipid chain lengths, this study provides a framework for designing next-generation antimicrobial agents to address the global antibiotic resistance crisis, advancing modern therapeutic strategies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005655","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":"HMGB1 B-Box Domain Associates Promote Protein-Polyelectrolyte Interactions.","authors":"Marten Kagelmacher, Marina Pigaleva, Ricardo Zarate, Leïla Bechtella, Kevin Pagel, Beate Koksch, Jens Dernedde, Andreas Herrmann, Thomas Risse","doi":"10.1021/acs.jpcb.5c02892","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02892","url":null,"abstract":"<p><p>HMGB1, a nuclear DNA-binding protein, can be secreted by activated immune cells or passively released from damaged cells. In such cases, HMGB1 functions as an alarmin that activates the immune system. Excessive inflammation may lead to pathogenesis, whereas this response can be dampened by polyanion binding, which impedes further receptor recognition. Moreover, HMGB1 is known to form liquid droplets in the cellular environment─a phase separation directly linked to its proper function. While the A-Box domain is believed to be primarily responsible for heparin binding due to its conserved binding site, the association and phase separation behavior of HMGB1 may be mediated by the B-box domain, owing to its extended hydrophobic regions. In this study, we first demonstrated that the B-box protein forms 30 nm large self-associates while maintaining its structure. Next, using molecularly sensitive EPR spectroscopy, we showed that the presence of these protein associates significantly enhances interactions with heparin. Notably, the local conformational changes induced by heparin are similar in both individual protein chains and their self-associated forms. To explain this effect, AlphaFold modeling was employed, revealing that the formation of protein multimers induces charge redistribution, resulting in an extended positively charged region that enhances electrostatic attraction to negatively charged polyanions such as heparin.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008044","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":"The important interplay between metal ions and the intermediate filament protein vimentin.","authors":"Estely J Carranza, Dylan T Murray, Marie C Heffern","doi":"10.1007/s00775-025-02124-x","DOIUrl":"https://doi.org/10.1007/s00775-025-02124-x","url":null,"abstract":"<p><p>Vimentin is a principal intermediate filament (IF) protein that is essential for maintaining cytoskeleton architecture and cellular mechanical integrity. Growing evidence is revealing that metal ions play critical roles in modulating the structure, assembly, and mechanics of vimentin IFs. Despite this, a detailed molecular-level understanding of vimentin-metal interactions and its functional consequences remains incomplete. This review summarizes the current knowledge of metal-induced effects on the structural and mechanical properties of vimentin and highlights how post-translational modifications and cytoskeletal dynamics may alter these metal-protein interactions. Advancing our understanding of the interplay between metal ions and vimentin IFs will enhance our comprehension of the complex mechanisms governing the versatile functions of vimentin and other IF proteins in health and disease.</p>","PeriodicalId":603,"journal":{"name":"Journal of Biological Inorganic Chemistry","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}