{"title":"Infrared and ultraviolet spectroscopic characterization of a key intermediate during DNA repair by (6-4) photolyase.","authors":"Daichi Yamada, Ai Kadono, Tatsumi Maeno, Wataru Sato, Sachiko Yanagisawa, Toshihiko Hamamura, Yasuteru Shigeta, Junpei Yamamoto, Minoru Kubo","doi":"10.1038/s42004-025-01625-9","DOIUrl":"10.1038/s42004-025-01625-9","url":null,"abstract":"<p><p>Ultraviolet (UV) irradiation of DNA causes genotoxic photolesions, such as carcinogenic pyrimidine(6-4)pyrimidone photoproducts ((6-4)PPs). In many organisms, (6-4)PPs are repaired by (6-4) photolyases, which contain a flavin chromophore and use blue light energy to initiate the catalytic reaction. Although (6-4)PP repair has been shown to require the input of two successive photons, details of the mechanism remain elusive. Here, we applied recently developed time-resolved UV and infrared (IR) spectroscopic techniques to capture a key intermediate that awaits the second photon in the repair reaction of Xenopus laevis (6-4) photolyase. The results indicate that the intermediate is formed within 500 μs following the initial absorption of a photon and contains a four-membered oxetane ring that bridges two adjacent pyrimidine bases. These findings shed light on the molecular basis of DNA repair involving two-photon activation.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"256"},"PeriodicalIF":6.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12397333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945589","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}
Armin Amirsadeghi, Raffaella Parlato, Anna Kenbeek, Ana Rita Gaspar, Marta Oggioni, Alessia Lasorsa, Adrivit Mukherjee, Malak Jaber, Małgorzata K Włodarczyk-Biegun, Patrick C A van der Wel, Marleen Kamperman, Guillermo Monreal Santiago
{"title":"Crosslinking, salt-induced aging, and secondary structure formation in Peptide-containing coacervates inspired by spider silk.","authors":"Armin Amirsadeghi, Raffaella Parlato, Anna Kenbeek, Ana Rita Gaspar, Marta Oggioni, Alessia Lasorsa, Adrivit Mukherjee, Malak Jaber, Małgorzata K Włodarczyk-Biegun, Patrick C A van der Wel, Marleen Kamperman, Guillermo Monreal Santiago","doi":"10.1038/s42004-025-01634-8","DOIUrl":"10.1038/s42004-025-01634-8","url":null,"abstract":"<p><p>Spider silks are exceptional biomaterials: biocompatible, biodegradable, and with remarkable mechanical properties. Unfortunately, attempts to replicate them tend to fail due to the difficulty of synthesizing the proteins that constitute them, and to an incomplete understanding of their processing conditions. Here, we report a synthetic system inspired by spider silk, consisting of a synthetic polyelectrolyte with grafted oligoalanine chains. We have used this peptide-polyelectrolyte conjugate to produce complex coacervates in an analogous process to the liquid-liquid phase separation (LLPS) observed during the natural processing of spider silk. We have characterized these coacervates using rheology, tack test, and solid-state NMR spectroscopy, observing α-helixes and β-sheets. These secondary structures crosslink the material, improving its mechanical properties and its processability, for example, for 3D printing. Furthermore, the peptide-based crosslinks cause distinctive behaviours - such as salt-induced aging. Our approach contributes to the fundamental understanding of the role that LLPS and peptide crosslinks play in spider silk, and to the development of new soft materials crosslinked by peptide aggregation.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"264"},"PeriodicalIF":6.2,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12394569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945605","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}
Mary C Jones, Leide P Cavalcanti, Gregory N Smith, Robert Dalgliesh, Stephen R Euston, Filipe Vilela, Valeria Arrighi, Gareth O Lloyd
{"title":"Self-sorting and co-assembly control in multicomponent supramolecular hydrogels with dual monomer and polymer statistical distribution.","authors":"Mary C Jones, Leide P Cavalcanti, Gregory N Smith, Robert Dalgliesh, Stephen R Euston, Filipe Vilela, Valeria Arrighi, Gareth O Lloyd","doi":"10.1038/s42004-025-01657-1","DOIUrl":"10.1038/s42004-025-01657-1","url":null,"abstract":"<p><p>Multicomponent supramolecular polymer gels are a class of soft matter materials which form via the assembly of two or more small molecules. Different structures can be generated with interesting potential functions and applications. Insight into the assembly mechanism is key in the design of these systems for specific applications. Herein, a series of hydrogels with diverse structures and functionalities were synthesised. Using dynamic covalent chemistry as a key tool we show that it is possible to control the monomer assembly, forming both self-sorted and co-assembled polymers and gels from the same initial components. The hierarchical structure of the gels is difficult to elucidate. We emphasise the significance of small-angle neutron scattering (SANS) and spin-echo SANS (SESANS) measurements in characterising these intricate assemblies and demonstrate that these techniques are able to differentiate among self-sorted and co-assembled structures even when using chemically similar components.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"265"},"PeriodicalIF":6.2,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12394493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945621","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}
Elizabeth Donahue, Tomáš Malina, Emma Smith, Jakub Pšenčík, Emily A Sprague-Klein
{"title":"Photophysics of plasmonically enhanced self-assembled artificial light-harvesting nanoantennas.","authors":"Elizabeth Donahue, Tomáš Malina, Emma Smith, Jakub Pšenčík, Emily A Sprague-Klein","doi":"10.1038/s42004-025-01664-2","DOIUrl":"10.1038/s42004-025-01664-2","url":null,"abstract":"<p><p>The design of efficient artificial light-harvesting antennas is essential for enabling the widespread use of solar energy. Natural photosynthetic systems offer valuable inspiration, but many rely on complex pigment-protein interactions and have limited spectral coverage, which pose challenges for rational design. Chlorosome mimics, which are self-assembling pigment aggregates inspired by green photosynthetic bacteria, offer structural simplicity, flexible tunability, and strong excitonic coupling through pigment-pigment interactions. However, these pigment aggregates suffer from limited absorption in the green and near-infrared regions and, similarly to other light-harvesting systems, reduced energy transfer efficiency at high donor concentrations. One promising strategy to overcome these limitations is the integration of plasmonic nanoparticles, which enhance local electromagnetic fields, increase spectral coverage, and make new energetic pathways accessible. Although plasmonic enhancement has been widely studied in pigment-protein complexes like Photosystem I and light-harvesting complexes (LHCs), its application to pigment-pigment self-assembled systems remains largely unexplored. This perspective presents recent advances in biomimetic light-harvesting design with chlorosome mimics and explores the potential for plasmonic enhancement of photophysics in these systems. We examine the structure of chlorosomes and their artificial mimics to understand the role of pigment-pigment interactions in facilitating highly efficient energy transfer.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"263"},"PeriodicalIF":6.2,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12394525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945658","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}
Bin Li, Lin Zhang, Huaixin Hao, Yishi Yu, Yuxiao Guo, Zhipeng Wang, Chao Xu
{"title":"Exploiting the coordination chemistry of high-valent americium for actinide/lanthanide separations.","authors":"Bin Li, Lin Zhang, Huaixin Hao, Yishi Yu, Yuxiao Guo, Zhipeng Wang, Chao Xu","doi":"10.1038/s42004-025-01668-y","DOIUrl":"10.1038/s42004-025-01668-y","url":null,"abstract":"<p><p>Efficient americium (Am)/lanthanide (Ln) separation is highly pursued in advanced nuclear fuel cycle for minimizing the long-term radiotoxicity of nuclear waste and maximizing the utilization of nuclear resources. However, such a task is extremely challenging given the chemical similarity between the inherent thermodynamically stable Am(III) and Ln(III) ions. In recent years, interest in Am/Ln separation through oxidizing Am(III) to higher-valent states is reigniting due to theoretically considerable separation efficiency of this approach. This review summarizes the developments in preparation and stabilization of high-valent Am, especially the progresses in the exploitation of the coordination chemistry of these high-valent Am for effective Am/Ln separation. This review aims to inspire the search for efficient redox and coordination systems with more robust Am/Ln separation performance.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"260"},"PeriodicalIF":6.2,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12391460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945630","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":"Photostability of organic fluorophore influenced by adjacent amino acid residues.","authors":"Yongzhen Hei, Banglong Wang, Yichen He, Wenjuan Wang, Yi Xue, Chunlai Chen","doi":"10.1038/s42004-025-01661-5","DOIUrl":"10.1038/s42004-025-01661-5","url":null,"abstract":"<p><p>Fluorescence microscopy represents a highly effective tool for examining the microscopic world. Modern microscopic techniques provide advanced temporal and spatial resolutions, while placing high demands on the photostability of fluorophores. Although it is well-known that the photostability of fluorophores is sensitive to their environment, the influence of nearby residues on the photostability of organic fluorophores attached to proteins is not yet fully understood. This study focuses on the influence of residues adjacent to the maleimide-derived fluorophore, specifically attached to cysteine residues in proteins. Under our experimental conditions, methionine, tryptophan, phenylalanine, valine, and leucine were all found to reduce the photostability, whereas glutamate was found to enhance the photostability. To put these experimental observations into perspective, we performed molecular dynamics simulations that offer insights into the mechanistic effects of adjacent residues.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"262"},"PeriodicalIF":6.2,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12391357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945655","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}
Wenzheng Jin, Jiaming Tu, Bei Zhang, Xuri Wu, Yijun Chen
{"title":"Gene conversion-associated successive engineering of modular polyketide synthases.","authors":"Wenzheng Jin, Jiaming Tu, Bei Zhang, Xuri Wu, Yijun Chen","doi":"10.1038/s42004-025-01671-3","DOIUrl":"10.1038/s42004-025-01671-3","url":null,"abstract":"<p><p>Modular polyketide synthases (PKSs) can produce various secondary metabolites in a collinearity fashion. Although rational engineering of modular PKS can ultimately create a diverse array of compounds, de novo generation of defined structures usually results in the loss or remarkable decline of productivity due primarily to the incompatibility of different elements. Here, we present a modular PKS engineering strategy driven by an evolutionary event of gene conversion to accomplish successive engineering of the modular PKS in cinnamomycin biosynthetic gene cluster (cmm BGC). By simulating the gene conversion process, cmm BGC is consecutively reprogrammed to generate a macrolide with predicted structural features. Moreover, the intra-module KS domain is demonstrated to associate with the proofreading of extender units. Collectively, the gene conversion-associated approach may shed a light on modular PKS engineering.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"261"},"PeriodicalIF":6.2,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12391348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945618","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":"Post-polymerization modification enabling library synthesis of highly isotactic polyacrylamides carrying different pendant groups.","authors":"Yuehang Pan, Makoto Ouchi","doi":"10.1038/s42004-025-01663-3","DOIUrl":"10.1038/s42004-025-01663-3","url":null,"abstract":"<p><p>The tacticity of vinyl polymers, i.e., the regularity of the side-chain stereochemistry, plays a crucial role in determining their physical properties. For example, the crystalline properties of isotactic polypropylene endow it with outstanding mechanical properties. In general, stereo-regulation during polymerization is greatly affected by even slight differences in the steric demand and/or position of the polar groups of the monomer side chains. In other words, no universal strategy to precisely control the tacticity for a given monomer with different pendant groups has been developed so far. Here, we provide a ground-breaking method for a library synthesis of highly isotactic polyacrylamides (99% meso dyad) with various pendant groups, including polar structures and di-substituted motifs. For that purpose, we designed an acrylamide monomer with a pendant that is sufficiently bulky to control the polymer tacticity that can be replaced by another pendant after polymerization. The transformable bulky monomer underwent iso-specific radical polymerization and subsequent aminolysis with a primary or secondary amine afforded a series of isotactic polyacrylamides derived from the added amine. Moreover, we clarified the isotacticity-dependent physical properties of the resulting polymers, such as their glass-transition temperature, crystalline properties, and solubility/thermo-responsibility in water, through a comparison with the corresponding atactic polyacrylamides.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"259"},"PeriodicalIF":6.2,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12381277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945592","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}
Mathieu Gascoin, Mariya Romanova, Ibrahim Cheik Njifon, Michel Freyss
{"title":"DFT+U investigation of local configurations and oxidation states of Cr in Cr-doped UO<sub>2</sub>.","authors":"Mathieu Gascoin, Mariya Romanova, Ibrahim Cheik Njifon, Michel Freyss","doi":"10.1038/s42004-025-01642-8","DOIUrl":"10.1038/s42004-025-01642-8","url":null,"abstract":"<p><p>Doping UO<sub>2</sub> with Cr modifies the material's microstructure, enhancing its properties and making Cr-doped UO<sub>2</sub> a promising candidate as accident-tolerant nuclear fuel (ATF). Numerous studies have examined the oxidation state and localization of Cr in UO<sub>2</sub> but often yield inconsistent results, identifying either Cr<sup>2+</sup> or Cr<sup>3+</sup> as the most stable oxidation state. In the present study, DFT+U is employed to model the incorporation of Cr in the UO<sub>2</sub> matrix, providing insights into the oxidation state of Cr in UO<sub>2</sub>, in relation to the local atomic configurations. In particular, we investigate the <math> <msubsup><mrow><mi>Cr</mi></mrow> <mrow><mi>x</mi></mrow> <mrow><mn>3</mn> <mo>+</mo></mrow> </msubsup> </math> <math> <msubsup><mrow><mi>U</mi></mrow> <mrow><mn>1</mn> <mo>-</mo> <mi>x</mi></mrow> <mrow><mn>4</mn> <mo>+</mo></mrow> </msubsup> </math> O<sub>2-0.5x</sub> local configuration recently proposed by EPR and XANES experiments, alongside other theoretical configurations. Cr<sup>3+</sup> is found to be the most favorable oxidation state in this configuration, agreeing with the most recent experimental data. This work clarifies the controversy over Cr oxidation states and incorporation sites within UO<sub>2</sub>, offering critical data for developing efficient and safer nuclear fuels.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"257"},"PeriodicalIF":6.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12378233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945599","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}
Mark Hemmings, Michał Zieliński, Tolou Golkar, Jonathan Blanchet, Angelos Pistofidis, Kim Munro, T Martin Schmeing, D Scott Bohle, Albert M Berghuis
{"title":"Enzyme-mediated aminoglycoside resistance without target mimicry.","authors":"Mark Hemmings, Michał Zieliński, Tolou Golkar, Jonathan Blanchet, Angelos Pistofidis, Kim Munro, T Martin Schmeing, D Scott Bohle, Albert M Berghuis","doi":"10.1038/s42004-025-01666-0","DOIUrl":"10.1038/s42004-025-01666-0","url":null,"abstract":"<p><p>The primary mode of resistance to aminoglycoside antibiotics is through chemical modification catalyzed by aminoglycoside-modifying enzymes. Numerous structural studies of these enzymes have invariably shown that they bind aminoglycosides in the same lowest-energy conformation as the intended target for these antibiotics, the A site of the bacterial ribosome. Presumably, the binding mode mimicry enables these enzymes to compete successfully with the target, thus conferring effective resistance. Here we present the first structural and functional studies of two aminoglycoside-modifying enzymes that do not use target mimicry, AAC(3)-Ia and AAC(3)-XIa. X-ray diffraction studies reveal that these enzymes bind aminoglycoside antibiotics in a conformation where the central 2-deoxystreptamine ring is in boat conformation. The effect of this non-canonical binding mode on the enzymes' ability to modify antibiotics is assessed in silico and in vitro, and its impact for conferring resistance is assessed in vivo. Overall, the results show that target mimicry, while advantageous, is not an essential strategy for aminoglycoside-modifying enzymes to be effective in conferring resistance.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"258"},"PeriodicalIF":6.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12378234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945660","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}