Pub Date : 2024-10-04DOI: 10.1038/s42004-024-01312-1
Janos Wasternack, Hendrik V Schröder, J Felix Witte, Mihkel Ilisson, Henrik Hupatz, Julian F Hille, Marius Gaedke, Arto M Valkonen, Sebastian Sobottka, Alexander Krappe, Mario Schubert, Beate Paulus, Kari Rissanen, Biprajit Sarkar, Siegfried Eigler, Ute Resch-Genger, Christoph A Schalley
In nature, molecular environments in proteins can sterically protect and stabilize reactive species such as organic radicals through non-covalent interactions. Here, we report a near-infrared fluorescent rotaxane in which the stabilization of a chemically labile squaraine fluorophore by the coordination of a tetralactam macrocycle can be controlled chemically and electrochemically. The rotaxane can be switched between two co-conformations in which the wheel either stabilizes or exposes the fluorophore. Coordination by the wheel affects the squaraine's stability across four redox states and renders the radical anion significantly more stable-by a factor of 6.7-than without protection by a mechanically bonded wheel. Furthermore, the fluorescence properties can be tuned by the redox reactions in a stepwise manner. Mechanically interlocked molecules provide an excellent scaffold to stabilize and selectively expose reactive species in a co-conformational switching process controlled by external stimuli.
{"title":"Switchable protection and exposure of a sensitive squaraine dye within a redox active rotaxane.","authors":"Janos Wasternack, Hendrik V Schröder, J Felix Witte, Mihkel Ilisson, Henrik Hupatz, Julian F Hille, Marius Gaedke, Arto M Valkonen, Sebastian Sobottka, Alexander Krappe, Mario Schubert, Beate Paulus, Kari Rissanen, Biprajit Sarkar, Siegfried Eigler, Ute Resch-Genger, Christoph A Schalley","doi":"10.1038/s42004-024-01312-1","DOIUrl":"https://doi.org/10.1038/s42004-024-01312-1","url":null,"abstract":"<p><p>In nature, molecular environments in proteins can sterically protect and stabilize reactive species such as organic radicals through non-covalent interactions. Here, we report a near-infrared fluorescent rotaxane in which the stabilization of a chemically labile squaraine fluorophore by the coordination of a tetralactam macrocycle can be controlled chemically and electrochemically. The rotaxane can be switched between two co-conformations in which the wheel either stabilizes or exposes the fluorophore. Coordination by the wheel affects the squaraine's stability across four redox states and renders the radical anion significantly more stable-by a factor of 6.7-than without protection by a mechanically bonded wheel. Furthermore, the fluorescence properties can be tuned by the redox reactions in a stepwise manner. Mechanically interlocked molecules provide an excellent scaffold to stabilize and selectively expose reactive species in a co-conformational switching process controlled by external stimuli.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375235","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}
Pub Date : 2024-10-04DOI: 10.1038/s42004-024-01303-2
{"title":"Women in Chemistry: Q&A with Dr Shira Joudan.","authors":"","doi":"10.1038/s42004-024-01303-2","DOIUrl":"https://doi.org/10.1038/s42004-024-01303-2","url":null,"abstract":"","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375236","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}
Pub Date : 2024-10-02DOI: 10.1038/s42004-024-01286-0
Nimrod Moiseyev
The ability to slow down or enhance chemical reactions, by a seemingly simple setup of reactions inside a cavity made of two parallel mirrors is fascinating. Unfortunately, currently, theory and experiment have not yet fully converged. Since theory and experiment perfectly match for atom/molecular collisions in gas phase the enhancing chemical reactions in gas phase through its coupling to quantized electromagnetic modes in a dark cavity is investigated. Here the conditions and guidelines for selecting the proper type of reactions that can be enhanced by a dark cavity are provided. Showing that the asymmetric reaction rates of O + D2 → [ODD]# → OD + D and H + ArCl → [ArHCl]# → H + Ar + Cl can be enhanced by a dark cavity. On the other hand, an effect of the dark cavity on the symmetric reaction of hydrogen exchange in methane is predicted to be negligible. Notice that the theory is not limited to microwave cavities only. The ability to slow down or enhance chemical reactions inside a cavity made of two parallel mirrors is fascinating but remains somewhat enigmatic. Here, the author presents a theoretical concept aimed at helping experimentalists select chemical reactions whose rates can be enhanced inside a dark microwave cavity.
通过在两个平行镜面组成的空腔内进行看似简单的反应设置，减缓或增强化学反应的能力令人着迷。遗憾的是，目前理论与实验尚未完全融合。由于气相中原子/分子碰撞的理论和实验完全吻合，因此我们研究了通过与暗腔中的量子化电磁模式耦合来增强气相中的化学反应。这里提供了选择暗腔可增强的适当反应类型的条件和指南。结果表明，暗腔可以提高 O + D2 → [ODD]# → OD + D 和 H + ArCl → [ArHCl]# → H + Ar + Cl 的不对称反应速率。另一方面，暗腔对甲烷中氢交换对称反应的影响预计可以忽略不计。请注意，该理论并不仅限于微波空穴。
{"title":"Conditions for enhancement of gas phase chemical reactions inside a dark microwave cavity","authors":"Nimrod Moiseyev","doi":"10.1038/s42004-024-01286-0","DOIUrl":"10.1038/s42004-024-01286-0","url":null,"abstract":"The ability to slow down or enhance chemical reactions, by a seemingly simple setup of reactions inside a cavity made of two parallel mirrors is fascinating. Unfortunately, currently, theory and experiment have not yet fully converged. Since theory and experiment perfectly match for atom/molecular collisions in gas phase the enhancing chemical reactions in gas phase through its coupling to quantized electromagnetic modes in a dark cavity is investigated. Here the conditions and guidelines for selecting the proper type of reactions that can be enhanced by a dark cavity are provided. Showing that the asymmetric reaction rates of O + D2 → [ODD]# → OD + D and H + ArCl → [ArHCl]# → H + Ar + Cl can be enhanced by a dark cavity. On the other hand, an effect of the dark cavity on the symmetric reaction of hydrogen exchange in methane is predicted to be negligible. Notice that the theory is not limited to microwave cavities only. The ability to slow down or enhance chemical reactions inside a cavity made of two parallel mirrors is fascinating but remains somewhat enigmatic. Here, the author presents a theoretical concept aimed at helping experimentalists select chemical reactions whose rates can be enhanced inside a dark microwave cavity.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01286-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364715","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}
Pub Date : 2024-10-02DOI: 10.1038/s42004-024-01305-0
Gerardo M. Casanola-Martin, Anas Karuth, Hai Pham-The, Humbert González-Díaz, Dean C. Webster, Bakhtiyor Rasulev
Glass transition temperature of polymers, Tg, is an important thermophysical property, which sometimes can be difficult to measure experimentally. In this regard, data-driven machine learning approaches are important alternatives to assess Tg values, in a high-throughput way. In this study, a large dataset of more than 900 polymers with reported glass transition temperature (Tg) was assembled from various public sources in order to develop a predictive model depicting the structure-property relationships. The collected dataset was curated, explored via cluster analysis, and then split into training and test sets for validation purposes and then polymer structures characterized by molecular descriptors. To find the models, several machine learning techniques, including multiple linear regression (MLR), k-nearest neighbor (k-NN), support vector machine (SVM), random forest (RF), gaussian processes for regression (GPR), and multi-layer perceptron (MLP) were explored. As result, a model with the subset of 15 descriptors accurately predicting the glass transition temperatures was developed. The electronic effect indices were determined to be important properties that positively contribute to the Tg values. The SVM-based model showed the best performance with determination coefficients (R2) of 0.813 and 0.770, for training and test sets, respectively. Also, the SVM model showed the lowest estimation error, RMSE = 0.062. In addition, the developed structure-property model was implemented as a web app to be used as an online computational tool to design and evaluate new homopolymers with desired glass transition profiles. Glass transition temperatures (Tg) of polymers are important thermophysical descriptors, but they can be difficult to determine experimentally. Here, the authors develop a data-driven support vector machine structure-property model to assess Tg values in a high-throughput manner, and implement the model into a web app.
{"title":"Machine learning analysis of a large set of homopolymers to predict glass transition temperatures","authors":"Gerardo M. Casanola-Martin, Anas Karuth, Hai Pham-The, Humbert González-Díaz, Dean C. Webster, Bakhtiyor Rasulev","doi":"10.1038/s42004-024-01305-0","DOIUrl":"10.1038/s42004-024-01305-0","url":null,"abstract":"Glass transition temperature of polymers, Tg, is an important thermophysical property, which sometimes can be difficult to measure experimentally. In this regard, data-driven machine learning approaches are important alternatives to assess Tg values, in a high-throughput way. In this study, a large dataset of more than 900 polymers with reported glass transition temperature (Tg) was assembled from various public sources in order to develop a predictive model depicting the structure-property relationships. The collected dataset was curated, explored via cluster analysis, and then split into training and test sets for validation purposes and then polymer structures characterized by molecular descriptors. To find the models, several machine learning techniques, including multiple linear regression (MLR), k-nearest neighbor (k-NN), support vector machine (SVM), random forest (RF), gaussian processes for regression (GPR), and multi-layer perceptron (MLP) were explored. As result, a model with the subset of 15 descriptors accurately predicting the glass transition temperatures was developed. The electronic effect indices were determined to be important properties that positively contribute to the Tg values. The SVM-based model showed the best performance with determination coefficients (R2) of 0.813 and 0.770, for training and test sets, respectively. Also, the SVM model showed the lowest estimation error, RMSE = 0.062. In addition, the developed structure-property model was implemented as a web app to be used as an online computational tool to design and evaluate new homopolymers with desired glass transition profiles. Glass transition temperatures (Tg) of polymers are important thermophysical descriptors, but they can be difficult to determine experimentally. Here, the authors develop a data-driven support vector machine structure-property model to assess Tg values in a high-throughput manner, and implement the model into a web app.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01305-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364716","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}
Pub Date : 2024-10-01DOI: 10.1038/s42004-024-01287-z
Tricia Breen Carmichael (she/her) is a Professor in the Department of Chemistry and Biochemistry at the University of Windsor.
特里西娅-布林-卡迈克尔（她/她）是温莎大学化学与生物化学系教授。
{"title":"Women in chemistry: Q&A with Professor Tricia Breen Carmichael","authors":"","doi":"10.1038/s42004-024-01287-z","DOIUrl":"10.1038/s42004-024-01287-z","url":null,"abstract":"Tricia Breen Carmichael (she/her) is a Professor in the Department of Chemistry and Biochemistry at the University of Windsor.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01287-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142360087","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}
Pub Date : 2024-09-30DOI: 10.1038/s42004-024-01308-x
Adrian Sanchez-Fernandez, Ignacio Insua, Javier Montenegro
As in natural cytoskeletons, the cooperative assembly of fibrillar networks can be hosted inside compartments to engineer biomimetic functions, such as mechanical actuation, transport, and reaction templating. Coacervates impose an optimal liquid-liquid phase separation within the aqueous continuum, functioning as membrane-less compartments that can organise such self-assembling processes as well as the exchange of information with their environment. Furthermore, biological fibrillation can often be controlled or assisted by intracellular compartments. Thus, the reconstitution of analogues of natural filaments in simplified artificial compartments, such as coacervates, offer a suitable model to unravel, mimic, and potentially exploit cellular functions. This perspective summarises the latest developments towards assembling fibrillar networks under confinement inside coacervates and related compartments, including a selection of examples ranging from biological to fully synthetic monomers. Comparative analysis between coacervates, lipid vesicles, and droplet emulsions showcases the interplay between supramolecular fibres and the boundaries of the corresponding compartment. Combining inspiration from natural systems and the custom properties of tailored synthetic fibrillators, rational monomer and compartment design will contribute towards engineering increasingly complex and more realistic artificial protocells. The bottom-up reconstitution of natural filaments within simplified artificial cellular compartments, such as coacervates, offer a model to study, mimic, and potentially exploit cellular functions. Here, the authors summarize the latest developments towards assembling confined fibrillar networks inside coacervates and related compartments, including a selection of examples ranging from biological to fully synthetic building blocks.
{"title":"Supramolecular fibrillation in coacervates and other confined systems towards biomimetic function","authors":"Adrian Sanchez-Fernandez, Ignacio Insua, Javier Montenegro","doi":"10.1038/s42004-024-01308-x","DOIUrl":"10.1038/s42004-024-01308-x","url":null,"abstract":"As in natural cytoskeletons, the cooperative assembly of fibrillar networks can be hosted inside compartments to engineer biomimetic functions, such as mechanical actuation, transport, and reaction templating. Coacervates impose an optimal liquid-liquid phase separation within the aqueous continuum, functioning as membrane-less compartments that can organise such self-assembling processes as well as the exchange of information with their environment. Furthermore, biological fibrillation can often be controlled or assisted by intracellular compartments. Thus, the reconstitution of analogues of natural filaments in simplified artificial compartments, such as coacervates, offer a suitable model to unravel, mimic, and potentially exploit cellular functions. This perspective summarises the latest developments towards assembling fibrillar networks under confinement inside coacervates and related compartments, including a selection of examples ranging from biological to fully synthetic monomers. Comparative analysis between coacervates, lipid vesicles, and droplet emulsions showcases the interplay between supramolecular fibres and the boundaries of the corresponding compartment. Combining inspiration from natural systems and the custom properties of tailored synthetic fibrillators, rational monomer and compartment design will contribute towards engineering increasingly complex and more realistic artificial protocells. The bottom-up reconstitution of natural filaments within simplified artificial cellular compartments, such as coacervates, offer a model to study, mimic, and potentially exploit cellular functions. Here, the authors summarize the latest developments towards assembling confined fibrillar networks inside coacervates and related compartments, including a selection of examples ranging from biological to fully synthetic building blocks.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01308-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329477","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}
Pub Date : 2024-09-30DOI: 10.1038/s42004-024-01309-w
Umbertoluca Ranieri, Christophe Bellin, Lewis J. Conway, Richard Gaal, John S. Loveday, Andreas Hermann, Abhay Shukla, Livia E. Bove
Ammonium fluoride (NH₄F) exhibits a variety of crystalline phases depending on temperature and pressure. By employing Raman spectroscopy and synchrotron X-ray diffraction beyond megabar pressures (up to 140 GPa), we have here observed a novel dense solid phase of NH₄F, characterised by the tetragonal P4/nmm structure also observed in other ammonium halides under less extreme pressure conditions, typically a few GPa. Using detailed ab-initio calculations and reevaluating earlier theoretical models pertaining to other ammonium halides, we examine the microscopic mechanisms underlying the transition from the low-pressure cubic phase (P-43m) to the newly identified high-pressure tetragonal phase (P4/nmm). Notably, NH₄F exhibits distinctive properties compared to its counterparts, resulting in a significantly broader pressure range over which this transition unfolds, facilitating the identification of its various stages. Our analysis points to a synergistic interplay driving the transition to the P4/nmm phase, which we name phase VIII. At intermediate pressures (around 40 GPa), a displacive transition of fluorine ions initiates a tetragonal distortion of the cubic phase. Subsequently, at higher pressures (around 115 GPa), every second ammonium ion undergoes a rotational shift, adopting an anti-tetrahedral arrangement. This coupled effect orchestrates the transition process, leading to the formation of the tetragonal phase. Solid ammonium fluoride has fascinating structural similarities with water ice, despite its ionic character. Here, the authors investigate NH4F at room temperature and high pressure, and report a new tetragonal phase formed through displacive transition of fluorine ions and subsequent rotation of ammonium ions in ‘antiferromagnetic’ units at ~115 GPa, which is unlike any form of ice.
{"title":"Structural phase transition in NH₄F under extreme pressure conditions","authors":"Umbertoluca Ranieri, Christophe Bellin, Lewis J. Conway, Richard Gaal, John S. Loveday, Andreas Hermann, Abhay Shukla, Livia E. Bove","doi":"10.1038/s42004-024-01309-w","DOIUrl":"10.1038/s42004-024-01309-w","url":null,"abstract":"Ammonium fluoride (NH₄F) exhibits a variety of crystalline phases depending on temperature and pressure. By employing Raman spectroscopy and synchrotron X-ray diffraction beyond megabar pressures (up to 140 GPa), we have here observed a novel dense solid phase of NH₄F, characterised by the tetragonal P4/nmm structure also observed in other ammonium halides under less extreme pressure conditions, typically a few GPa. Using detailed ab-initio calculations and reevaluating earlier theoretical models pertaining to other ammonium halides, we examine the microscopic mechanisms underlying the transition from the low-pressure cubic phase (P-43m) to the newly identified high-pressure tetragonal phase (P4/nmm). Notably, NH₄F exhibits distinctive properties compared to its counterparts, resulting in a significantly broader pressure range over which this transition unfolds, facilitating the identification of its various stages. Our analysis points to a synergistic interplay driving the transition to the P4/nmm phase, which we name phase VIII. At intermediate pressures (around 40 GPa), a displacive transition of fluorine ions initiates a tetragonal distortion of the cubic phase. Subsequently, at higher pressures (around 115 GPa), every second ammonium ion undergoes a rotational shift, adopting an anti-tetrahedral arrangement. This coupled effect orchestrates the transition process, leading to the formation of the tetragonal phase. Solid ammonium fluoride has fascinating structural similarities with water ice, despite its ionic character. Here, the authors investigate NH4F at room temperature and high pressure, and report a new tetragonal phase formed through displacive transition of fluorine ions and subsequent rotation of ammonium ions in ‘antiferromagnetic’ units at ~115 GPa, which is unlike any form of ice.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01309-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329456","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}
Pub Date : 2024-09-30DOI: 10.1038/s42004-024-01307-y
Professor Hongjing Dou is a full Professor at the Institute of Composite Materials, School of Materials Science and Engineering at Shanghai Jiao Tong University, China, where she leads a research group focused on bionanomaterials and their biomedical applications.
{"title":"Women in chemistry: Q&A with Professor Hongjing Dou","authors":"","doi":"10.1038/s42004-024-01307-y","DOIUrl":"10.1038/s42004-024-01307-y","url":null,"abstract":"Professor Hongjing Dou is a full Professor at the Institute of Composite Materials, School of Materials Science and Engineering at Shanghai Jiao Tong University, China, where she leads a research group focused on bionanomaterials and their biomedical applications.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01307-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329462","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}
Pub Date : 2024-09-30DOI: 10.1038/s42004-024-01311-2
Yi Han, Yaojie Guo, Nan Zhang, Fan Xu, Jarukitt Limwachiranon, Zhenzhen Xiong, Liru Xu, Xu-Ming Mao, Daniel H. Scharf
Fungal natural products from various species often feature hydroxamic acid motifs that have the ability to chelate iron. These compounds have an array of medicinally and ecologically relevant activities. Through genome mining, gene deletion in the host Aspergillus terreus, and heterologous expression experiments, this study has revealed that a nonribosomal peptide synthetase (NRPS) TamA and a specialized cytochrome P450 monooxygenase TamB catalyze the sequential biosynthetic reactions in the formation of terramides A-C, a series of diketopiperazines (DKPs) with hydroxamic acid motifs. Feeding experiments showed that TamB catalyzes an unprecedented di-hydroxylation of the amide nitrogens in the diketopiperazine core. This tailoring reaction led to the formation of two bidentate iron-binding sites per molecule with an unusual iron-binding stoichiometry. The structure of the terramide A-Fe complex was characterized by liquid chromatography-mass spectrometry (LC-MS), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy and electron paramagnetic resonance spectroscopy (EPR). Antimicrobial assays showed that the iron-binding motifs are crucial for the activity against bacteria and fungi. Murine infection experiments indicated that terramide production is crucial for the virulence of A. terreus and could be a potential antifungal drug target. Terramides A-C are produced by Aspergillus terreus and feature hydroxamic acid motifs in diketopiperazines to chelate iron; however, their biosynthesis is not fully understood. Here, the authors probe the function of two key enzymes TamA and TamB and propose the biosynthesis of terramides A-C as well as their function in the virulence of A. terreus.
{"title":"Biosynthesis of iron-chelating terramides A-C and their role in Aspergillus terreus infection","authors":"Yi Han, Yaojie Guo, Nan Zhang, Fan Xu, Jarukitt Limwachiranon, Zhenzhen Xiong, Liru Xu, Xu-Ming Mao, Daniel H. Scharf","doi":"10.1038/s42004-024-01311-2","DOIUrl":"10.1038/s42004-024-01311-2","url":null,"abstract":"Fungal natural products from various species often feature hydroxamic acid motifs that have the ability to chelate iron. These compounds have an array of medicinally and ecologically relevant activities. Through genome mining, gene deletion in the host Aspergillus terreus, and heterologous expression experiments, this study has revealed that a nonribosomal peptide synthetase (NRPS) TamA and a specialized cytochrome P450 monooxygenase TamB catalyze the sequential biosynthetic reactions in the formation of terramides A-C, a series of diketopiperazines (DKPs) with hydroxamic acid motifs. Feeding experiments showed that TamB catalyzes an unprecedented di-hydroxylation of the amide nitrogens in the diketopiperazine core. This tailoring reaction led to the formation of two bidentate iron-binding sites per molecule with an unusual iron-binding stoichiometry. The structure of the terramide A-Fe complex was characterized by liquid chromatography-mass spectrometry (LC-MS), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy and electron paramagnetic resonance spectroscopy (EPR). Antimicrobial assays showed that the iron-binding motifs are crucial for the activity against bacteria and fungi. Murine infection experiments indicated that terramide production is crucial for the virulence of A. terreus and could be a potential antifungal drug target. Terramides A-C are produced by Aspergillus terreus and feature hydroxamic acid motifs in diketopiperazines to chelate iron; however, their biosynthesis is not fully understood. Here, the authors probe the function of two key enzymes TamA and TamB and propose the biosynthesis of terramides A-C as well as their function in the virulence of A. terreus.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01311-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329467","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}
Pub Date : 2024-09-30DOI: 10.1038/s42004-024-01304-1
Atanu Baksi, Hasan Zerze, Aman Agrawal, Alamgir Karim, Gül H. Zerze
Complex coacervates play essential roles in various biological processes and applications. Although substantial progress has been made in understanding the molecular interactions driving complex coacervation, the mechanisms stabilizing coacervates against coalescence remain experimentally challenging and not fully elucidated. We recently showed that polydiallyldimethylammonium chloride (PDDA) and adenosine triphosphate (ATP) coacervates stabilize upon their transfer to deionized (DI) water. Here, we perform molecular dynamics simulations of PDDA-ATP coacervates in supernatant and DI water, to understand the ion dynamics and structure within stable coacervates. We found that transferring the coacervates to DI water results in an immediate ejection of a significant fraction of small ions (Na+ and Cl−) from the surface of the coacervates to DI water. We also observed a notable reduction in the mobility of these counterions in coacervates when in DI water, both in the cluster-forming and slab simulations, together with a lowered displacement of PDDA and ATP. These results suggest that the initial ejection of the ions from the coacervates in DI water may induce an interfacial skin layer formation, inhibiting further mobility of ions in the skin layer. Transferring coacervates based on polydiallyldimethylammonium chloride and adenosine triphosphate into deionized water has been experimentally demonstrated to stabilize them against coalescence. Here, molecular modeling and simulations are used to study the coacervation and stabilization of the relevant polyelectrolyte mixture, systematically investigating the structural and dynamic properties that lead to stability.
复合凝聚态在各种生物过程和应用中发挥着至关重要的作用。尽管在理解驱动复合凝聚的分子相互作用方面取得了重大进展，但稳定凝聚体防止凝聚的机制仍具有实验挑战性，尚未完全阐明。我们最近的研究表明，聚二烯丙基二甲基氯化铵（PDDA）和三磷酸腺苷（ATP）凝聚体在转移到去离子水中后会变得稳定。在此，我们对上清液和去离子水中的 PDDA-ATP 凝聚态进行了分子动力学模拟，以了解稳定凝聚态中的离子动力学和结构。我们发现，将共蒸物转移到去离子水中会导致大量小离子（Na+ 和 Cl-）立即从共蒸物表面喷射到去离子水中。在成团模拟和板块模拟中，我们还观察到这些反离子在去离子水中的流动性明显降低，同时 PDDA 和 ATP 的位移也降低了。这些结果表明，离子最初从去离子水中的共凝聚体中喷出时，可能会诱发界面表皮层的形成，从而抑制离子在表皮层中的进一步移动。实验证明，将基于聚二烯丙基二甲基氯化铵和三磷酸腺苷的凝聚态水转移到去离子水中可以使其稳定，防止凝聚。在此，我们利用分子建模和模拟来研究相关聚电解质混合物的凝聚和稳定，系统地研究了导致稳定的结构和动态特性。
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