Irena Roterman, Michal Brylinski, Fabio Polticelli, A. D. de Brevern
{"title":"Editorial: Structure and function of trans-membrane proteins","authors":"Irena Roterman, Michal Brylinski, Fabio Polticelli, A. D. de Brevern","doi":"10.3389/fchem.2024.1414079","DOIUrl":"https://doi.org/10.3389/fchem.2024.1414079","url":null,"abstract":"","PeriodicalId":507928,"journal":{"name":"Frontiers in Chemistry","volume":"208 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141002051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Editorial: Computational and experimental insights in proton and ion translocating bioenergetic systems","authors":"Vivek Sharma, Petra Hellwig, Manuela Pereira","doi":"10.3389/fchem.2024.1384385","DOIUrl":"https://doi.org/10.3389/fchem.2024.1384385","url":null,"abstract":"","PeriodicalId":507928,"journal":{"name":"Frontiers in Chemistry","volume":"129 51","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140078629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Basudev Baral, A. Altaee, Konstantinos Simeonidis, A. Samal
{"title":"Editorial: Shape and size dependent nanostructures for environmental applications","authors":"Basudev Baral, A. Altaee, Konstantinos Simeonidis, A. Samal","doi":"10.3389/fchem.2024.1362033","DOIUrl":"https://doi.org/10.3389/fchem.2024.1362033","url":null,"abstract":"","PeriodicalId":507928,"journal":{"name":"Frontiers in Chemistry","volume":"20 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139609154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in ChemistryPub Date : 2022-06-14eCollection Date: 2022-01-01DOI: 10.3389/fchem.2022.921787
Alejandro Sanz, Amelia Linares, Mari Cruz García-Gutiérrez, Aurora Nogales, Sandra Paszkiewicz, Agata Zubkiewicz, Anna Szymczyk, Tiberio A Ezquerra
{"title":"Relaxation Dynamics of Biomass-Derived Copolymers With Promising Gas-Barrier Properties.","authors":"Alejandro Sanz, Amelia Linares, Mari Cruz García-Gutiérrez, Aurora Nogales, Sandra Paszkiewicz, Agata Zubkiewicz, Anna Szymczyk, Tiberio A Ezquerra","doi":"10.3389/fchem.2022.921787","DOIUrl":"https://doi.org/10.3389/fchem.2022.921787","url":null,"abstract":"<p><p>This article presents an experimental study on the relaxation dynamics of a series of random copolymers based on bio-friendly comonomers with interesting gas barrier properties. We analyze the relaxation response in the glassy and ultraviscous regime of poly (trimethylene furanoate/sebacate) random copolymers via dielectric spectroscopy. We report lower values of dynamic fragility [a dimensionless index introduced in 1985 (Angell, Relaxations in Complex Systems, 1985)] in comparison to popular polyesters widely used in industry, such as poly (ethylene terephthalate), suggesting that the amorphous phase of these furanoate-based polyesters adopt an efficient chain packing. This is consistent with their low permeability to gases. We also discuss on different equations (phenomenological and theory-based approaches) for fitting the temperature-evolution of the alpha relaxation time.</p>","PeriodicalId":507928,"journal":{"name":"Frontiers in Chemistry","volume":" ","pages":"921787"},"PeriodicalIF":5.5,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9237226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40551280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in ChemistryPub Date : 2021-05-04eCollection Date: 2021-01-01DOI: 10.3389/fchem.2021.650651
Xiaojing Wu, Jérôme Hénin, Laura Baciou, Marc Baaden, Fabien Cailliez, Aurélien de la Lande
{"title":"Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.","authors":"Xiaojing Wu, Jérôme Hénin, Laura Baciou, Marc Baaden, Fabien Cailliez, Aurélien de la Lande","doi":"10.3389/fchem.2021.650651","DOIUrl":"https://doi.org/10.3389/fchem.2021.650651","url":null,"abstract":"<p><p>NOX5 is a member of the NADPH oxidase family which is dedicated to the production of reactive oxygen species. The molecular mechanisms governing transmembrane electron transfer (ET) that permits to shuttle electrons over the biological membrane have remained elusive for a long time. Using computer simulations, we report conformational dynamics of NOX5 embedded within a realistic membrane environment. We assess the stability of the protein within the membrane and monitor the existence of cavities that could accommodate dioxygen molecules. We investigate the heme-to-heme electron transfer. We find a reaction free energy of a few tenths of eV (ca. -0.3 eV) and a reorganization free energy of around 1.1 eV (0.8 eV after including electrostatic induction corrections). The former indicates thermodynamically favorable ET, while the latter falls in the expected values for transmembrane inter-heme ET. We estimate the electronic coupling to fall in the range of the μeV. We identify electron tunneling pathways showing that not only the W378 residue is playing a central role, but also F348. Finally, we reveal the existence of two connected O<sub>2-</sub>binding pockets near the outer heme with fast exchange between the two sites on the nanosecond timescale. We show that when the terminal heme is reduced, O<sub>2</sub> binds closer to it, affording a more efficient tunneling pathway than when the terminal heme is oxidized, thereby providing an efficient mechanism to catalyze superoxide production in the final step. Overall, our study reveals some key molecular mechanisms permitting reactive oxygen species production by NOX5 and paves the road for further investigation of ET processes in the wide family of NADPH oxidases by computer simulations.</p>","PeriodicalId":507928,"journal":{"name":"Frontiers in Chemistry","volume":" ","pages":"650651"},"PeriodicalIF":5.5,"publicationDate":"2021-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8129163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39002684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in ChemistryPub Date : 2020-12-10eCollection Date: 2020-01-01DOI: 10.3389/fchem.2020.590184
Chao Yang, Jiri Brabec, Libor Veis, David B Williams-Young, Karol Kowalski
{"title":"Solving Coupled Cluster Equations by the Newton Krylov Method.","authors":"Chao Yang, Jiri Brabec, Libor Veis, David B Williams-Young, Karol Kowalski","doi":"10.3389/fchem.2020.590184","DOIUrl":"https://doi.org/10.3389/fchem.2020.590184","url":null,"abstract":"<p><p>We describe using the Newton Krylov method to solve the coupled cluster equation. The method uses a Krylov iterative method to compute the Newton correction to the approximate coupled cluster amplitude. The multiplication of the Jacobian with a vector, which is required in each step of a Krylov iterative method such as the Generalized Minimum Residual (GMRES) method, is carried out through a finite difference approximation, and requires an additional residual evaluation. The overall cost of the method is determined by the sum of the inner Krylov and outer Newton iterations. We discuss the termination criterion used for the inner iteration and show how to apply pre-conditioners to accelerate convergence. We will also examine the use of regularization technique to improve the stability of convergence and compare the method with the widely used direct inversion of iterative subspace (DIIS) methods through numerical examples.</p>","PeriodicalId":507928,"journal":{"name":"Frontiers in Chemistry","volume":" ","pages":"590184"},"PeriodicalIF":5.5,"publicationDate":"2020-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38751135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}