Article
Chemistry, Multidisciplinary
Yi Zhang, Thirakorn Mokkawes, Sam P. de Visser
Summary: DFT calculations reveal a novel mechanism of aromatic defluorination by P450 Compound I, involving either an epoxide intermediate or a 1,2-fluorine shift in an electrophilic intermediate. The presence of a proton donor is crucial, as a strong Fe-F bond can be formed in the absence of one. This study provides insights into the potential application of cytochrome P450 enzymes in biocatalysis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Rong-Zhen Liao, Jing-Xuan Zhang, Zhenyang Lin, Per E. M. Siegbahn
Summary: QM/MM calculations were used to investigate the reduction of acetylene to ethylene catalyzed by the DCCPCh enzyme with an [Fe8S9] double-cubane cluster. Various reaction pathways involving different oxidation states and protonation states were analyzed to find the most favorable one. The reaction proceeds via a special double-electron transfer induced proton transfer mechanism with the anti-ferromagnetically coupled [Fe8S8] cluster delivering electrons to the substrate.
JOURNAL OF CATALYSIS
(2021)
Article
Biochemistry & Molecular Biology
Felix Kaspar, Darian S. Wolff, Peter Neubauer, Anke Kurreck, Vickery L. Arcus
Summary: In this study, a kinetic characterization of a specific enzyme system revealed a measurable change in activation heat capacity in the reaction system, with stability across different medium pH and substrate charge. Furthermore, the results showed that a single halide substitution had minimal impact on ΔC-p double dagger but significantly decreased the activation enthalpy, resulting in a substantial increase in reaction rate.
Review
Biotechnology & Applied Microbiology
Philipp Wendering, Zoran Nikoloski
Summary: Temperature has an impact on cellular processes, and understanding the genetic and molecular mechanisms involved can help mitigate future climate effects. This study provides a systematic review of modeling efforts to investigate temperature effects on various levels of cellular metabolism, comparing computational approaches and theories and discussing their applications in biotechnology. The article also highlights the potential benefits of integrating machine learning and models of different cellular layers to improve insights into temperature effects.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Chemistry, Physical
Die Bai, Man Li, Rong-Zhen Liao
Summary: The merging of transition-metal-catalyzed C-H bond activation with electro-oxidation has become a promising approach for oxidative C-H bond functionalization. However, the specific effects of electro-oxidation on the reaction mechanism of transition-metal catalysis have rarely been studied. In this computational study, the rhodium-catalyzed electrochemical C-H phosphorylation of 2-phenylpyridine by diphenylphosphine oxide was investigated to reveal the mechanistic details. The calculations showed that C-H activation prefers to occur at the Rh(III) state, P-H activation at the Rh(IV) state, and reductive elimination at the Rh(V) state. The mechanistic insights obtained from this study are valuable for understanding transition-metal-catalyzed electro-oxidative C-H bond functionalization.
Article
Energy & Fuels
Jianwei Zhu, Xue Li, Zilong Liu, Xiaoliang Sun, Li Zhao, Yanyan Shi, Guanggang Zhou, Zhenhua Rui, Guiwu Lu
Summary: This study investigated the influencing mechanism of amino acids on the decomposition of methane hydrates through molecular dynamics simulations. The results showed that glycine exhibited excellent performance in accelerating the decomposition of hydrates. Temperature promoted hydrate decomposition, while pressure had both inhibiting and facilitation effects.
Article
Chemistry, Applied
Jing Shen, Robert E. Hayes, Natalia Semagina
Summary: The oxygen storage capacity of exhaust gas treatment catalysts is crucial for stabilizing catalytic activity and improving engine performance, particularly at sub-stoichiometric oxygen-to-fuel ratios. Co3O4 catalysts demonstrate insensitivity of methane conversion to oxygen variations, while the Pd/Co3O4 catalyst shows the best performance at temperatures between 400 and 550 degrees Celsius.
Article
Green & Sustainable Science & Technology
Mingna Zheng, Yanwei Li, Rui Xue, Weiliang Dong, Qingzhu Zhang, Wenxing Wang
Summary: Enzymatic depolymerization is an important method for dealing with PET pollution, but the understanding of depolymerization mechanism of environment-relevant PET waste and the influence of PET size on depolymerization efficiency is still limited. This study used nanosized model substrate to investigate the PET depolymerization process and elucidated the effects of PET size and active site features on activation energy barriers. These findings provide important insights for the development of rational enzyme engineering strategies for environmentally friendly and efficient removal of PET.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Chemistry, Multidisciplinary
Xiaoyang Chen, Zhiguo Wang, Yujiao Lou, Yongzhen Peng, Qiaoyan Zhu, Jian Xu, Qi Wu
Summary: This study successfully achieved an intramolecular stereoselective Stetter reaction catalyzed by benzaldehyde lyase through rational structure screening of various ThDP-dependent enzymes using molecular dynamics simulations. The optimized novel enzyme function exhibited high productivity (up to 99 %) and stereoselectivity (up to 99:1 e.r.).
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Jun-Lin Shi, Shi-Qin Xiang, Dai-Jian Su, Xiaohong Liu, Wei Zhang, Liu-Bin Zhao
Summary: Theoretical simulations suggested that Au-Mo alloy materials act as high-performance electrocatalysts for nitrogen reduction reaction (NRR) by simultaneously promoting NRR and suppressing HER. Adjusting the atomic proportion in alloys could optimize catalytic activity for NRR and HER.
Article
Engineering, Chemical
Xinyu Liu, Hongliang Sheng, Song He, Chunhua Du, Yuansheng Ma, Chichi Ruan, Chunxiang He, Huaming Dai, Yajun Huang, Yuelei Pan
Summary: The pyrolysis kinetics and thermodynamics of hydrophobic silica aerogels under N2 environment were studied using three model-free methods. Based on the calculated kinetic parameters, the pyrolysis mechanism of silica aerogels was discussed. The volatile products of silica aerogel pyrolysis were found to mainly consist of hydrocarbons generated by the decomposition of hydrophobic groups (methyl groups) on the surface. The effects of pyrolysis on the properties of silica aerogels were investigated based on various analysis results.
CHINESE JOURNAL OF CHEMICAL ENGINEERING
(2023)
Article
Materials Science, Multidisciplinary
Xiaoliang Sun, Guanggang Zhou, Zilong Liu, Jianwei Zhu, Fengzhi Guo, Junqing Chen, Wenhao He, Ning Wang, Ge Zhao, Guiwu Lu
Summary: This study systematically investigated the effect of ethanol concentration on methane hydrate decomposition using molecular dynamics simulations. The results showed that the addition of ethanol facilitated methane bubble formation and accelerated hydrate decomposition. Increasing ethanol concentration led to a higher degree of decomposition of the hydrate system.
JOURNAL OF MATERIALS RESEARCH AND TECHNOLOGY-JMR&T
(2021)
Article
Chemistry, Inorganic & Nuclear
Yongsheng Wang, Xinyu Wang, Lipeng Zhang, Yufeng Zhang, Zhaoxiang Xu, Lianyue Lu, Junling Huang, Likun Yin, Wei Zhu, Zhongbin Zhuang
Summary: Iron phosphide nanoparticles are a promising noble metal-free electrocatalyst for the hydrogen evolution reaction, but often face challenges such as limited surface area and oxidative passivation. The structural parameters of oxide precursors have been found to be correlated with the electrochemically active surface area, phase purity, surface oxidation, and hollow morphology of FeP catalysts, thereby affecting their activity. Among the FeP hollow nanoparticles studied, those prepared using Fe3O4 precursor exhibited the highest overall activity, while those prepared using Fe2O3 precursor showed the highest turnover frequency.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Bas Terlingen, Ramon Oord, Mathieu Ahr, Eline Hutter, Coert van Lare, Bert M. Weckhuysen
Summary: The commercialization of CH4 valorization processes is currently hindered by the lack of suitable catalysts. Lanthanide-based catalysts, especially EuOCl, show promising catalytic activity and selectivity in the oxychlorination of CH4. Increasing the HCl concentration can enhance the catalytic performance, making EuOCl a potential candidate for economically viable CH4 valorization process.
Article
Environmental Sciences
Chaoyang Liu, Haixia Tian, Xiaoyue Gu, Ni Li, Xiaoning Zhao, Mei Lei, Hattan Alharbi, Mallavarapu Megharaj, Wenxiang He, Yakov Kuzyakov
Summary: Soil enzymes play a crucial role in carbon and nutrient cycling and are sensitive to warming. This study examines the enzyme responses to warming based on the Arrhenius law and physiological theory. The results show that enzyme catalytic efficiency remains stable at low temperatures and increases at higher temperatures, highlighting the importance of considering physiological theory in understanding enzyme activities under warming.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Juan C. Aledo, Francisco R. Canton, Francisco J. Veredas
SCIENTIFIC REPORTS
(2015)
Article
Biochemistry & Molecular Biology
Juan Carlos Aledo
Article
Evolutionary Biology
Juan Carlos Aledo, Hector Valverde, Manuel Ruiz-Camacho, Ian Morilla, Francisco Demetrio Lopez
GENOME BIOLOGY AND EVOLUTION
(2014)
Article
Multidisciplinary Sciences
Francisco J. Veredas, Francisco R. Canton, J. Carlos Aledo
SCIENTIFIC REPORTS
(2017)
Review
Biochemistry & Molecular Biology
Juan C. Aledo
Article
Biochemistry & Molecular Biology
Juan C. Aledo
Summary: This paper discusses how to correctly determine the K-m and V-max of a michaelian enzyme, avoiding common pitfalls. Analysis of experimental data from biochemistry students revealed significant variations in results, but proper analysis could yield reliable estimates for the kinetic parameters.
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2021)
Article
Biochemical Research Methods
Juan Carlos Aledo
Summary: The software package ptm is designed for studying methionine sulfoxidation, but can be used for analyzing other posttranslational modifications as well. By integrating information from multiple databases, ptm allows for programmatic analysis of thousands of proteins and addresses site- and protein-centric hypotheses related to PTMs.
Review
Biochemistry & Molecular Biology
Juan Carlos Aledo
Summary: Membraneless organelles are non-stoichiometric supramolecular structures in micron scale that can be rapidly assembled/disassembled in response to specific stimuli. Liquid-liquid phase separation provides a physical framework to understand the molecular forces underlying the process and how they can be tuned according to cellular needs, playing a crucial role in cell compartmentalization and RNA metabolism. Proteins with low complexity domains enriched in methionine amino acids undergo reversible methionine sulfoxidation, affecting the assembly/disassembly of biomolecular condensates.
Article
Biochemical Research Methods
Juan Carlos Aledo
Summary: renz is an easy-to-use software package for accurate and efficient estimation of enzyme kinetic parameters. It fills the gap between highly specialized and general-purpose software, providing different methods for users to choose.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Juan Carlos Aledo
Summary: Methionine-rich prion-like proteins exhibit modular nature with larger molecular sizes and higher spatial compaction compared to average human proteins. Computational evidence suggests that the high compactness might be due to the aggregation of methionine residues, indicating a potential redox regulation. Gene ontology and network analyses reveal that methionine-rich prion-like proteins share more gene ontology terms among themselves than with non-methionine-rich counterparts.
Article
Biochemistry & Molecular Biology
Pablo Aledo, Juan Carlos Aledo
Summary: This study proposes a neutral continuous fitness-stability model inspired by the Arrhenius law to explain the observed amino acid substitution rates. The model suggests that the rate of substitution depends on a pre-exponential factor and an exponential term reflecting relative fitness. By analyzing stability changes in proteins and their disease-causing potential, the study found a significant positive correlation between energy values and the fitness effect of substitutions, supporting the validity of the model.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Jose Miguel Valderrama-Martin, Francisco Ortigosa, Juan Carlos Aledo, Concepcion Avila, Francisco M. Canovas, Rafael A. Canas
Summary: The pine (Pinus pinaster) GS1 (PpGS1b.2) gene was identified and shown to have a high sequence identity with the GS1b.1 gene in conifers. Phylogenetic analysis revealed that PpGS1b.2 is restricted to Pinus and Picea genera. Gene expression data suggested a putative role of PpGS1b.2 in plant development, similar to other GS1b genes from angiosperms. Structural and kinetic analysis showed differences between GS1b.1 and GS1b.2 despite their high sequence homology.
Article
Biochemical Research Methods
Juan C. Aledo, Francisco R. Canton, Francisco J. Veredas
BMC BIOINFORMATICS
(2017)
Article
Evolutionary Biology
Juan Carlos Aledo
BMC EVOLUTIONARY BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Juan Carlos Aledo
