Article
Chemistry, Physical
Angus J. Robertson, F. Aaron Cruz-Navarrete, Henry P. Wood, Nikita Vekaria, Andrea M. Hounslow, Claudine Bisson, Matthew J. Cliff, Nicola J. Baxter, Jonathan P. Waltho
Summary: Understanding the factors contributing to the high catalytic efficiencies of enzymes is crucial for catalysis and enzyme design. This study investigates the relationship between binding a phosphodianion group in a distal site, adopting a closed enzyme form, and catalytic proficiency. The results suggest that binding of a phosphodianion group in the distal site stimulates domain closure and stabilizes the closed active form, leading to high catalytic efficiencies.
Article
Multidisciplinary Sciences
Hengjun Cui, Andreas U. Mueller, Marc Leibundgut, Jiawen Tian, Nenad Ban, Eilika Weber-Ban
Summary: This study presents crystal structures of Dop in different functional states, providing insights into the catalytic mechanism of this enzyme. Pupylation and depupylation are reversible protein modification processes mainly acting in members of Actinobacteria.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Jinlong Li, Sijia Wang, Cui Liu, Yixin Li, Yu Wei, Gang Fu, Pi Liu, Hongwu Ma, Dawei Huang, Jianping Lin, Dawei Zhang
Summary: In this study, a computation-driven strategy for optimizing enzyme structures based on simulation-based iterative saturation mutagenesis (ISM) has been proposed. This strategy aims to stabilize the spatial effects of the transition state (TS) by using a transition state analogue (TSA) as a placeholder. The approach was successfully applied to redesign the structure of chitinase and significantly increase its catalytic activity.
Article
Multidisciplinary Sciences
Satoshi Kimura, Veerasak Srisuknimit, Kacie McCarty, Peter C. Dedon, Philip J. Kranzusch, Matthew K. Waldor
Summary: This study characterizes the C-to-psi conversion RNA editing process and its regulation, highlighting the role of the TrcP enzyme and modification network in optimizing translation efficiency.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Yi Shuang Wang, Wan Zheng, Nan Jiang, Yun Xia Jin, Zi Kang Meng, Meng Xin Sun, Yu Liang Zong, Tong Xu, Jiapeng Zhu, Ren Xiang Tan
Summary: This study discovered a new class of enzymes called ChaP that can catalyze the deconstruction of intradiol-like o-quinones and release CO2. Experimental evidence showed that by mutating and replacing specific residues, the enzyme's reaction trajectory and regioselectivity can be altered. The results of this study highlight the catalytic versatility and enzymatic plasticity of VOC enzymes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Xin Xin, Chen Li, Delu Gao, Dunyou Wang
Summary: The study investigates the catalytic power of haloalkane dehalogenase reaction with distinctive descriptors, showing that catalytic power increases with the number of residues; water solvent hinders reactivity; reactive descriptors can describe and predict the catalytic performance for enzyme catalysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Andrew J. O'Donnell, Ruiqi Huang, Jessica J. Barboline, Todd J. Barkman
Summary: Resurrected ancient enzymes of the caffeine synthase shed light on how ancestral biosynthetic catalytic capabilities lead to the convergent evolution of similar biochemical pathways. It appears that modern-day pathways likely originated from ancestral pathways with different inferred flux, and the modern enzymes independently evolved via gene duplication with convergent catalytic characteristics differentiating multiple ancestral activities through mutations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Chemistry, Physical
Isaac Daniel, Bohyeon Kim, Mark Douthwaite, Samuel Pattisson, Richard Lewis, Joseph Cline, David Morgan, Donald Bethell, Christopher Kiely, Steven Mcintosh, Graham Hutchings
Summary: The cooperative redox enhancement effects in Au-Pd systems play a crucial role in promoting bimetallic catalysis in thermochemical oxidation. The electrochemical polarization of two disparate catalytic sites leads to an observed activity enhancement in thermochemical systems, increasing the driving force of each of the composite half reactions in oxidative dehydrogenation.
Article
Chemistry, Physical
Ritesh Singh Maurya, Swetha Jayanthi, Ch Gupta Chandaluri, T. P. Radhakrishnan
Summary: The impact of the mode of assembly of molecules on the properties and functions of molecular materials is a fundamental problem that was investigated through a novel diaminodicyanoquinodimethane derivative in this study. The compound exhibited enhanced fluorescence in the crystalline state, with a noticeable weak and red-shifted fluorescence in the amorphous state. The transformation from amorphous to crystalline state was monitored through imaging techniques and confirmed by diffraction methods.
CHEMISTRY OF MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Guo Qing Tang, Jessica J. H. Elder, Jordan Douglas, Charles W. Carter Jr
Summary: LeuRS is a Class I aaRS that synthesizes leucyl-tRNA for protein synthesis. Signature sequences HxGH and KMSKS stabilize transition-states in amino acid activation and tRNA aminoacylation. Mutations in these signatures have opposite effects in LeuRS and its ancestral model LeuAC, suggesting domain motion in catalysis by LeuRS. The gain of function in LeuAC is attributed to the coordination of HxGH and KMSKS by the anticodon-binding and multiple insertion modules.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Materials Science, Multidisciplinary
Xiaoming Zhang, Lirong Wang, Minghang Li, Weizhen Meng, Ying Liu, Xuefang Dai, Guodong Liu, Yuantong Gu, Junxian Liu, Liangzhi Kou
Summary: This study identifies that the density of topological surface states (TSS) at the Fermi level can serve as a universal catalytic descriptor in metal diborides. The catalytic activity for the hydrogen evolution reaction (HER) is linearly correlated with the projected TSSs on corresponding surfaces, regardless of the material types.
Article
Chemistry, Physical
William Hadinata Lie, Yang Yuwei, Jodie A. Yuwono, Constantine Tsounis, Muhammad Zubair, Joshua Wright, Lars Thomsen, Priyank Kumar, Nicholas Bedford
Summary: Several transition metal oxides and hydroxides have shown promising electrocatalytic activity for the oxidation of 5-hydroxymethyl furfural (HMF), an important biomass-derived compound. However, little is known about the factors influencing the reactivity and selectivity of these materials for HMF electrooxidation (HMFOR). In this study, Co, Ni and Cu-based Prussian blue analogue (PBA) electrocatalysts were investigated to understand their intrinsic electronic contributions to HMFOR activity. Cu-phase PBAs exhibited the highest faradaic efficiency for generating 2,5-furandicarboxylic acid (FDCA) during HMF oxidation. The presence of nucleophilic OH* species on the electrocatalyst's surface was identified as an important factor affecting the activity and selectivity towards FDCA. These findings provide insights into the design of high-performance HMFOR catalysts without relying on catalysts with high oxygen evolution reaction (OER) activity.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Multidisciplinary Sciences
Craig J. Markin, Daniel A. Mokhtari, Siyuan Du, Tzanko Doukov, Fanny Sunden, Jordan A. Cook, Polly M. Fordyce, Daniel Herschlag
Summary: Using high-throughput microfluidic enzyme kinetics, the impacts of single site mutations on the alkaline phosphatase PafA's affinity for two transition state analogs were measured. Active site and active-site-contacting residues had similar effects on catalysis and analog binding, while distal residues that reduced catalysis had little impact on binding and some even increased affinity. A model suggests that distal mutations alter the enzyme's conformation, accommodating larger analogs. These findings indicate the importance of both active site and distal residues in enzyme engineering.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Shalini Tomar, Sudip Chakraborty
Summary: The demand for an electrochemical water-splitting mechanism is increasing due to the growth in green and renewable energy conversion needs. However, developing efficient electrocatalysts remains a major challenge. In this study, DFT was used to investigate the catalytic activities of ZrS2, ZrSe2, and ZrTe2 layered structures for the HER, OER, and ORR reactions. The effects of non-metal functionalization were also examined. The findings provide valuable insights for designing cost-effective and efficient 2D electrocatalysts.
SUSTAINABLE ENERGY & FUELS
(2023)
Article
Biology
Atefeh Ghorbani, S. Javad Khataeipour, Monica H. Solbakken, David N. G. Huebert, Minasadat Khoddami, Khalil Eslamloo, Cassandra Collins, Tiago Hori, Sissel Jentoft, Matthew L. Rise, Mani Larijani
Summary: Research has found that in certain fish species, the important enzyme AID is either inactive or lacks catalytic activity, indicating that secondary antibody diversification is not absolutely conserved in all jawed vertebrates. The inactivation of AID in fish may be an immune adaptation strategy evolved due to their unique reproductive behaviors.