Nature Catalysis最新文献_第5页

The structural basis of pyridoxal-5′-phosphate-dependent β-NAD-alkylating enzymes 依赖吡哆醛-5′-磷酸的β-NAD-烷基化酶的结构基础

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-09-02 DOI: 10.1038/s41929-024-01221-5

Takayoshi Awakawa, Takahiro Mori, Lena Barra, Yusef Ahmed, Richiro Ushimaru, Yaojie Gao, Naruhiko Adachi, Toshiya Senda, Tohru Terada, Dean J. Tantillo, Ikuro Abe

{"title":"The structural basis of pyridoxal-5′-phosphate-dependent β-NAD-alkylating enzymes","authors":"Takayoshi Awakawa, Takahiro Mori, Lena Barra, Yusef Ahmed, Richiro Ushimaru, Yaojie Gao, Naruhiko Adachi, Toshiya Senda, Tohru Terada, Dean J. Tantillo, Ikuro Abe","doi":"10.1038/s41929-024-01221-5","DOIUrl":"10.1038/s41929-024-01221-5","url":null,"abstract":"SbzP is a unique pyridoxal-5′-phosphate-dependent enzyme, which catalyses a [3+2] annulation between the pyridinium ring of β-nicotinamide adenine dinucleotide (β-NAD) and an electron rich β,γ-unsaturated quinonoid derived from S-adenosylmethionine in natural product azaindane antibiotics biosynthesis. The SbzP-mediated annulation has been proposed to be a rare tandem C–C bond formation, but its structural basis and catalytic mechanism remain largely unknown. Here we report the β-NAD-complexed structure of PseP (SbzP homologue), identified by cryo-electron microscopy. Structure-based mutagenesis, stopped-flow analysis, thermal shift and surface plasmon resonance analysis identified the important residues for the substrate binding. Molecular dynamics simulations provided insights regarding how the enzyme orients the Cγ of the unsaturated quinonoid to β-NAD. In addition, density functional theory calculations confirmed that the proposed stepwise mechanism is more likely than a pericyclization mechanism. This study provides the structural basis of a pyridoxal-5′-phosphate-dependent enzyme that catalyses nucleophilic Cγ addition and β-NAD processing in natural product biosynthesis. Recently, the pyridoxal-5′-phosphate-dependent enzyme SbzP was reported to catalyse a [3+2]-annulation reaction yielding β-NAD-derived antibiotics. Now, cryo-electron microscopy structures of a stable homologue and computational simulations provide structural and mechanistic insights into this enzymatic reaction.","PeriodicalId":18845,"journal":{"name":"Nature Catalysis","volume":"7 10","pages":"1099-1108"},"PeriodicalIF":42.8,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41929-024-01221-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142117989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states 机器学习生成的动力学模型能准确描述细胞内的代谢状态

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-30 DOI: 10.1038/s41929-024-01220-6

Subham Choudhury, Bharath Narayanan, Michael Moret, Vassily Hatzimanikatis, Ljubisa Miskovic

{"title":"Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states","authors":"Subham Choudhury, Bharath Narayanan, Michael Moret, Vassily Hatzimanikatis, Ljubisa Miskovic","doi":"10.1038/s41929-024-01220-6","DOIUrl":"10.1038/s41929-024-01220-6","url":null,"abstract":"Generating large omics datasets has become routine for gaining insights into cellular processes, yet deciphering these datasets to determine metabolic states remains challenging. Kinetic models can help integrate omics data by explicitly linking metabolite concentrations, metabolic fluxes and enzyme levels. Nevertheless, determining the kinetic parameters that underlie cellular physiology poses notable obstacles to the widespread use of these mathematical representations of metabolism. Here we present RENAISSANCE, a generative machine learning framework for efficiently parameterizing large-scale kinetic models with dynamic properties matching experimental observations. Through seamless integration of diverse omics data and other relevant information, including extracellular medium composition, physicochemical data and expertise of domain specialists, RENAISSANCE accurately characterizes intracellular metabolic states in Escherichia coli. It also estimates missing kinetic parameters and reconciles them with sparse experimental data, substantially reducing parameter uncertainty and improving accuracy. This framework will be valuable for researchers studying metabolic variations involving changes in metabolite and enzyme levels and enzyme activity in health and biotechnology. Despite the availability of large omics datasets, determining intracellular metabolic states is challenging. Now a generative machine learning framework called RENAISSANCE has been developed to estimate missing kinetic parameters and determine time-resolved metabolic reaction rates and metabolite concentrations without requiring training data.","PeriodicalId":18845,"journal":{"name":"Nature Catalysis","volume":"7 10","pages":"1086-1098"},"PeriodicalIF":42.8,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41929-024-01220-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Understanding the interplay between electrocatalytic C(sp3)‒C(sp3) fragmentation and oxygenation reactions 了解电催化 C(sp3)-C(sp3)碎片化和加氧反应之间的相互作用

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-29 DOI: 10.1038/s41929-024-01218-0

Christine Lucky, Shengli Jiang, Chien-Rung Shih, Victor M. Zavala, Marcel Schreier

{"title":"Understanding the interplay between electrocatalytic C(sp3)‒C(sp3) fragmentation and oxygenation reactions","authors":"Christine Lucky, Shengli Jiang, Chien-Rung Shih, Victor M. Zavala, Marcel Schreier","doi":"10.1038/s41929-024-01218-0","DOIUrl":"10.1038/s41929-024-01218-0","url":null,"abstract":"Achieving the selective electrocatalytic activation of C(sp3)–C(sp3) and C(sp3)−H bonds is key to enabling the electricity-driven synthesis of chemicals, the sustainable upgrading of plastics and the development of fuel cells operating on energy-dense liquid fuels. When exposed to electrodes under oxidative bias, hydrocarbons undergo both C–C bond fragmentation and oxygenation. Currently, we lack control over the bifurcation of these pathways. Here we provide insights into the complex network of alkyl transformation reactions, showing that under oxidizing potentials, adsorbed butane transforms to adsorbed CHx fragments, which can be desorbed as methane before oxidation to adsorbed CO. Identifying the branchpoint between C‒C fragmentation and oxygenation allowed us to steer selectivity by applying pulsed potentials tailored to the desorption potential of specific adsorbates and the kinetics of intermediate oxidation. Our findings provide design criteria for improved fuel cell catalysts and open the door to selective C‒C cleavage in electrosynthetic pathways. The electrochemical activation of alkanes on metal catalysts is a complex process that is not fully understood. Now an electrochemical protocol is put forward to isolate the adsorption, fragmentation and oxygenation potential-dependent steps of butane activation on a platinum electrode and derive its intricate reaction network.","PeriodicalId":18845,"journal":{"name":"Nature Catalysis","volume":"7 9","pages":"1021-1031"},"PeriodicalIF":42.8,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142089960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Organocatalytic acylation of remote arene C–H bonds 远端芳烃 C-H 键的有机催化酰化反应

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01195-4

引用次数: 0

Radical control for enantioselective Csp3–Csp3 cross-coupling 对映选择性 Csp3-Csp3 交叉偶联的辐射控制

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01208-2

Ju Byeong Chae, Annika R. Holm, Liviu M. Mirica

引用次数: 0

Reshaping catalysis beyond the conventional 超越传统，重塑催化

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01212-6

Amani M. Ebrahim

引用次数: 0

A structured catalyst for anion exchange membrane water electrolysis 用于阴离子交换膜电解水的结构催化剂

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01210-8

引用次数: 0

Harnessing electron-rich arenes in nickel photoredox catalysis 在镍光氧化催化中利用富电子烯烃

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01196-3

Sneha Nayak, Laura K. G. Ackerman-Biegasiewicz

引用次数: 0

Identifying restructured motifs on iridium oxide catalyst surfaces for water electrolysis 识别电解水用氧化铱催化剂表面的重组图案

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01201-9

引用次数: 0

Atomically dispersed ruthenium hydride on beta zeolite as catalysts for the isomerization of muconates 原子分散的氢化钌在β沸石上作为短碳酸盐异构化的催化剂

IF 42.8 1区化学

Nature Catalysis Pub Date : 2024-08-19 DOI: 10.1038/s41929-024-01205-5

Ibrahim Khalil, Marco Giulio Rigamonti, Kwinten Janssens, Aram Bugaev, Daniel Arenas Esteban, Sven Robijns, Thibaut Donckels, Mostafa Torka Beydokhti, Sara Bals, Dirk De Vos, Michiel Dusselier

{"title":"Atomically dispersed ruthenium hydride on beta zeolite as catalysts for the isomerization of muconates","authors":"Ibrahim Khalil, Marco Giulio Rigamonti, Kwinten Janssens, Aram Bugaev, Daniel Arenas Esteban, Sven Robijns, Thibaut Donckels, Mostafa Torka Beydokhti, Sara Bals, Dirk De Vos, Michiel Dusselier","doi":"10.1038/s41929-024-01205-5","DOIUrl":"10.1038/s41929-024-01205-5","url":null,"abstract":"Searching for sustainable polymers requires access to biomass-based monomers. In that sense, glucose-derived cis,cis-muconic acid stands as a high-potential intermediate. However, to unlock its potential, an isomerization to the value-added trans,trans-isomer, trans,trans-muconic acid, is required. Here we develop atomically dispersed low-loaded Ru on beta zeolite catalysts that produce trans,trans-muconate in ethanol with total conversion (to equilibrium) and a selectivity of >95%. We reach very high turnovers per Ru and productivity rates of 427 mM h−1 (~85 g l−1 h−1), surpassing the bio-based cis,cis-muconic acid production rates by an order of magnitude. By coupling isomerization to Diels–Alder cycloaddition, terephthalate intermediates are produced in around 90% yields, circumventing the isomer equilibrium. Isomerization is promoted by Ru hydride species where the hydrides are generated from the alcohol solvent, as evidenced by Fourier transform infrared spectroscopy. Beyond isomerization, the Ru–zeolite and its hydride-forming capacity could be of use as a heterogeneous catalyst for other hydride chemistries, demonstrated by a successful hydride transfer hydrogenation. Muconic acid is an important bio-based chemical; however its applications are limited by the lack of efficient methods to access its trans,trans-isomer. Here the authors address this problem with a catalyst based on single Ru atoms dispersed on zeolite BEA that is capable of unlocking hydride chemistries.","PeriodicalId":18845,"journal":{"name":"Nature Catalysis","volume":"7 8","pages":"921-933"},"PeriodicalIF":42.8,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0