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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 Q1 CHEMISTRY, PHYSICAL 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
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.
SbzP 是一种独特的依赖于吡哆醛-5′-磷酸的酶,在天然产品氮杂环丁烷抗生素的生物合成过程中,它能催化β-烟酰胺腺嘌呤二核苷酸(β-NAD)的吡啶环与来自 S-腺苷蛋氨酸的富电子β,γ-不饱和类醌之间的[3+2]环化反应。SbzP 介导的环化被认为是一种罕见的串联 C-C 键形成,但其结构基础和催化机理在很大程度上仍然未知。在此,我们报告了通过冷冻电镜鉴定的 PseP(SbzP 同源物)β-NAD 复合物结构。基于结构的诱变、停流分析、热位移和表面等离子体共振分析确定了底物结合的重要残基。分子动力学模拟揭示了酶如何将不饱和类醌的 Cγ 定向到 β-NAD。此外,密度泛函理论计算证实,所提出的逐步机制比周环化机制更有可能。这项研究为一种依赖于吡哆醛-5′-磷酸的酶提供了结构基础,这种酶在天然产物的生物合成过程中催化亲核 Cγ 加成和 β-NAD 处理。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-30 DOI: 10.1038/s41929-024-01220-6
Subham Choudhury, Bharath Narayanan, Michael Moret, Vassily Hatzimanikatis, Ljubisa Miskovic
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.
生成大型全息数据集已成为深入了解细胞过程的例行工作,然而破译这些数据集以确定代谢状态仍具有挑战性。动力学模型可以明确地将代谢物浓度、代谢通量和酶水平联系起来,从而帮助整合全微观数据。然而,确定细胞生理学的动力学参数对这些代谢数学表征的广泛应用构成了明显的障碍。在这里,我们介绍了 RENAISSANCE,这是一种生成式机器学习框架,用于高效地为具有与实验观察相匹配的动态特性的大规模动力学模型设置参数。RENAISSANCE 通过无缝整合各种 omics 数据和其他相关信息(包括细胞外培养基成分、理化数据和领域专家的专业知识),准确描述了大肠杆菌的细胞内代谢状态。它还能估算缺失的动力学参数,并将其与稀少的实验数据相协调,从而大大降低参数的不确定性,提高准确性。这一框架对于研究代谢变化(涉及代谢物和酶水平的变化以及健康和生物技术领域的酶活性)的研究人员非常有价值。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-29 DOI: 10.1038/s41929-024-01218-0
Christine Lucky, Shengli Jiang, Chien-Rung Shih, Victor M. Zavala, Marcel Schreier
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.
实现 C(sp3)-C(sp3)和 C(sp3)-H 键的选择性电催化活化,是实现电力驱动的化学品合成、塑料的可持续升级以及开发使用高能量液体燃料的燃料电池的关键。当碳氢化合物暴露于氧化偏压下的电极时,会发生 C-C 键断裂和氧合反应。目前,我们对这些途径的分叉缺乏控制。在此,我们对烷基转化反应的复杂网络进行了深入研究,结果表明在氧化电位下,吸附的丁烷会转化为吸附的 CHx 片段,在氧化为吸附的 CO 之前,CHx 片段会被解吸为甲烷。确定了 C-C 断裂和氧合之间的支点后,我们就可以根据特定吸附物的解吸电位和中间氧化的动力学原理,通过应用脉冲电位来控制选择性。我们的发现为改进燃料电池催化剂提供了设计标准,并为电合成途径中选择性 C-C 裂解打开了大门。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01195-4
Site-selective acylation of remote arene C(sp2)−H bonds is achieved through N-heterocyclic carbene organocatalysis. This catalytic transformation proceeds through a nitrogen radical-mediated pathway and enables the late-stage modification of drugs, amino acids and peptides under mild conditions.
通过 N-杂环碳烯有机催化实现了远端芳烃 C(sp2)-H 键的位点选择性酰化。这种催化转化通过氮自由基介导的途径进行,可在温和的条件下对药物、氨基酸和肽进行后期修饰。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01208-2
Ju Byeong Chae, Annika R. Holm, Liviu M. Mirica
The enantioselective formation of Csp3–Csp3 bonds is still a substantial challenge in the synthesis of complex molecules. Now, a photocatalytic system has been developed for the enantioselective alkylation of α-amino Csp3−H bonds that promotes the generation of two different alkyl radicals, followed by their cross-coupling at a chiral nickel centre.
在复杂分子的合成过程中,Csp3-Csp3 键的对映选择性形成仍然是一个巨大的挑战。现在,我们已经开发出一种光催化系统,用于α-氨基 Csp3-H 键的对映选择性烷基化,该系统可促进生成两种不同的烷基自由基,然后在手性镍中心进行交叉偶联。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01212-6
Amani M. Ebrahim
The catalysis Gordon Research Conference is a much-anticipated biennial gathering of the community to discuss the frontiers in design and development of catalytic materials and processes. Amani Ebrahim briefly touches upon this year’s themes centred on enabling technologies for sustainable societies.
催化戈登研究大会是备受瞩目的两年一度的学术盛会,旨在讨论催化材料和工艺设计与开发的前沿问题。Amani Ebrahim 简要介绍了今年的主题,即可持续社会的使能技术。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01210-8
A heterogeneous nucleation strategy is used to synthesize a NiFe oxygen evolution reaction catalyst for anion exchange membrane water electrolysis. The resulting catalyst has high electrochemical activity and achieves a stable performance for over 21 months owing to a dense interlayer, which anchors the catalytic layer to the metal substrate.
利用异质成核策略合成了一种用于阴离子交换膜水电解的镍铁氧体进化反应催化剂。由于致密的中间层将催化层固定在金属基底上,因此生成的催化剂具有很高的电化学活性,并能在 21 个月内保持稳定的性能。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01196-3
Sneha Nayak, Laura K. G. Ackerman-Biegasiewicz
Nickel photoredox catalysis is often limited to electron-deficient and neutral arenes. Arylthianthrenium salts can now be used as redox-active reagents to afford general reactivity with electron-rich arenes.
镍的光氧化催化作用通常仅限于缺电子和中性的烯烃。现在,芳基噻蒽盐可用作氧化还原活性试剂,与电子丰富的烯烃发生一般反应。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2024-08-27 DOI: 10.1038/s41929-024-01201-9
Using electron- and X-ray-based characterization techniques, three paracrystalline structural motifs are shown to form at the surface of amorphized iridium oxide catalysts upon use for water electrolysis in acidic conditions. An iridium oxide catalyst containing only these paracrystalline structural motifs achieves enhanced performance, making more efficient use of its limited iridium content.
利用基于电子和 X 射线的表征技术,在酸性条件下用于水电解时,非晶态氧化铱催化剂表面会形成三种副晶结构图案。仅含有这些副晶结构图案的氧化铱催化剂性能得到了提高,使其有限的铱含量得到了更有效的利用。
{"title":"Identifying restructured motifs on iridium oxide catalyst surfaces for water electrolysis","authors":"","doi":"10.1038/s41929-024-01201-9","DOIUrl":"10.1038/s41929-024-01201-9","url":null,"abstract":"Using electron- and X-ray-based characterization techniques, three paracrystalline structural motifs are shown to form at the surface of amorphized iridium oxide catalysts upon use for water electrolysis in acidic conditions. An iridium oxide catalyst containing only these paracrystalline structural motifs achieves enhanced performance, making more efficient use of its limited iridium content.","PeriodicalId":18845,"journal":{"name":"Nature Catalysis","volume":"7 8","pages":"862-863"},"PeriodicalIF":42.8,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142084600","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
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 Q1 CHEMISTRY, PHYSICAL 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
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.
寻找可持续聚合物需要获得基于生物质的单体。从这个意义上说,葡萄糖衍生的顺式、顺式粘多酸是一种极具潜力的中间体。然而,要释放其潜力,需要将其异构化为高附加值的反式、反式异构体--反式、反式粘多酸。在此,我们开发了原子分散低负载 Ru 的β沸石催化剂,可在乙醇中生产反式、反式粘多酸,总转化率(达到平衡)和选择性高达 95%。我们的单位 Ru 转化率非常高,生产率达到 427 mM h-1(约 85 g l-1 h-1),比生物基顺式、顺式粘多酸生产率高出一个数量级。通过将异构化与 Diels-Alder 环加成耦合,对苯二甲酸盐中间体的产量约为 90%,避开了异构体平衡。傅立叶变换红外光谱证明,Ru 氢化物可促进异构化,而氢化物是从醇溶剂中生成的。除了异构化,Ru 沸石及其氢化物形成能力还可用作其他氢化物化学的异质催化剂,氢化物转移加氢反应的成功就证明了这一点。
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Nature Catalysis
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