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Molecular basis for the diversification of lincosamide biosynthesis by pyridoxal phosphate-dependent enzymes 磷酸吡哆醛依赖酶合成利可沙胺多样化的分子基础
IF 21.8 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-06 DOI: 10.1038/s41557-024-01687-7
Takahiro Mori, Yoshitaka Moriwaki, Kosuke Sakurada, Shuang Lyu, Stanislav Kadlcik, Jiri Janata, Aninda Mazumdar, Marketa Koberska, Tohru Terada, Zdenek Kamenik, Ikuro Abe

The biosynthesis of the lincosamide antibiotics lincomycin A and celesticetin involves the pyridoxal-5′-phosphate (PLP)-dependent enzymes LmbF and CcbF, which are responsible for bifurcation of the biosynthetic pathways. Despite recognizing the same S-glycosyl-l-cysteine structure of the substrates, LmbF catalyses thiol formation through β-elimination, whereas CcbF produces S-acetaldehyde through decarboxylation-coupled oxidative deamination. The structural basis for the diversification mechanism remains largely unexplored. Here we conduct structure–function analyses of LmbF and CcbF. X-ray crystal structures, docking and molecular dynamics simulations reveal that active-site aromatic residues play important roles in controlling the substrate binding mode and the reaction outcome. Furthermore, the reaction selectivity and oxygen-utilization of LmbF and CcbF were rationally engineered through structure- and calculation-based mutagenesis. Thus, the catalytic function of CcbF was switched to that of LmbF, and, remarkably, both LmbF and CcbF variants gained the oxidative-amidation activity to produce an unnatural S-acetamide derivative of lincosamide.

lincoamide抗生素lincomycin A和celticsetin的生物合成涉及吡哆醛-5 ' -磷酸(PLP)依赖性酶LmbF和CcbF,它们负责生物合成途径的分叉。尽管识别出底物相同的s -糖基-l-半胱氨酸结构,但LmbF通过β消除催化硫醇形成,而CcbF通过脱羧偶联氧化脱胺产生s -乙醛。多样化机制的结构基础在很大程度上仍未得到探索。本文对LmbF和CcbF进行了结构-功能分析。x射线晶体结构、对接和分子动力学模拟表明,活性位点芳香族残基在控制底物结合模式和反应结果中起着重要作用。此外,通过基于结构和计算的诱变,合理设计LmbF和CcbF的反应选择性和氧利用率。因此,CcbF的催化功能被转换为LmbF的催化功能,并且值得注意的是,LmbF和CcbF变体都获得了氧化酰胺化活性,从而产生了非天然的lincosamide的s -乙酰胺衍生物。
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引用次数: 0
Protein prediction takes the prize 蛋白质预测获奖
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-02 DOI: 10.1038/s41557-024-01699-3
Stacey Paiva
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引用次数: 0
The mystery of crotonyl-CoA 巴豆酰辅酶a的奥秘
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-02 DOI: 10.1038/s41557-024-01678-8
Marinda Westerveld, Rita Petracca
Marinda Westerveld and Rita Petracca describe the current understanding of the biosynthesis of crotonyl-coenzyme A.
Marinda Westerveld和Rita Petracca描述了目前对巴豆酰辅酶A的生物合成的理解。
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引用次数: 0
Electrochemical formation of bis(fluorosulfonyl)imide-derived solid-electrolyte interphase at Li-metal potential 锂金属电位下双(氟磺酰基)亚胺衍生固体-电解质间相的电化学形成
IF 21.8 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-02 DOI: 10.1038/s41557-024-01689-5
Weilai Yu, Kuan-Yu Lin, David T. Boyle, Michael T. Tang, Yi Cui, Yuelang Chen, Zhiao Yu, Rong Xu, Yangju Lin, Guangxia Feng, Zhuojun Huang, Lukas Michalek, Weiyu Li, Stephen J. Harris, Jyh-Chiang Jiang, Frank Abild-Pedersen, Jian Qin, Yi Cui, Zhenan Bao

Lithium bis(fluorosulfonyl)imide-based liquid electrolytes are promising for realizing high coulombic efficiency and long cycle life in next-generation Li-metal batteries. However, the role of anions in the formation of the solid–electrolyte interphase remains unclear. Here we combine electrochemical analyses and X-ray photoelectron spectroscopy measurements, both with and without sample washing, together with computational simulations, to propose the reaction pathways of electrolyte decomposition and correlate the interphase component solubility with the efficacy of passivation. We discover that not all the products derived from interphase-forming reactions are incorporated into the resulting passivation layer, with a notable portion present in the liquid electrolyte. We also find that the high-performance electrolytes can afford a sufficiently passivating interphase with minimized electrolyte decomposition, by incorporating more anion-decomposition products. Overall, this work presents a systematic approach of coupling electrochemical and surface analyses to paint a comprehensive picture of solid–electrolyte interphase formation, while identifying the key attributes of high-performance electrolytes to guide future designs.

氟磺酰亚胺锂基液体电解质有望在下一代锂金属电池中实现高库仑效率和长循环寿命。然而,阴离子在固-电解质间相形成中的作用尚不清楚。在这里,我们结合电化学分析和x射线光电子能谱测量,在有和没有样品洗涤的情况下,结合计算模拟,提出了电解质分解的反应途径,并将相间组分的溶解度与钝化效果联系起来。我们发现,并非所有形成相间反应的产物都被纳入到所产生的钝化层中,其中很大一部分存在于液体电解质中。我们还发现,通过加入更多的阴离子分解产物,高性能电解质可以提供充分钝化的界面相,使电解质分解最小化。总的来说,这项工作提出了一种耦合电化学和表面分析的系统方法,以描绘固体电解质界面形成的全面图景,同时确定高性能电解质的关键属性,以指导未来的设计。
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引用次数: 0
Evolving learning styles 不断发展的学习方式
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-02 DOI: 10.1038/s41557-024-01679-7
Shira Joudan
In grad school, there is time to focus on learning about your field and your project — and to keep up with the literature. Now, as an assistant professor, Shira Joudan explains how learning science is necessarily different as they manage multiple projects and a busy schedule.
在研究生院,有时间专注于学习你的领域和你的项目——并跟上文献的步伐。现在,作为一名助理教授,Shira Joudan解释说,当他们管理多个项目和繁忙的日程时,学习科学必然是不同的。
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引用次数: 0
Phase separation and ageing of glycine-rich protein from tick adhesive 蜱虫黏合剂中富含甘氨酸蛋白的相分离与老化
IF 21.8 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-11-29 DOI: 10.1038/s41557-024-01686-8
Ketan A. Ganar, Manali Nandy, Polina Turbina, Chang Chen, Dennis Suylen, Elisa Nihoul, Emily Louise Pascoe, Stan van der Beelen, Maarten Plaum, Leendert van den Bos, Constantianus J. M. Koenraadt, Ingrid Dijkgraaf, Siddharth Deshpande

Hard ticks feed on their host for multiple days. To ensure firm attachment, they secrete a protein-rich saliva that eventually forms a solid cement cone. The underlying mechanism of this liquid-to-solid transition is currently not understood. This study focuses on the phase transitions of a disordered glycine-rich protein (GRP) found in tick saliva. We show that GRP undergoes liquid–liquid phase separation via simple coacervation to form biomolecular condensates in salty environments. Cation–π and ππ interactions mediated by periodically placed arginine and aromatic amino-acid residues are the primary driving forces that promote phase separation. Interestingly, GRP condensates exhibit ageing by undergoing liquid-to-gel transition over time and exhibit adhesive properties, similar to the naturally occurring cement cone. Finally, we provide evidence for protein-rich condensates in natural tick saliva. Our findings provide a starting point to gain further insights into the bioadhesion of ticks, to develop novel tick control strategies, and towards achieving biomedical applications such as tissue sealants.

硬蜱以宿主为食好几天。为了确保牢固的附着,它们分泌一种富含蛋白质的唾液,最终形成一个坚固的水泥锥体。这种从液体到固体转变的潜在机制目前还不清楚。本研究的重点是在蜱虫唾液中发现的一种富含甘氨酸的蛋白(GRP)的相变。研究表明,GRP在含盐环境中通过简单的凝聚作用进行液液相分离,形成生物分子凝聚物。周期性放置的精氨酸和芳香氨基酸残基介导的阳离子-π和π -π相互作用是促进相分离的主要驱动力。有趣的是,GRP凝析物随着时间的推移会经历液体到凝胶的转变,并表现出与天然水泥锥相似的粘合性能,从而表现出老化。最后,我们提供了天然蜱唾液中富含蛋白质凝聚物的证据。我们的研究结果为进一步了解蜱虫的生物粘附性、开发新的蜱虫控制策略以及实现生物医学应用(如组织密封剂)提供了一个起点。
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引用次数: 0
DNA catch bonds demonstrate the art of getting stuck DNA捕获键展示了卡住的艺术
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-11-29 DOI: 10.1038/s41557-024-01683-x
Russell J. Wilson, Kerstin G. Blank
Biological systems have evolved bonds that strengthen under load, enabling cells to adhere in high shear flow. A DNA-based artificial motif has now been designed to mimic these catch bonds.
生物系统已经进化出在负载下加强的键,使细胞能够在高剪切流中粘附。一种基于dna的人工基序现在被设计用来模拟这些捕获键。
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引用次数: 0
Competitive exclusion among self-replicating molecules curtails the tendency of chemistry to diversify 自我复制分子之间的竞争性排斥抑制了化学多样化的趋势
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-11-29 DOI: 10.1038/s41557-024-01664-0
Marcel J. Eleveld, Yannick Geiger, Juntian Wu, Armin Kiani, Gaël Schaeffer, Sijbren Otto
The transition of chemistry into biology is poorly understood. Key questions include how the inherently divergent nature of chemical reactions can be curtailed, and whether Darwinian principles from biology extend to chemistry. Addressing both questions simultaneously, we now show that the evolutionary principle of competitive exclusion, which states that a single niche can be stably occupied by only one species, also applies to self-replicating chemical systems, and that this principle diminishes the tendency of chemistry to diversify. Specifically, we report two systems in which three different self-replicator quasi-species emerge in a largely stochastic fashion from a mixture of two building blocks (resources). Competitive exclusion leads to the selection of only a single quasi-species when all replicators rely to the same extent on both resources. When one of the quasi-species preferentially uses one resource and another quasi-species specializes in the other (resource partitioning), these replicator quasi-species effectively occupy different niches and were found to coexist in an evolutionary stable steady state. It is unclear whether Darwinian principles extend to chemistry and if they can direct chemistry to produce specific products. Now it has been shown that competition between self-replicating molecules can result in the survival of the fittest product or coexistence of a small subset of products, depending on how resources are partitioned between the replicators.
人们对化学向生物学的转变知之甚少。关键问题包括如何减少化学反应固有的差异性,以及生物学中的达尔文原理是否延伸到化学中。同时解决这两个问题,我们现在表明,竞争排斥的进化原则,即一个单一的生态位只能由一个物种稳定地占据,也适用于自我复制的化学系统,并且这一原则削弱了化学多样化的趋势。具体来说,我们报告了两个系统,其中三个不同的自我复制准物种以一种很大程度上随机的方式从两个构建块(资源)的混合中出现。当所有复制因子对两种资源的依赖程度相同时,竞争性排斥会导致只选择一个准物种。当一个准物种优先使用一种资源而另一个准物种专门使用另一种资源(资源分配)时,这些复制子准物种有效地占据不同的生态位,并在进化稳定状态下共存。
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引用次数: 0
Designing artificial fluorescent proteins and biosensors by genetically encoding molecular rotor-based amino acids 通过对基于分子转子的氨基酸进行基因编码,设计人工荧光蛋白和生物传感器
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-11-28 DOI: 10.1038/s41557-024-01675-x
Liming Hu, Wenbing Cao, Yihaofan Jiang, Wenkang Cai, Xiaoding Lou, Tao Liu
Fluorescent proteins are indispensable tools in biological and medical research. The fluorophores are typically encoded by the primary amino acid sequence, from which a fluorescent molecular rotor structure forms upon protein folding. Here, inspired by the fluorogenic property exhibited by native fluorophores, we designed a collection of fluorogenic non-canonical amino acids that feature this molecular rotor structure—termed fluorescent molecular rotor amino acids (FMR-AAs)—akin to native fluorescent protein fluorophores. By incorporating FMR-AAs into target proteins through an expanded genetic code, we use them as encoded fluorophore analogues within a confined protein microenvironment, thus readily transforming diverse non-fluorescent proteins into artificial fluorescent proteins. We also use FMR-AAs in selected proteins as sensitive fluorescent probes for monitoring protein–protein interactions and detecting protein conformational changes in vitro and in living cells. This approach enables the generation of artificial fluorescent proteins and the development of biosensors from potentially any protein of interest with minor modifications. The toolbox of artificial fluorescent proteins can be expanded by engineering mimics of the molecular rotor-based fluorophore found in the green fluorescent protein (GFP) into diverse protein scaffolds. Now, by genetically encoding mimics of the GFP fluorophore, any protein of interest can be modified to fluoresce either under select circumstances or always (when folded).
荧光蛋白是生物和医学研究中不可或缺的工具。荧光蛋白通常由主氨基酸序列编码,在蛋白质折叠时形成荧光分子转子结构。受原生荧光团的致荧光特性启发,我们设计了一系列具有这种分子转子结构的致荧光非经典氨基酸--荧光分子转子氨基酸(FMR-AAs)--与原生荧光蛋白荧光团类似。我们通过扩展遗传密码将 FMR-AAs 加入目标蛋白质中,将其用作受限蛋白质微环境中的编码荧光团类似物,从而轻松地将各种非荧光蛋白质转化为人工荧光蛋白质。我们还将选定蛋白质中的 FMR-AAs 用作灵敏的荧光探针,用于监测蛋白质与蛋白质之间的相互作用,以及检测体外和活细胞中蛋白质构象的变化。通过这种方法,只需稍加改动,就能生成人工荧光蛋白,并利用可能感兴趣的任何蛋白质开发生物传感器。
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引用次数: 0
Asymmetric dearomative single-atom skeletal editing of indoles and pyrroles 吲哚和吡咯的不对称去原子单原子骨架编辑
IF 21.8 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-11-28 DOI: 10.1038/s41557-024-01680-0
Xiaolong Zhang, Qingmin Song, Shaopeng Liu, Paramasivam Sivaguru, Zhaohong Liu, Yong Yang, Yongyue Ning, Edward A. Anderson, Graham de Ruiter, Xihe Bi

Heterocycle skeletal editing has recently emerged as a powerful tactic for achieving heterocycle-to-heterocycle transmutation without the need for multistep de novo heterocycle synthesis. However, the enantioselective skeletal editing of heteroarenes through single-atom logic remains challenging. Here we report the enantiodivergent dearomative skeletal editing of indoles and pyrroles via an asymmetric carbon-atom insertion, using trifluoromethyl N-triftosylhydrazones as carbene precursors. This strategy provides a straightforward methodology to access enantiomerically enriched six-membered N-heterocycles containing a trifluoromethylated quaternary stereocentre from planar N-heteroarenes. The synthetic utility of this enantiodivergent methodology was demonstrated by a broad evaluation of reaction scope, product derivatization and concise syntheses of drug analogues. Mechanistic studies reveal that the excellent asymmetric induction arises from the initial cyclopropanation step. The asymmetric single-atom insertion strategy is expected to have a broad impact on the field of single-atom skeletal editing and catalytic asymmetric dearomatization of aromatic compounds.

近年来,杂环骨架编辑已成为无需多步从头合成杂环即可实现杂环到杂环嬗变的有力手段。然而,通过单原子逻辑对杂环进行对映选择性骨架编辑仍然具有挑战性。在此,我们报告了以三氟甲基 N-三十烷基肼为碳烯前体,通过不对称碳原子插入,对吲哚和吡咯进行对映选择性非对映骨架编辑的方法。这种策略提供了一种直接的方法,可以从平面 N-heteroarenes 中获得对映体富集的六元 N-heterocycles ,其中包含一个三氟甲基化的四元立体中心。通过对反应范围、产品衍生化和药物类似物的简易合成进行广泛评估,证明了这种对映异构方法的合成实用性。机理研究表明,最初的环丙烷化步骤产生了极佳的不对称诱导效果。不对称单原子插入策略有望在单原子骨架编辑和催化芳香化合物不对称脱芳香领域产生广泛影响。
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引用次数: 0
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Nature chemistry
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