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[前沿资讯 ] 蛋白冠调控纳米酶活性研究获新进展 进入全文
科学网
近日，国家纳米科学中心陈春英院士、吴晓春研究员和中国科学院高能物理研究所王黎明研究员团队合作，在蛋白冠调控纳米酶活性研究领域获新进展，相关研究已在《美国化学会志》发表。 纳米酶是一类具有类似天然酶催化活性的功能性纳米材料。目前，已有上千种具有类酶活性的纳米材料被陆续报道并应用于疾病诊断和治疗、生物检测。如何精准地调控纳米酶的催化活性一直是纳米酶设计、功能开发与应用的关键科学问题。在生物医学应用中，纳米酶很可能与生物体液接触，在表面吸附多种类型的蛋白质形成“蛋白冠”。由于多数纳米酶的催化位点位于表面，而蛋白冠在表面吸附形成物理屏障，很可能占据催化位点，但蛋白冠能否影响纳米酶的催化活性并不清楚。 基于此，研究人员以聚二甲基二烯丙基氯化铵(PDDAC)包覆的金铂纳米棒作为模型纳米酶，研究了蛋白冠对纳米酶催化活性的调控作用。发现血浆蛋白冠能显著抑制多种类酶活性，且其抑制效应依赖于蛋白的形状。在纳米酶表面，吸附的纤维蛋白原、纤连蛋白等纤维状蛋白比血清白蛋白等球形蛋白对催化活性的抑制效果更强，原因是纤维状蛋白形成的蛋白网络更致密、孔隙更小，导致参与催化反应的底物更难从孔隙渗透、底物与纳米酶表面接触的机率更小，从而对催化活性的抑制效果更显著。这种蛋白冠抑制纳米酶催化活性现象，首次揭示吸附蛋白的形状是关键调控因素, 为纳米酶的理性设计、功能开发与生物医学应用提供了新的视角和思考。
[学术文献 ] A New-Generation Base Editor with an Expanded Editing Window for Microbial Cell Evolution In Vivo Based on CRISPR‒Cas12b Engineering 进入全文
Advanced Science
Base editors (BEs) are widely used as revolutionary genome manipulation tools for cell evolution. To screen the targeted individuals, it is often necessary to expand the editing window to ensure highly diverse variant library. However, current BEs suffer from a limited editing window of 5–6 bases, corresponding to only 2–3 amino acids. Here, by engineering the CRISPR‒Cas12b, the study develops dCas12b-based CRISPRi system, which can efficiently repress gene expression by blocking the initiation and elongation of gene transcription. Further, based on dCas12b, a new-generation of BEs with an expanded editing window is established, covering the entire protospacer or more. The expanded editing window results from the smaller steric hindrance compared with other Cas proteins. The universality of the new BE is successfully validated in Bacillus subtilis and Escherichia coli. As a proof of concept, a spectinomycin-resistant E. coli strain (BL21) and a 6.49-fold increased protein secretion efficiency in E. coli JM109 are successfully obtained by using the new BE. The study, by tremendously expanding the editing window of BEs, increased the capacity of the variant library exponentially, greatly increasing the screening efficiency for microbial cell evolution.
[学术文献 ] Opportunities and challenges in design and optimization of protein function 进入全文
Nature Reviews Molecular Cell Biology
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calculations, as well as machine learning tools, have dramatically improved protein engineering and design. In this Review, we discuss how these methods have enabled the design of increasingly complex structures and therapeutically relevant activities. Additionally, protein optimization methods have improved the stability and activity of complex eukaryotic proteins. Thanks to their increased reliability, computational design methods have been applied to improve therapeutics and enzymes for green chemistry and have generated vaccine antigens, antivirals and drug-delivery nano-vehicles. Moreover, the high success of design methods reflects an increased understanding of basic rules that govern the relationships among protein sequence, structure and function. However, de novo design is still limited mostly to α-helix bundles, restricting its potential to generate sophisticated enzymes and diverse protein and small-molecule binders. Designing complex protein structures is a challenging but necessary next step if we are to realize our objective of generating new-to-nature activities.
[前沿资讯 ] 北京大学生命科学学院阐明磷酸化酶激酶PhK的组装与激活机制 进入全文
北京大学
PhK是第一个被纯化的蛋白激酶，也是最大、最复杂的蛋白激酶之一，总分子量为1.3兆道尔顿。它包含α、β、γ和δ四个亚基。其中，α和β亚基是结构亚基；γ亚基具有激酶活性，由一个持续激活的N端激酶结构域（KD）和一个C端调节结构域（CRD）组成；δ亚基为钙调蛋白，但其特殊之处在于无论Ca2+是否存在，δ亚基都能紧密结合在PhK中，作为其不可或缺的组成部分4,5。Ca2+可能通过与钙调蛋白结合产生的构象变化激活PhK。尽管关于PhK的研究已经持续近70年，但其具体的组装方式和激活的分子机理仍不完全清楚。2024年3月28日，北京大学生命科学学院肖俊宇课题组在Nature Communications期刊发表题为“Architecture and activation of human muscle phosphorylase kinase”的论文，揭示了PhK全酶的组装和激酶活性自抑制机制，并提出了PhK的Ca2+激活模型。
[学术文献 ] Gut-Derived Exosomes Mediate the Microbiota Dysbiosis-Induced Spermatogenesis Impairment by Targeting Meioc in Mice 进入全文
Advanced Science
iseases like obesity and intestinal inflammation diseases are accompanied by dysbiosis of the gut microbiota (DSGM), which leads to various complications, including systemic metabolic disorders. DSGM reportedly impairs the fertility of male mice; however, the regulatory mechanism is unclear. Exosomes are molecular mediators of intercellular communication, but the regulation of spermatogenesis by non-reproductive tissue-originated exosomes remains unknown. The present study shows that DSGM altered the miRNA expression profile of mouse circulating exosomes and impaired spermatogenesis. Moreover, the single-cell sequencing results indicate that circulating exosomes from mice with DSGM impaired spermatogenesis, while circulating exosomes from wild mice improved spermatogenesis by promoting meiosis. Further study demonstrates that DSGM leads to abnormal upregulation of miR-211-5p in gut-derived circulating exosomes, which inhibited the expression of meiosis-specific with coiled-coil domain (Meioc) in the testes and impaired spermatogenesis by disturbing meiosis process. In summary, this study defines the important role of gut-derived exosomes in connecting the "gut-testis" axis. This study proposes a new concept of the gut exosome testis axis. Following dysbiosis of gut microbiota, miR-211-5p loaded in the gut-derived circulating exosomes is increased abnormally and transported to the testicular seminiferous tubules through the blood circulation, targeting and inhibiting the expression of Meioc, consequently disturbing the meiosis process and impairing spermatogenesis.
[前沿资讯 ] 非模块化脂肪酸合酶参与生成新型核糖体肽类天然产物 进入全文
科学网
核糖体肽类天然产物（RiPPs）是天然来源的具有丰富化学结构和生物活性的多肽化合物。目前，融合多种天然产物合成机制的RiPPs生物合成途径还鲜有报道。美国伊利诺伊大学香槟分校的赵惠民教授团队从自然界中发现并鉴定了一类兼具RiPPs和脂肪酸合成机制的杂合生物合成途径，可生成具有特殊脂酰基修饰的环状多肽lipoavitides，并发现了具有良好底物适应性、可作为多肽化合物改造潜在工具的酰基转移酶。相关成果“Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides”发表在2024年3月25日的Nature Chemistry期刊上。
