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View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases 来自 PEAKs 的观点:PEAK 伪激酶家族结构研究的启示
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-24 DOI: 10.1016/j.sbi.2024.102932
Isabelle S. Lucet , Roger J. Daly
The PEAK family of pseudokinase scaffolds, comprising PEAK1 (originally termed SgK269), PEAK2 (SgK223, the human orthologue of rat Pragmin) and PEAK3 (C19orf35), have emerged as important regulators and integrators of cellular signaling and also play oncogenic roles in a variety of human cancers. These proteins undergo both homo- and heterotypic association that act to diversify signal output. Recently, structural and functional characterization of PEAK3 and its protein–protein interactions have shed light on PEAK signaling dynamics and the interdependency of PEAK family members, how PEAK dimerization regulates the binding of downstream effectors, and how 14-3-3 binding acts to regulate PEAK3 signal output. These important advances form the basis of this review.
伪激酶支架 PEAK 家族包括 PEAK1(原名 SgK269)、PEAK2(SgK223,大鼠 Pragmin 的人类直向同源物)和 PEAK3(C19orf35),它们已成为细胞信号传导的重要调节器和整合器,并在多种人类癌症中发挥致癌作用。这些蛋白会发生同型和异型结合,从而使信号输出多样化。最近,PEAK3 及其蛋白-蛋白相互作用的结构和功能特征研究揭示了 PEAK 信号动态和 PEAK 家族成员的相互依存关系、PEAK 二聚化如何调节下游效应物的结合以及 14-3-3 结合如何调节 PEAK3 信号输出。这些重要进展构成了本综述的基础。
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引用次数: 0
Transcriptional machinery as an architect of genome structure 转录机制是基因组结构的设计师
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-21 DOI: 10.1016/j.sbi.2024.102920
Nadezda A. Fursova, Daniel R. Larson

Chromatin organization, facilitated by compartmentalization and loop extrusion, is crucial for proper gene expression and cell viability. Transcription has long been considered important for shaping genome architecture due to its pervasive activity across the genome and impact on the local chromatin environment. Although earlier studies suggested a minimal contribution of transcription to shaping global genome structure, recent insights from high-resolution chromatin contact mapping, polymer simulations, and acute perturbations have revealed its critical role in dynamic chromatin organization at the level of active genes and enhancer-promoter interactions. In this review, we discuss these latest advances, highlighting the direct interplay between transcriptional machinery and loop extrusion. Finally, we explore how transcription of genes and non-coding regulatory elements may contribute to the specificity of gene regulation, focusing on enhancers as sites of targeted cohesin loading.

通过分区和环挤压促进的染色质组织对于正常的基因表达和细胞活力至关重要。长期以来,转录一直被认为是塑造基因组结构的重要因素,因为转录在整个基因组中普遍活跃,并对局部染色质环境产生影响。虽然早期的研究表明转录对塑造全局基因组结构的贡献微乎其微,但最近从高分辨率染色质接触图谱、聚合物模拟和急性扰动中获得的见解揭示了转录在活跃基因和增强子-启动子相互作用水平的动态染色质组织中的关键作用。在这篇综述中,我们将讨论这些最新进展,强调转录机制与环挤压之间的直接相互作用。最后,我们探讨了基因转录和非编码调控元件如何促进基因调控的特异性,重点关注增强子作为靶向凝聚素加载位点的作用。
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引用次数: 0
The next revolution in computational simulations: Harnessing AI and quantum computing in molecular dynamics 计算模拟的下一次革命:在分子动力学中利用人工智能和量子计算
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-21 DOI: 10.1016/j.sbi.2024.102919
Anna Lappala

The integration of artificial intelligence, machine learning and quantum computing into molecular dynamics simulations is catalyzing a revolution in computational biology, improving the accuracy and efficiency of simulations. This review describes the advancements and applications of these technologies to process vast molecular dynamics simulation datasets, adapt parameters of simulations and gain insight into complex biological processes. These advances include the use of predictive force fields, adaptive algorithms and quantum-assisted methodologies. While the integration of artificial intelligence and quantum computing with MD simulations provides insightful and stimulating improvements to our understanding of molecular mechanisms, it could introduce new issues related to data quality, interpretability of models and computational complexity. Modern multidisciplinary approaches are needed to navigate these challenges and exploit the potential of these emerging technologies for MD simulations of biomolecular systems.

将人工智能、机器学习和量子计算整合到分子动力学模拟中,正在催化计算生物学的一场革命,提高模拟的准确性和效率。本综述介绍了这些技术在处理庞大的分子动力学模拟数据集、调整模拟参数和深入了解复杂生物过程方面的进展和应用。这些进步包括使用预测力场、自适应算法和量子辅助方法。虽然人工智能和量子计算与 MD 模拟的整合为我们了解分子机理提供了富有洞察力和激励性的改进,但也可能带来与数据质量、模型可解释性和计算复杂性有关的新问题。需要采用现代多学科方法来应对这些挑战,并挖掘这些新兴技术在生物分子系统 MD 模拟方面的潜力。
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引用次数: 0
Structural and dynamic studies of chromatin by solid-state NMR spectroscopy 利用固态核磁共振光谱对染色质进行结构和动态研究
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-17 DOI: 10.1016/j.sbi.2024.102921
Christopher P. Jaroniec

Chromatin is a complex of DNA with histone proteins organized into nucleosomes that regulates genome accessibility and controls transcription, replication and repair by dynamically switching between open and compact states as a function of different parameters including histone post-translational modifications and interactions with chromatin modulators. Continuing advances in structural biology techniques including X-ray crystallography, cryo-electron microscopy and nuclear magnetic resonance (NMR) spectroscopy have facilitated studies of chromatin systems, in spite of challenges posed by their large size and dynamic nature, yielding important functional and mechanistic insights. In this review we highlight recent applications of magic angle spinning solid-state NMR – an emerging technique that is uniquely-suited toward providing atomistic information for rigid and flexible regions within biomacromolecular assemblies – to detailed characterization of structure, conformational dynamics and interactions for histone core and tail domains in condensed nucleosomes and oligonucleosome arrays mimicking chromatin at high densities characteristic of the cellular environment.

染色质是 DNA 与组蛋白组成核小体的复合物,它调节基因组的可及性,并控制转录、复制和修复,通过在开放状态和紧密状态之间动态切换作为不同参数(包括组蛋白翻译后修饰以及与染色质调节剂的相互作用)的函数。结构生物学技术(包括 X 射线晶体学、低温电子显微镜和核磁共振(NMR)光谱)的不断进步促进了染色质系统的研究,尽管其庞大的体积和动态性质带来了挑战,但仍产生了重要的功能和机理见解。在这篇综述中,我们将重点介绍魔角旋转固态核磁共振的最新应用--这种新兴技术非常适合为生物大分子组装体中的刚性和柔性区域提供原子信息--在细胞环境特有的高密度条件下,对凝聚核小体和寡核苷酸阵列中组蛋白核心和尾域的结构、构象动力学和相互作用进行详细表征。
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引用次数: 0
Single particle cryo-EM map and model validation: It's not crystal clear 单颗粒低温电子显微镜图和模型验证:并非清澈见底
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-17 DOI: 10.1016/j.sbi.2024.102918
Gabriel C. Lander

The application of single particle cryogenic electron microscopy (cryo-EM) to structure determination continues to have a transformative impact on our understanding on biological systems. While there has been a great deal of algorithmic development focused on improving attainable resolutions and streamlining atomic model building, there has not been commensurate development of validation metrics to ensure the accuracy of our cryo-EM maps and models. This review emphasizes the persistent issues that currently complicate single particle cryo-EM structure validation, and highlights the metrics that are gaining broad acceptance by the community. This article aims to underscore the need for further development of validation criteria and the potential role of machine learning methodologies in confidently assessing the quality of cryo-EM structures.

单颗粒低温电子显微镜(cryo-EM)在结构确定方面的应用将继续对我们了解生物系统产生变革性影响。虽然在提高可实现分辨率和简化原子模型构建方面进行了大量算法开发,但在确保低温电子显微镜图谱和模型准确性的验证指标方面却没有相应的发展。本综述强调了目前使单颗粒低温电子显微镜结构验证复杂化的顽固问题,并重点介绍了正在被业界广泛接受的指标。本文旨在强调进一步制定验证标准的必要性,以及机器学习方法在自信地评估冷冻电镜结构质量方面的潜在作用。
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引用次数: 0
Combining single-molecule and structural studies reveals protein and DNA conformations and assemblies that govern DNA mismatch repair 结合单分子和结构研究揭示支配 DNA 错配修复的蛋白质和 DNA 构象与组合
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-10 DOI: 10.1016/j.sbi.2024.102917
Dorothy A. Erie , Keith R. Weninger

DNA mismatch repair (MMR) requires coordinated sequential actions of multiple proteins during a window of time after the replication apparatus makes an error and before the newly synthesized DNA undergoes chromosome compaction and/or methylation of dGATC sites in some γ-proteobacteria. In this review, we focus on the steps carried out by MutS and MutL homologs that initiate repair. We connect new structural data to early and recent single-molecule FRET and atomic force microscopy (AFM) studies to reveal insights into how signaling within the MMR cascade connects MutS homolog recognition of a mismatch to downstream repair. We present unified models of MMR initiation that account for the differences in the strand discrimination signals between methyl- and non-methyl-directed MMR.

在一些γ-蛋白细菌中,DNA错配修复(MMR)需要在复制装置出错后、新合成的DNA进行染色体压实和/或dGATC位点甲基化之前的一段时间内,由多个蛋白质协调依次进行。在这篇综述中,我们重点讨论了 MutS 和 MutL 同源物启动修复的步骤。我们将新的结构数据与早期和近期的单分子 FRET 和原子力显微镜(AFM)研究联系起来,揭示了 MMR 级联中的信号传递是如何将 MutS 同源物对错配的识别与下游修复联系起来的。我们提出了 MMR 启动的统一模型,这些模型解释了甲基导向和非甲基导向 MMR 之间链分辨信号的差异。
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引用次数: 0
Cryo-EM: A window into the dynamic world of RNA molecules 低温电子显微镜:了解 RNA 分子动态世界的窗口
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-03 DOI: 10.1016/j.sbi.2024.102916
Xiaojing Zhang, Shanshan Li, Kaiming Zhang

RNAs are critical for complex cellular functions, characterized by their structural versatility and ability to undergo conformational transitions in response to cellular cues. The elusive structures of RNAs are being unraveled with unprecedented clarity, thanks to the technological advancements in structural biology, including nuclear magnetic resonance (NMR), X-ray crystallography, cryo-electron microscopy (cryo-EM) etc. This review focuses on examining the revolutionary impact of cryo-EM on our comprehension of RNA structural dynamics, underscoring the technique's contributions to structural biology and envisioning the future trajectory of this rapidly evolving field.

RNA 对于复杂的细胞功能至关重要,其特点是结构多变,能够根据细胞线索发生构象转变。由于结构生物学技术的进步,包括核磁共振(NMR)、X 射线晶体学、冷冻电镜(cryo-EM)等,难以捉摸的 RNA 结构正以前所未有的清晰度被揭开。这篇综述重点探讨了冷冻电镜技术对我们理解 RNA 结构动力学的革命性影响,强调了该技术对结构生物学的贡献,并展望了这一快速发展领域的未来轨迹。
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引用次数: 0
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER) 膜对 HIV-1 包膜近端外部区域(MPER)抗原呈递的影响
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-21 DOI: 10.1016/j.sbi.2024.102897
Cesar A. López , S. Munir Alam , Cynthia A. Derdeyn , Barton F. Haynes , Sandrasegaram Gnanakaran

The membrane proximal external region (MPER) of the HIV envelope glycoproteins has generated renewed interest after a recent phase I vaccine trial that presented MPER lipid-peptide epitopes demonstrated promise to elicit a broad neutralization response. The antigenicity of MPER is intimately associated with the membrane, and its presentation relies significantly on the lipid composition. This review brings together recent findings on the influence of membranes on the conformation of MPER and its recognition by broadly neutralizing antibodies. Specifically, the review highlights the importance of properly accounting for the balance between protein–protein and membrane–protein interactions in vaccine design.

最近的一项 I 期疫苗试验显示,呈现 MPER 脂质肽表位的疫苗有望引起广泛的中和反应,这使人们对 HIV 包膜糖蛋白的膜近端外部区域 (MPER) 重新产生了兴趣。MPER 的抗原性与膜密切相关,其表现形式在很大程度上依赖于脂质成分。本综述汇集了有关膜对 MPER 构象的影响及其被广泛中和抗体识别的最新研究成果。具体来说,综述强调了在疫苗设计中适当考虑蛋白质-蛋白质和膜-蛋白质相互作用平衡的重要性。
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引用次数: 0
Untangling the pseudoknots of SARS-CoV-2: Insights into structural heterogeneity and plasticity 解开 SARS-CoV-2 的假结:洞察结构异质性和可塑性
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-21 DOI: 10.1016/j.sbi.2024.102912
Justin Aruda , Scott L. Grote , Silvi Rouskin

Since the onset of the COVID-19 pandemic, one productive area of research has focused on the intricate two- and three-dimensional structures taken on by SARS-CoV-2's RNA genome. These structures control essential viral processes, making them tempting targets for therapeutic intervention. This review focuses on two such structured regions, the frameshift stimulation element (FSE), which controls the translation of viral protein, and the 3′ untranslated region (3′ UTR), which is thought to regulate genome replication. For the FSE, we discuss its canonical pseudoknot's threaded and unthreaded topologies, as well as the diversity of competing two-dimensional structures formed by local and long-distance base pairing. For the 3′ UTR, we review the evidence both for and against the formation of its replication-enabling pseudoknot.

自 COVID-19 大流行以来,一个富有成效的研究领域集中在 SARS-CoV-2 的 RNA 基因组所具有的错综复杂的二维和三维结构上。这些结构控制着病毒的基本过程,使其成为治疗干预的诱人目标。本综述将重点讨论两个这样的结构区域,即控制病毒蛋白质翻译的换帧刺激元件(FSE)和被认为能调节基因组复制的 3′ 非翻译区(3′ UTR)。对于 FSE,我们讨论了其典型的假结的螺纹和非螺纹拓扑结构,以及由局部和长距离碱基配对形成的竞争性二维结构的多样性。对于 3′ UTR,我们回顾了支持和反对形成其复制功能假结的证据。
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引用次数: 0
Dynamic interactions drive early spliceosome assembly 动态相互作用推动早期剪接体的组装
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-20 DOI: 10.1016/j.sbi.2024.102907
Santiago Martínez-Lumbreras , Clara Morguet , Michael Sattler

Splicing is a critical processing step during pre-mRNA maturation in eukaryotes. The correct selection of splice sites during the early steps of spliceosome assembly is highly important and crucial for the regulation of alternative splicing. Splice site recognition and alternative splicing depend on cis-regulatory sequence elements in the RNA and trans-acting splicing factors that recognize these elements and crosstalk with the canonical splicing machinery. Structural mechanisms involving early spliceosome complexes are governed by dynamic RNA structures, protein-RNA interactions and conformational flexibility of multidomain RNA binding proteins. Here, we highlight structural studies and integrative structural biology approaches, which provide complementary information from cryo-EM, NMR, small angle scattering, and X-ray crystallography to elucidate mechanisms in the regulation of early spliceosome assembly and quality control, highlighting the role of conformational dynamics.

剪接是真核生物中前 mRNA 成熟过程中的一个关键处理步骤。在剪接体组装的早期步骤中,正确选择剪接位点非常重要,对替代剪接的调控也至关重要。剪接位点的识别和替代剪接取决于 RNA 中的顺式调控序列元件以及识别这些元件并与典型剪接机制发生串联的反式作用剪接因子。涉及早期剪接体复合物的结构机制受动态 RNA 结构、蛋白质-RNA 相互作用以及多域 RNA 结合蛋白构象灵活性的制约。在此,我们重点介绍结构研究和综合结构生物学方法,这些方法提供了低温电子显微镜、核磁共振、小角散射和 X 射线晶体学的互补信息,以阐明早期剪接体组装和质量控制的调控机制,并强调构象动态的作用。
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引用次数: 0
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Current opinion in structural biology
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