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Modeling flexible RNA 3D structures and RNA-protein complexes 建模柔性RNA三维结构和RNA-蛋白复合物
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-16 DOI: 10.1016/j.sbi.2025.103137
Rui João Loureiro, Satyabrata Maiti, Kuntal Mondal, Sunandan Mukherjee, Janusz M. Bujnicki
RNA and RNA–protein (RNP) complexes are central to many cellular processes, but the determination of their structures remains challenging due to RNA flexibility and interaction diversity. This review highlights recent computational advances, particularly from the past two years, in predicting and analyzing RNA and RNP structures. We discuss template-based modeling, docking, molecular simulations, and deep learning approaches, with an emphasis on emerging hybrid methods that integrate these strategies. Special attention is given to tools for modeling conformational heterogeneity, folding pathways, and dynamic binding. We also outline machine learning and simulation techniques for ensemble prediction and explore future directions including quantum-enhanced modeling. Together, these developments are enabling more accurate and scalable modeling of both the static and dynamic aspects of RNA and RNP complexes.
RNA和RNA -蛋白(RNP)复合物是许多细胞过程的核心,但由于RNA的灵活性和相互作用的多样性,确定其结构仍然具有挑战性。这篇综述强调了最近的计算进展,特别是过去两年,在预测和分析RNA和RNP结构方面。我们讨论了基于模板的建模、对接、分子模拟和深度学习方法,重点介绍了整合这些策略的新兴混合方法。特别注意的是建模的工具构象异质性,折叠途径,和动态结合。我们还概述了集成预测的机器学习和模拟技术,并探索了未来的方向,包括量子增强建模。总之,这些发展使RNA和RNP复合物的静态和动态方面的建模更加准确和可扩展。
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引用次数: 0
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives 蛋白质- rna适体识别和建模的进展:当前趋势和未来展望
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-14 DOI: 10.1016/j.sbi.2025.103133
Liming Qiu , Xiaoqin Zou
RNA aptamers possess a remarkable ability to selectively target a diverse spectrum of biomolecules with exceptional affinity and specificity. Their distinctive physical and chemical attributes have driven extensive research into their therapeutic, diagnostic, and analytical applications. However, experimental approaches alone are insufficient to meet the growing demand. As a result, accurate and efficient computational methods are playing an increasingly vital role in RNA aptamer sequence design and structural modeling. Recent breakthroughs in biomolecular structure prediction, particularly through deep learning, have further spurred the development of innovative algorithms. In this review, we summarize current computational models for RNA aptamer structure prediction and design, highlighting recent advances in the field.
RNA适配体具有非凡的亲和力和特异性,能够选择性地靶向多种生物分子。它们独特的物理和化学特性推动了对其治疗、诊断和分析应用的广泛研究。然而,仅靠实验方法不足以满足日益增长的需求。因此,精确、高效的计算方法在RNA适体序列设计和结构建模中发挥着越来越重要的作用。最近在生物分子结构预测方面的突破,特别是通过深度学习,进一步刺激了创新算法的发展。在这篇综述中,我们总结了目前用于RNA适体结构预测和设计的计算模型,重点介绍了该领域的最新进展。
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引用次数: 0
Generative AI techniques for conformational diversity and evolutionary adaptation of proteins 蛋白质构象多样性和进化适应的生成人工智能技术
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-14 DOI: 10.1016/j.sbi.2025.103135
Alfie-Louise R. Brownless , Dariia Yehorova , Colin L. Welsh , Shina Caroline Lynn Kamerlin
The advent of AlphaFold and consumer large language models have elicited unprecedented development of artificial intelligence (AI). AI has had substantial impact in every area of research, including in molecular biology. This is principally in thanks to contributions to the Protein Data Bank and various genome sequence databases, providing an astronomical amount of data for model training. These databases contain evolutionary information explicitly and implicitly, allowing accurate predictions and deep insights into biological questions. Here, we describe recent state-of-the-art applications of AI that exploit evolutionary relationships. This includes structure prediction and design, conformational ensemble generation, and functional site identification. We present a brief snapshot of AI usage in studying protein structure and dynamics, a field that is advancing at breakneck speed.
AlphaFold和消费级大语言模型的出现,引发了人工智能(AI)的空前发展。人工智能在包括分子生物学在内的每个研究领域都产生了重大影响。这主要是由于对蛋白质数据库和各种基因组序列数据库的贡献,为模型训练提供了天文数字的数据量。这些数据库明确地或隐含地包含了进化信息,允许对生物学问题进行准确的预测和深入的了解。在这里,我们描述了利用进化关系的人工智能的最新应用。这包括结构预测和设计、构象集合生成和功能位点识别。我们简要介绍了人工智能在研究蛋白质结构和动力学方面的应用,这一领域正在以惊人的速度发展。
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引用次数: 0
Global dynamics behind enzyme catalysis, evolution, and design 酶催化、进化和设计背后的全球动力学
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-12 DOI: 10.1016/j.sbi.2025.103131
Burcu Aykac Fas , Zeynep Erge Akbas Buz , Turkan Haliloglu
Enzymes are inherently dynamic entities, with their functions intricately governed by the interplay between conformational dynamics - ranging from local residue fluctuations to global motions - and biochemical activity. Deciphering how such dynamics coordinate higher-order cooperativity across multiple timescales to drive catalysis remains a fundamental challenge. This mini-review highlights the role of large-scale, collective motions involving domain-level displacements and hinge-based rearrangements, which not only facilitate substrate recognition, transformation, and release, but also emerge from and propagate through multidirectional allosteric interactions. Such dynamic mechanochemical coupling reflects evolutionary memory and provides a blueprint for enzyme design innovations.
酶本质上是动态的实体,其功能受到构象动力学(从局部残留波动到全局运动)和生化活性之间相互作用的复杂控制。破译这种动力学如何在多个时间尺度上协调高阶协同性来驱动催化仍然是一个根本性的挑战。这篇综述强调了涉及域水平位移和基于铰链的重排的大规模集体运动的作用,这些运动不仅促进了底物的识别、转化和释放,而且还通过多向变构相互作用产生和传播。这种动态的机械化学耦合反映了进化记忆,并为酶设计创新提供了蓝图。
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引用次数: 0
Advances in native cell membrane nanoparticles system 天然细胞膜纳米颗粒体系的研究进展
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-06 DOI: 10.1016/j.sbi.2025.103130
Weihua Qiu , Youzhong Guo
The native cell membrane nanoparticles (NCMN) system utilizes membrane-active polymers specifically designed and optimized to extract and stabilize membrane proteins in the form of NCMN particlesfor biochemical and biophysical characterization. The NCMN system is a genuine and advanced detergent-free approach inspired by the membrane activity of the styrene–maleic acid copolymers (SMA), distinguishing it from the nanodisc technology, Salipro technology, and Peptidisc technology. This review introduces the current advancements in the NCMN system, including the development of NCMN polymers, the application of the NCMN system for single-particle cryo-EM analysis, and the functional characterization of membrane proteins.
天然细胞膜纳米颗粒(NCMN)系统利用专门设计和优化的膜活性聚合物,以NCMN颗粒的形式提取和稳定膜蛋白,用于生化和生物物理表征。NCMN系统是一种真正先进的无洗涤剂方法,其灵感来自于苯乙烯-马来酸共聚物(SMA)的膜活性,将其与纳米盘技术、Salipro技术和肽盘技术区分开来。本文介绍了NCMN系统的最新进展,包括NCMN聚合物的发展,NCMN系统在单颗粒低温电镜分析中的应用,以及膜蛋白的功能表征。
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引用次数: 0
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design 纳米圆盘中的HIV-1 gp160:揭示结构和指导疫苗设计
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-05 DOI: 10.1016/j.sbi.2025.103122
Nancy M. Elbaz, Mahmoud L. Nasr
The stabilization of HIV-1 gp160 trimers (Env) within phospholipid bilayer nanodiscs has provided critical structural insights into the membrane-proximal external region (MPER) and the broader dynamics of gp160. Cryo-EM and molecular simulations reveal that the membrane context preserves the MPER architecture and captures spontaneous trimer asymmetry, as well as ectodomain tilting. These dynamic properties expose vulnerable epitopes that are targeted by broadly neutralizing antibodies (bnAbs). Studies using nanodiscs have highlighted how interactions with the membrane affect the structure of gp160, the accessibility of epitopes, and the mechanisms of neutralization, providing important insights for immunogen design. Unlike soluble SOSIP and IDL constructs, full-length nanodisc-embedded gp160 maintains its native stability, flexibility, and the complete set of neutralization epitopes, suggesting that membrane-mimicking platforms are essential for the rational design of next-generation HIV vaccines targeting conserved regions, such as the MPER.
磷脂双层纳米圆盘内HIV-1 gp160三聚体(Env)的稳定为膜近端外区(MPER)和gp160更广泛的动力学提供了关键的结构见解。低温电镜和分子模拟表明,膜环境保留了MPER结构,并捕获了自发的三聚体不对称,以及外畴倾斜。这些动态特性暴露了易受攻击的表位,这些表位是广泛中和抗体(bnAbs)的目标。利用纳米片的研究强调了与膜的相互作用如何影响gp160的结构、表位的可及性和中和机制,为免疫原设计提供了重要的见解。与可溶性SOSIP和IDL构建物不同,全长纳米圆盘嵌入的gp160保持了其固有的稳定性、灵活性和完整的中和表位,这表明膜模拟平台对于合理设计针对保守区域(如MPER)的下一代HIV疫苗至关重要。
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引用次数: 0
Frustration, dynamics, and catalysis 挫折,动力和催化
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-05 DOI: 10.1016/j.sbi.2025.103127
R. Gonzalo Parra , Diego U. Ferreiro
The controlled dissipation of chemical potentials is the fundamental way cells make a living. Enzyme-mediated catalysis allows the various transformations to proceed at biologically relevant rates with remarkable precision and efficiency. Theory, experiments, and computational studies coincide to show that local frustration is a useful concept to relate protein dynamics with catalytic power. Local frustration gives rise to the asperities of the energy landscapes that can harness the thermal fluctuations to guide the functional protein motions. We review here recent advances into these relationships from various fields of protein science. The biologically relevant dynamics is tuned by the evolution of protein sequences that modulate local frustration patterns to near-optimal values.
控制化学势的耗散是细胞生存的基本方式。酶介导的催化使各种转化以生物学相关的速度进行,具有显著的精度和效率。理论、实验和计算研究一致表明,局部挫折是一个有用的概念,将蛋白质动力学与催化力联系起来。局部挫折导致能量景观的凹凸不平,可以利用热波动来指导功能性蛋白质的运动。在此,我们回顾了蛋白质科学各个领域对这些关系的最新进展。生物相关的动态是通过蛋白质序列的进化来调节局部挫折模式到接近最佳值。
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引用次数: 0
Optogenetic enzymes: A deep dive into design and impact 光遗传酶:深入研究设计和影响
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-05 DOI: 10.1016/j.sbi.2025.103126
Tanaya Basu Roy , Mana Heidari , Nikolay V. Dokholyan
Optogenetically regulated enzymes offer unprecedented spatiotemporal control over protein activity, intermolecular interactions, and intracellular signaling. Many design strategies have been developed for their fabrication based on the principles of intrinsic allostery, oligomerization or ‘split’ status, intracellular compartmentalization, and steric hindrance. In addition to employing photosensory domains as part of the traditional optogenetic toolset, the specificity of effector domains has also been leveraged for endogenous applications. Here, we discuss the dynamics of light activation while providing a bird's eye view of the crafting approaches, targets, and impact of optogenetic enzymes in orchestrating cellular functions, as well as the bottlenecks and an outlook into the future.
光遗传学调节酶提供了前所未有的时空控制蛋白质活性,分子间相互作用和细胞内信号。基于内在变构、寡聚或“分裂”状态、细胞内区隔化和空间位阻的原理,已经开发了许多设计策略。除了利用光敏结构域作为传统光遗传学工具集的一部分外,效应结构域的特异性也被用于内源性应用。在这里,我们讨论了光激活的动力学,同时提供了制作方法,目标和光遗传酶在协调细胞功能中的影响的鸟瞰图,以及瓶颈和对未来的展望。
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引用次数: 0
Orchestrating function: Concerted dynamics, allostery, and catalysis in protein tyrosine phosphatases 协调功能:蛋白酪氨酸磷酸酶的协调动力学、变构和催化作用。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-04 DOI: 10.1016/j.sbi.2025.103125
Virgil A. Woods , Shivani Sharma , Alexis M. Lemberikman , Daniel A. Keedy
Protein tyrosine phosphatases (PTPs) are a family of enzymes that play critical roles in intracellular signaling and regulation. PTPs are conformationally dynamic, exhibiting motions of catalytic loops and additional regions of the structurally conserved catalytic domain. However, many questions remain about how dynamics contribute to catalysis and allostery in PTPs, how these behaviors vary among evolutionarily divergent PTP family members, and how mutations and ligands reshape dynamics to modulate PTP function. Recently, our understanding in these areas has expanded significantly, thanks to novel applications of existing methods and emergence of new approaches in structural biology and biophysics. Here we review exciting advances in this realm from the last few years. We organize our commentary both by experimental and computational methodologies, including solution techniques, avant-garde crystallography, molecular dynamics simulations, and bioinformatics, and also by scientific focus, including regulatory mechanisms, mutations and protein engineering, and small-molecule ligands such as allosteric modulators.
蛋白酪氨酸磷酸酶(PTPs)是一个在细胞内信号传导和调控中起关键作用的酶家族。PTPs是构象动态的,表现出催化环的运动和结构保守的催化域的附加区域。然而,关于动力学如何促进PTP的催化和变构,这些行为在进化不同的PTP家族成员中如何变化,以及突变和配体如何重塑动力学以调节PTP功能,仍然存在许多问题。最近,由于结构生物学和生物物理学中现有方法的新应用和新方法的出现,我们对这些领域的理解有了显著的扩展。在这里,我们回顾了过去几年在这一领域取得的令人兴奋的进展。我们通过实验和计算方法组织我们的评论,包括溶液技术,前卫晶体学,分子动力学模拟和生物信息学,以及科学焦点,包括调节机制,突变和蛋白质工程,以及小分子配体,如变构调节剂。
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引用次数: 0
Emerging paradigms in the lateral and transverse organization in biological membrane and their functional implications: Connecting the dots with biomolecular simulations 生物膜横向和横向组织的新范式及其功能含义:用生物分子模拟连接点
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-07-31 DOI: 10.1016/j.sbi.2025.103128
Anand Srivastava
Since the publication of the first papers in the early 1990s, molecular simulation as a reliable biophysical tool in the area of membrane biophysics has come a long way. Advances in simulation algorithms, coupled with exascale computing have pushed the size and time scales of biomolecular membrane simulations to scales where connections to experiments are made with higher fidelity. When integrated with experimental data in a theoretically well-grounded manner, current biomolecular simulations are providing indispensable insights that cannot be obtained through experiments alone. Here, I summarize some recent developments where simulations have allowed a deeper understanding in membrane spatiotemporal organization. I also discuss the need for transformative method developments to meet recent breakthroughs in experimental measurements at molecular scales.
自20世纪90年代初第一批论文发表以来,分子模拟作为一种可靠的生物物理工具在膜生物物理学领域取得了长足的发展。模拟算法的进步,加上百亿亿次计算,已经将生物分子膜模拟的大小和时间尺度推向了更高保真度的实验连接尺度。当以理论上有充分根据的方式与实验数据相结合时,当前的生物分子模拟提供了仅通过实验无法获得的不可或缺的见解。在这里,我总结了一些最近的发展,其中模拟允许对膜时空组织有更深的理解。我还讨论了变革方法发展的必要性,以满足最近在分子尺度上实验测量的突破。
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引用次数: 0
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Current opinion in structural biology
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