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NMR Studies of Biomolecular Systems 生物分子体系的核磁共振研究。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-15 DOI: 10.1016/j.jmb.2025.169489
Lewis E. Kay, Remco Sprangers
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引用次数: 0
Slow Dynamics Orchestrate Communication Between Binding Sites in the Condensation Domain of a Non-ribosomal Peptide Synthetase 慢动力学协调非核糖体肽合成酶缩合域结合位点之间的通信。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-11 DOI: 10.1016/j.jmb.2025.169484
Megha N. Karanth , Debajyoti De , John P. Kirkpatrick , Mark Jeeves , Teresa Carlomagno
Non-ribosomal peptide synthetases (NRPSs) are complex molecular machineries that synthesize non-proteinaceous peptides in microorganisms. These peptides (NRPs) usually present a wide range of biological activities and are highly regarded as potential anti-cancer and anti-infective agents. Because of their chemical complexity, derivatives of NRPs with tailored pharmacological properties are difficult to synthesize chemically, which has triggered efforts to understand the functional mechanisms of NRPS systems and develop protein engineering strategies aimed at enabling enzymatic synthesis of non-natural NRPs. A fundamental reaction step of NRPS systems is the formation of peptide bonds between amino-acid-like building blocks. This reaction is catalyzed by so-called condensation domains. The structures of several condensation domains and their complexes have been solved by crystallography and electron microscopy, but these structures have failed to provide the key to the design of artificial condensation domains. Here, we use NMR spectroscopy to reveal a complex network of dynamics in the condensation domain of the NRPS responsible for the synthesis of Tomaymycin and reveal how these motions mediate communication between the two substrate binding sites, providing a means to synchronize interactions for efficient catalysis. Our results underline the impact of dynamics, next to structure, on the function of enzymatic units and reinforce the need to consider conformational flexibility in the design of proteins with altered functions.
非核糖体肽合成酶(NRPSs)是微生物合成非蛋白肽的复杂分子机制。这些肽通常具有广泛的生物活性,被认为是潜在的抗癌和抗感染药物。由于其化学复杂性,具有定制药理特性的NRPs衍生物难以化学合成,这促使人们努力了解NRPs系统的功能机制,并开发旨在实现酶合成非天然NRPs的蛋白质工程策略。NRPS系统的一个基本反应步骤是在氨基酸类构建块之间形成肽键。这个反应是由所谓的缩合域催化的。通过晶体学和电子显微镜研究了几种缩合域及其配合物的结构,但这些结构未能为人工缩合域的设计提供关键。在这里,我们使用核磁共振波谱揭示了在负责合成托马霉素的NRPS的缩合域中一个复杂的动力学网络,并揭示了这些运动如何介导两个底物结合位点之间的通信,为有效催化提供了一种同步相互作用的方法。我们的研究结果强调了动力学的影响,其次是结构,对酶单位的功能,并加强了在设计功能改变的蛋白质时考虑构象灵活性的需要。
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引用次数: 0
Molecular Insights into CLD Domain Dynamics and Toxin Recruitment of the HlyA E. coli T1SS HlyA大肠杆菌T1SS CLD结构域动力学和毒素募集的分子研究
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-11 DOI: 10.1016/j.jmb.2025.169485
Rocco Gentile , Stephan Schott-Verdugo , Sakshi Khosa , Cigdem Günes , Michele Bonus , Jens Reiners , Sander H.J. Smits , Lutz Schmitt , Holger Gohlke
Escherichia coli is a Gram-negative opportunistic pathogen causing nosocomial infections through the production of various virulence factors. Type 1 secretion systems (T1SS) contribute to virulence by mediating the one-step secretion of unfolded substrates into the extracellular space, bypassing the periplasm. A well-studied example is the hemolysin A (HlyA) system, which secretes HlyA toxin in an unfolded state across the inner and outer membranes. T1SS typically comprise a homodimeric ABC transporter (HlyB), a membrane fusion protein (HlyD), and the outer membrane protein TolC. Some ABC transporters in T1SS also contain N-terminal C39 peptidase or peptidase-like (CLD) domains implicated in substrate interaction or activation. Recent cryo-EM studies have resolved the inner-membrane complex as trimer of HlyB homodimers with associated HlyD protomers. However, a full structural model including TolC remains unavailable. We present the first complete structural model of the HlyA T1SS, constructed using template- and MSA-based information and validated by SAXS. Molecular dynamics simulations provide insights into the function of the CLD domains, which are partially absent from existing cryo-EM structures. These domains may modulate transport by stabilizing specific conformations of the complex. Simulations with a C-terminal fragment of HlyA indicate that toxin binding occurs in the occluded conformation of HlyB, potentially initiating substrate transport through a single HlyB protomer before transitioning to an inward-facing state. HlyA binding also induces allosteric effects on HlyD, affecting key residues involved in TolC recruitment. These results indicate how substrate recognition and transport are coupled and may support the development of antimicrobial strategies targeting the T1SS.
大肠杆菌是一种革兰氏阴性条件致病菌,通过产生各种毒力因子引起医院感染。1型分泌系统(T1SS)通过介导未折叠底物的一步分泌进入细胞外空间,绕过外周质,从而促进毒力。溶血素A (HlyA)系统是一个被充分研究的例子,它在内外膜上以未展开的状态分泌HlyA毒素。T1SS通常由同二聚体ABC转运蛋白(HlyB)、膜融合蛋白(HlyD)和外膜蛋白TolC组成。T1SS中的一些ABC转运体也含有n端C39肽酶或肽酶样(CLD)结构域,与底物相互作用或激活有关。最近的低温电镜研究已将膜内复合物分解为HlyB同型二聚体与相关HlyD原体的三聚体。然而,包括TolC在内的完整结构模型仍然不可用。我们提出了HlyA T1SS的第一个完整的结构模型,该模型使用基于模板和msa的信息构建,并通过SAXS进行验证。分子动力学模拟提供了对CLD结构域功能的深入了解,这在现有的低温电镜结构中是部分缺失的。这些结构域可以通过稳定复合物的特定构象来调节转运。对HlyA c端片段的模拟表明,毒素结合发生在HlyB的封闭构象中,在过渡到内向状态之前,可能会通过单个HlyB原聚体启动底物运输。HlyA结合还诱导HlyD的变构效应,影响参与TolC募集的关键残基。这些结果表明底物识别和转运是如何耦合的,并可能支持针对T1SS的抗菌策略的开发。
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引用次数: 0
The Symmetric Structure of the Antigenic Loop in Type B HBV Surface Antigen 乙型肝炎病毒表面抗原抗原环的对称结构。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-10 DOI: 10.1016/j.jmb.2025.169483
Weiyu Tao , Xiao He , Lei Chen
Hepatitis B virus (HBV) is an enveloped virus with HBV surface antigen (HBsAg) as the only protein on its viral membrane. The extracellular antigenic loop (AGL) of HBsAg plays a crucial role in viral attachment to host cells, serves as the primary target for neutralizing antibodies (NAbs), and is subject to escape mutations. Previous studies have shown that the AGL exhibits two different structures (Type A and Type B) dictated by distinct disulfide bond linkage. However, due to the flexibility of some regions in previous structure, the complete model of AGLType B and its symmetry remain elusive. Here, we present the cryo-EM structure of AGLType B in complex with the Fab fragment of the NAb H020. The complete structure of AGLType B reveals its two-fold symmetry and it can bind two FabH020 fragments simultaneously. Further analysis elucidates the underlying mechanism of pan-serotype neutralizing capability of H020 and how escape mutations hinder its binding.
乙型肝炎病毒(HBV)是一种包膜病毒,其病毒膜上唯一的蛋白是HBV表面抗原(HBsAg)。HBsAg的细胞外抗原环(AGL)在病毒附着宿主细胞中起着至关重要的作用,是中和抗体(nab)的主要靶点,并且容易发生逃逸突变。先前的研究表明,AGL具有两种不同的结构(A型和B型),由不同的二硫键连接决定。然而,由于先前结构中某些区域的灵活性,AGLType B的完整模型及其对称性仍然难以捉摸。在这里,我们展示了与NAb H020的Fab片段配合物的AGLType B的低温电镜结构。AGLType B的完整结构显示其双重对称性,可以结合两个FabH020片段。进一步的分析阐明了H020泛血清型中和能力的潜在机制,以及逃逸突变如何阻碍其结合。
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引用次数: 0
Temporal Regulation of Signal Recognition Particle During Translation 翻译过程中信号识别粒子的时间调控。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-10 DOI: 10.1016/j.jmb.2025.169482
Ruilin Qian , Radoslaw J. Gora , Sowmya Chandrasekar, Shu-ou Shan
Signal recognition particle (SRP) is a universally conserved protein targeting machine that directs newly synthesized proteins to the endoplasmic reticulum (ER). SRP recognizes signal sequences on nascent ER proteins as they emerge from the ribosome and, in response, activates interaction with the SRP receptor (SR) at the ER membrane. Early work suggested that SRP loses targeting competence as the nascent chain elongates; however, the underlying molecular mechanism remains unclear. Here we address this question using a combination of steady-state and single-molecule fluorescence spectroscopy measurements. A Förster resonance energy transfer (FRET) assay revealed increased dynamic excursions of the signal sequence from SRP on ribosomes bearing longer nascent chains, leading to a suboptimal conformation of SRP and its impaired interaction kinetics with SR. In addition, the nascent polypeptide associated complex (NAC) amplifies the effects of longer nascent chains to further exclude SRP from ER targeting. Our findings reveal the profound effects of an elongating nascent polypeptide on the conformation and activity of SRP and a key role of NAC in the temporal regulation of SRP, which together impose a limited window for cotranslational ER protein targeting during protein synthesis.
信号识别颗粒(Signal recognition particle, SRP)是一种普遍保守的蛋白质靶向机器,它将新合成的蛋白质定向到内质网(endoplasmic network, ER)。SRP识别新生内质网蛋白上的信号序列,当它们从核糖体中出现时,作为响应,激活与内质网膜上的SRP受体(SR)的相互作用。早期的研究表明,随着新生链的延长,SRP失去了靶向能力;然而,潜在的分子机制尚不清楚。在这里,我们使用稳态和单分子荧光光谱测量的组合来解决这个问题。Förster共振能量转移(FRET)分析显示,SRP信号序列在携带较长新生链的核糖体上的动态偏移增加,导致SRP的次优构象及其与sr的相互作用动力学受损。此外,新生多肽相关复合物(NAC)放大了较长新生链的影响,进一步将SRP排除在ER靶向之外。我们的研究结果揭示了一个细长的新生多肽对SRP的构象和活性的深远影响,以及NAC在SRP的时间调控中的关键作用,这两个因素共同为蛋白质合成过程中共翻译ER蛋白靶向提供了一个有限的窗口。
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引用次数: 0
The Interdomain Loop Modulates Conformational Dynamics for the Antibiotic-resistant Activity of TEM-type Extended-spectrum β-lactamases 结构域间环调节tem型宽谱β-内酰胺酶耐药活性的构象动力学。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-09 DOI: 10.1016/j.jmb.2025.169481
Tsz-Fung Wong , Pui-Kin So , Wai-Po Kong , Zhong-Ping Yao
Extended-spectrum β-lactamases (ESBLs) are bacteria-produced enzymes that can hydrolyze and confer extra resistance to new generation β-lactam antibiotics. TEM-type ESBLs are clinically prevalent and have caused serious health problems worldwide. TEM-type ESBLs are the evolutionary products of wild-type TEM-1 β-lactamase mainly through individual or combined mutations of G238S, E104K and M182T, but how these mutations cause conformational dynamics changes of the enzymes and how these changes correlate to their extended-spectrum antibiotic resistance remain unclear. Using hydrogen/deuterium exchange mass spectrometry integrated with molecular dynamics simulation, we revealed the significant effects of these individual or combined mutations on the conformational dynamics of the all-α-domain, α/β-domain and interdomain loop of the enzymes. Particularly, we observed different conformational dynamics changes of the interdomain loop in response to different mutations and substrate binding, which indicated the important role of the interdomain loop in modulating conformational dynamics of ESBLs for the catalytic efficiency. These new findings shed new insights into the antibiotic-resistance mechanism of TEM-type ESBLs and designing of novel inhibitors, and provide clues for the evolutionary strategy of β-lactamases and the studies of proteins with similar linking loops.
广谱β-内酰胺酶(ESBLs)是细菌产生的酶,可以水解并赋予新一代β-内酰胺类抗生素额外的抗性。tem型esbl在临床上普遍存在,并在世界范围内引起了严重的健康问题。tem型ESBLs是野生型TEM-1 β-内酰胺酶主要通过G238S、E104K和M182T的单独或联合突变进化而来的产物,但这些突变如何引起酶的构象动力学变化以及这些变化与它们的广谱抗生素耐药性之间的关系尚不清楚。利用氢/氘交换质谱结合分子动力学模拟,我们揭示了这些单个或组合突变对酶的全α-结构域、α/β-结构域和结构域间环的构象动力学的显著影响。特别是,我们观察到不同突变和底物结合时结构域间环的不同构象动力学变化,这表明结构域间环在调节ESBLs的构象动力学中对催化效率的重要作用。这些新发现为tem型ESBLs的耐药机制和新型抑制剂的设计提供了新的见解,并为β-内酰胺酶的进化策略和具有类似连接环的蛋白质的研究提供了线索。
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引用次数: 0
Rising Stars: Molecular Mechanisms and Chemical Interventions of α-Synuclein Amyloid Aggregation in Parkinson’s Disease 新星:帕金森病α-突触核蛋白淀粉样蛋白聚集的分子机制和化学干预。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-09 DOI: 10.1016/j.jmb.2025.169475
Shengnan Zhang , Kaien Liu , Dan Li , Cong Liu
Parkinson’s disease (PD) is a prevalent neurodegenerative disorder characterized by progressive neuronal loss and pathological aggregation of α-synuclein (α-syn) into amyloid fibrils, which propagate between cells and drive disease progression. Over the past decade, our laboratory has implemented an integrated strategy—combining high-resolution structural biology, molecular biophysics, biochemical and cellular analyses, chemical biology approaches, and in vivo disease models—to elucidate the molecular basis of α-syn pathology. We first determined atomic-resolution structures of full-length α-syn fibrils, revealing diverse polymorphs shaped by familial mutations and post-translational modifications, and linking conformational heterogeneity to phenotypic and pathological diversity. We further elucidated the structural basis underlying the interaction between amyloid fibril and chemical ligands, enabling the rational development of imaging probes and therapeutic modulators. In parallel, we found that the conserved acidic C-terminal region of α-syn fibrils acts as a central interface for driving pathogenic engagement with multiple receptors for neural propagation and inflammation induction, while also binding the autophagy adaptor LC3B to disrupt p62-mediated selective autophagy. Targeting this interface with small molecule inhibitors alleviates α-syn–induced toxicity in cellular models. Together, these findings provide an integrated molecular roadmap for understanding α-syn pathology and advancing precision diagnostics and targeted interventions in PD and related synucleinopathies.
帕金森病(PD)是一种常见的神经退行性疾病,其特征是进行性神经元丧失和α-突触核蛋白(α-syn)病理聚集成淀粉样原纤维,淀粉样原纤维在细胞间繁殖并驱动疾病进展。在过去的十年中,我们的实验室实施了一项综合策略-结合高分辨率结构生物学,分子生物物理学,生化和细胞分析,化学生物学方法和体内疾病模型-来阐明α-syn病理的分子基础。我们首先确定了全长α-syn原纤维的原子分辨率结构,揭示了家族突变和翻译后修饰形成的多种多态性,并将构象异质性与表型和病理多样性联系起来。我们进一步阐明了淀粉样纤维与化学配体相互作用的结构基础,为成像探针和治疗调节剂的合理开发提供了基础。同时,我们发现α-syn原纤维的保守酸性c端区域作为中心界面,驱动病原与多个受体结合,以促进神经传播和炎症诱导,同时还结合自噬接头LC3B,破坏p62介导的选择性自噬。在细胞模型中,用小分子抑制剂靶向该界面可减轻α-syn诱导的毒性。总之,这些发现为了解PD和相关突触核蛋白病的α-syn病理、推进精确诊断和靶向干预提供了一个完整的分子路线图。
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引用次数: 0
Rising Stars: Bioinformatics of Post-translational Modifications 冉冉升起的新星:翻译后修饰的生物信息学。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-09 DOI: 10.1016/j.jmb.2025.169478
Yu Xue
Yu Xue is a professor in the College of Life Science and Technology at Huazhong University of Science and Technology, and hold a joint position in the Hubei Hongshan Laboratory at Huazhong Agricultural University. He received two B.E. degrees in polymer science and technology and computer science from the University of Science and Technology of China (USTC) in 2002, and a Ph.D. degree in cell biology from USTC in 2006. His major research interest is the computational analysis of post-translational modifications (PTMs) in proteins, a field he terms PTM bioinformatics. Since 2004, his group has developed a number of algorithms, including the Group-based Prediction System (GPS), for prediction of PTM sites and their functional relevance. They have also constructed several PTM-related databases and designed methods to analyze PTMomic data and infer key regulatory enzymes. Through extensive collaboration and their own experimental work, they have predicted and uncovered new PTM sites and regulators in dynamic biological processes. He served as a co-founder and secretary general of the Artificial Intelligence Biology (AIBIO) Sub-branch of the Biophysical Society of China. In 2023, he proposed the concept of “vit-molecular language”, drawing an analogy between PTM regulation and human natural languages. He anticipates that cutting-edge AI technology, combined with conventional bioinformatics and experimental approaches, will profoundly empower future PTM studies.
于雪,华中科技大学生命科学与技术学院教授,华中农业大学湖北洪山实验室联合研究员。2002年获中国科学技术大学高分子科学与技术和计算机科学两个学士学位,2006年获中国科学技术大学细胞生物学博士学位。他的主要研究兴趣是蛋白质翻译后修饰(PTM)的计算分析,他将该领域称为PTM生物信息学。自2004年以来,他的团队已经开发了许多算法,包括基于群体的预测系统(GPS),用于预测PTM站点及其功能相关性。他们还构建了几个与ptm相关的数据库,并设计了分析PTMomic数据和推断关键调控酶的方法。通过广泛的合作和他们自己的实验工作,他们预测并发现了动态生物过程中新的PTM位点和调节因子。曾任中国生物物理学会人工智能生物学分会(AIBIO)联合创始人兼秘书长。2023年,他提出了“反分子语言”的概念,将PTM调控与人类自然语言进行类比。他预计,尖端的人工智能技术,结合传统的生物信息学和实验方法,将极大地增强未来PTM研究的能力。
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引用次数: 0
ISWI is an Intrinsically Dynamic Nucleosome Remodeler That Induces Large-scale Histone Dynamics ISWI是一种内在动态的核小体重塑剂,可诱导大规模组蛋白动力学。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-08 DOI: 10.1016/j.jmb.2025.169480
Vincenzo R. Lobbia , Clara L. van Emmerik , María Cristina Trueba Sánchez , Johanna Ludwigsen , Felix Mueller-Planitz , Hugo van Ingen
The chromatin remodeler ISWI plays a crucial role in the maintenance of the dynamic chromatin landscape through its ability to alter nucleosome spacing. Nucleosome remodeling by ISWI involves the translocation of DNA over the histone octamer surface, without disassembly of the nucleosome. Despite the enormous progress in the structural characterization of this process in recent years, it remains unclear to what extent conformational changes in the histone proteins play a role in remodeling. In addition, the conformation and dynamics of regulatory NTR and NegC domains within the remodeler have proven difficult to obtain. Here, we studied the conformational dynamics of fruit fly ISWI and the nucleosome-ISWI complex using solution NMR spectroscopy. We find that the NTR contains a highly dynamic DNA-binding loop and that the NegC domain is packed against ATPase lobe 2 in the free enzyme. Methyl-TROSY data indicate that the ATPase lobes and the NegC domain have substantial μs-ms motions in the free enzyme suggesting that conformational changes during the catalytic cycle are intrinsically encoded. Comparison of histone methyl-TROSY spectra upon binding of different ISWI constructs indicates that binding of a de-inhibited ISWI construct induces largest conformational changes through the histone octamer, affecting histone-DNA and histone-histone contacts. Overall, these findings refine our understanding of the conformational landscape of ISWI and provide strong support for histone plasticity during remodeling to facilitate DNA translocation, highlighting the histone octamer as an allosteric unit.
染色质重塑剂ISWI通过改变核小体间距的能力,在维持动态染色质景观中起着至关重要的作用。ISWI对核小体的重塑涉及DNA在组蛋白八聚体表面的易位,而核小体没有解体。尽管近年来在这一过程的结构表征方面取得了巨大进展,但仍不清楚组蛋白的构象变化在多大程度上在重塑中起作用。此外,重塑器内调节NTR和NegC结构域的构象和动力学已被证明难以获得。本文利用溶液核磁共振波谱技术研究了果蝇ISWI和核小体-ISWI复合物的构象动力学。我们发现NTR包含一个高度动态的dna结合环,并且在游离酶中,NegC结构域被包装在atp酶叶2上。甲基- trosy数据表明,atp酶叶和NegC结构域在游离酶中有大量μs-ms的运动,表明催化循环过程中的构象变化是内在编码的。不同ISWI构建体结合后组蛋白甲基化- trosy光谱的比较表明,去抑制ISWI构建体的结合通过组蛋白八聚体诱导最大的构象变化,影响组蛋白- dna和组蛋白-组蛋白的接触。总的来说,这些发现完善了我们对ISWI构象景观的理解,并为组蛋白在重塑过程中的可塑性提供了强有力的支持,以促进DNA易位,突出了组蛋白八聚体作为一个变构单位。
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引用次数: 0
Unveiling Eukaryotic Membrane Proteins in High Resolution Using Peptide Solubilization 利用肽增溶技术高分辨率揭示真核膜蛋白。
IF 4.5 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-06 DOI: 10.1016/j.jmb.2025.169467
Jiahe Zang , Yiting Shi , Weiyu Tao , Xiaoyu Liu , Wenjun Guo , Lei Chen
Integral membrane proteins are vital for numerous biological functions and their structures are typically studied using X-ray crystallography and cryo-electron microscopy (cryo-EM). However, these techniques require the extraction of target membrane proteins from their native membranes using detergents, which might disrupt the lipid environments and alter protein behavior. In this study, we present a novel method for solubilizing membrane proteins using 4F peptide, thereby eliminating the need for detergents throughout the procedure. We demonstrate that the 4F peptide effectively solubilizes a range of membrane proteins and complexes into 4F-discs, while preserving their functionality and structural integrity. Converting these 4F-discs into nanodiscs further enhances particle homogeneity and facilitates high-resolution structural determination of membrane proteins. Our findings highlight the potential of membrane-solubilizing peptides to advance membrane protein research.
整体膜蛋白对许多生物功能至关重要,其结构通常使用x射线晶体学和冷冻电子显微镜(cryo-EM)进行研究。然而,这些技术需要使用洗涤剂从其天然膜中提取目标膜蛋白,这可能会破坏脂质环境并改变蛋白质行为。在这项研究中,我们提出了一种使用4F肽溶解膜蛋白的新方法,从而在整个过程中消除了对洗涤剂的需要。我们证明了4F肽有效地将一系列膜蛋白和复合物溶解到4F盘中,同时保持了它们的功能和结构完整性。将这些4f圆盘转化为纳米圆盘进一步增强了颗粒的均匀性,并促进了膜蛋白的高分辨率结构测定。我们的发现突出了膜溶肽在推进膜蛋白研究方面的潜力。
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引用次数: 0
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