Biochimica et biophysica acta. Proteins and proteomics最新文献_第3页

Biophysical characterization of Hpa1 protein from Xanthomonas orzyae 黄单胞菌Hpa1蛋白的生物物理特性研究。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-11-07 DOI: 10.1016/j.bbapap.2025.141111

Jaimini Patoliya , Khushali Thaker , Jahanvi Bajpai , Dhaval Patel , Nayan Jain , Prasant Kumar , Rushikesh Joshi

Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight in rice, secretes a suite of effectors via the Type III Secretion System (T3SS), among which harpin proteins like Hpa1 are key modulators of plant immunity. Unlike other T3SS effectors, Hpa1 lacks enzymatic activity and instead acts as a biostimulant, promoting growth and defense responses. In this study, the hpa1 gene was cloned from Xoo BXO1 strain and successfully expressed in E. coli Rosetta cells. The recombinant protein was purified using Ni-NTA chromatography, and SDS-PAGE, Western blotting, and MALDI-TOF analysis confirmed its molecular weight (∼16.5 kDa). Biophysical characterization revealed a predominance of α-helical content, with CD spectroscopy. Thermal and chemical unfolding of Hpa1 was evaluated using CD spectroscopy (with GuHCl) and ANS fluorescence (with GuHCl and urea), revealing moderate stability. pH-dependent stability assessed by fluorescence showed optimal structural retention at pH 5. TFE-induced structural modulation, studied by CD, demonstrated concentration-dependent α-helix enhancement. Thermal stability was assessed through four approaches: SDS-PAGE, CD at 222 nm, SYPRO Orange-based thermal shift assay, and HR-inducing activity in Nicotiana benthamiana. These results collectively confirmed that native Hpa1 conformation is not necessary for its function. These findings highlight its potential as a protein-based biostimulant for agricultural applications and its utility as a model for studying intrinsically disordered yet functionally stable proteins.

米黄单胞菌。水稻白叶枯病病原菌oryzae （Xoo）通过III型分泌系统（Type III分泌系统，T3SS）分泌一系列效应物，其中Hpa1等harpin蛋白是植物免疫的关键调节剂。与其他T3SS效应物不同，Hpa1缺乏酶活性，而是作为生物刺激物，促进生长和防御反应。本研究从Xoo BXO1菌株中克隆了hpa1基因，并在大肠杆菌Rosetta细胞中成功表达。重组蛋白经Ni-NTA层析纯化，SDS-PAGE、Western blotting和MALDI-TOF分析证实其分子量为~16.5 kDa。生物物理表征表明α-螺旋含量占主导地位。利用CD光谱（含GuHCl）和ANS荧光（含GuHCl和尿素）对Hpa1的热展开和化学展开进行了评估，结果显示Hpa1的稳定性中等。荧光测定的pH依赖性稳定性表明，pH为 5时结构保持最佳。CD研究了tfe诱导的结构调制，显示出浓度依赖性α-螺旋增强。通过四种方法评估热稳定性：SDS-PAGE、222 nm CD、SYPRO橙基热移法和benthamiana诱导hr活性。这些结果共同证实了天然Hpa1构象对其功能不是必需的。这些发现突出了它作为一种基于蛋白质的生物刺激素在农业应用中的潜力，以及它作为研究内在无序但功能稳定的蛋白质的模型的效用。

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引用次数: 0

Self-association of Apolipoprotein A-I studied with multiple-association models: A pyrene multiparametric analysis. 多关联模型研究载脂蛋白A- i的自关联：芘多参数分析。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-11-01 Epub Date: 2025-08-06 DOI: 10.1016/j.bbapap.2025.141093

Wilson A Tárraga, Lisandro J Falomir-Lockhart, Horacio A Garda, Marina C Gonzalez

Apolipoprotein A-I (apoA-I) is the main protein of high-density lipoprotein particles, conferring anti-atherogenic properties through reverse cholesterol transport. In its lipid-free state, apoA-I self-associates, a process implicated in normal physiology as well as in pathological conditions, such as amyloidosis. Although various mechanisms have been proposed to explain its self-association, there is still no consensus, and its functional implications remain unclear. Here, we employed a multi-parametric fluorescent probe to investigate apoA-I self-association. We used three single cysteine mutants located in different helixes: K107C (H4), K133C (H5), and F225C (H10); and labelled them with pyrene as detailed previously (Tárraga et al. Arch Biochem Biophys 699 (2021) 108748). Our original experiments revealed excimer emission between helixes H5 and H10 and polarity changes also in H4. By exploiting specific pyrene band emissions to monitor dimer association (via excimer formation) and microenvironment polarity (P-value), we tracked apoA-I oligomerization as a function of protein concentration. Several mathematical models of self-association were developed and compared using selection criteria to identify the simplest model reproducing apoA-I's complex behaviour in aqueous media: a Sequential Association submodel limited to a tetramer as the highest order oligomeric species and considering both dimers and tetramers as responsible for the excimer's emission. Multi-equilibria models enhanced the titration analysis, allowing estimation of association constants (Ka) and oligomeric species distribution. Our results support previous evidence that contacts among helixes, which stabilize discoidal HDL particles, are already present in lipid-free apoA-I, with dimeric species predominating, and possible tetrameric too. Further investigation of these species is essential to elucidate their physiological and pathological roles, such as in atherosclerosis.

载脂蛋白A-I （apoA-I）是高密度脂蛋白颗粒的主要蛋白，通过逆向胆固醇转运具有抗动脉粥样硬化特性。在无脂状态下，apoa - 1自我结合，这一过程涉及正常生理和病理条件，如淀粉样变性。尽管人们提出了各种机制来解释其自我关联，但仍未达成共识，其功能含义仍不清楚。在这里，我们采用多参数荧光探针来研究apoA-I的自关联。我们使用了三个位于不同螺旋上的单半胱氨酸突变体：K107C （H4）、K133C （H5）和F225C (H10)；如前所述，用芘标记它们（Tárraga等）。生物化学学报，699(2021)108748。我们最初的实验发现H5和H10螺旋之间的准分子发射和H4的极性也发生了变化。通过利用特定的芘带发射来监测二聚体结合（通过准分子形成）和微环境极性（p值），我们跟踪了apoA-I寡聚化作为蛋白质浓度的函数。研究人员开发了几种自结合的数学模型，并使用选择标准进行了比较，以确定再现apoA-I在水介质中复杂行为的最简单模型：一个顺序结合子模型，该模型将四聚体作为最高阶寡聚物，并考虑到二聚体和四聚体都负责准分子的发射。多平衡模型增强了滴定分析，允许估计缔合常数（Ka）和低聚物种分布。我们的研究结果支持了先前的证据，即在无脂apoa - 1中已经存在稳定盘状HDL颗粒的螺旋之间的接触，二聚体占主导地位，也可能是四聚体。进一步研究这些物种对于阐明其生理和病理作用至关重要，例如动脉粥样硬化。

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引用次数: 0

Drug–biomolecular interaction: Spectroscopic and computational insights into esomeprazole binding with human serum albumin 药物-生物分子相互作用：埃索美拉唑与人血清白蛋白结合的光谱和计算见解。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-31 DOI: 10.1016/j.bbapap.2025.141109

Anna Tanuja Safala Bodapati , Ragaiahgari Srinivas Reddy , Kandikonda Lavanya , Shravya Rao Madku , Rajdeep Chowdhury , Bijaya Ketan Sahoo

Cellular process relies on specific binding of drug molecules with desired biological receptors. Biomolecular receptors and drugs exhibit their biological functions upon their interactions. Understanding the binding parameters and energetics of the binding provides a plethora of information that may be helpful in drug design and discovery. Further, drug interaction with carrier proteins affects the pharmacokinetics and dynamics of other exogenous and endogenous drugs. In this work, we report the binding behavior of esomeprazole with human serum albumin using several biophysical techniques. Qualitative and quantitative aspects of the binding along with the binding energetics has been focused in extracting the thermodynamics parameters and key interaction force. The binding constants (K_b)obtained from Scatchard analysis are-1.17 × 10⁵, 7.49 × 10⁴, and 3.23 × 10⁴ M⁻¹ at 298, 303, 308 K respectively. Esomeprazole binds preferentially at site 1 in subdomain IIA of human serum albumin and was confirmed, supported by site-specific marker displacement studies and docking simulations. Negative value of change in free energy (∆G⁰) -32 kJ/mol at 298 K showed thermodynamically favourable interaction and outweigh of entropic factor (T∆S⁰ = 230.76 ± 3 kJ for T = 298 K) over the enthalpic contribution (∆H⁰ = −261.99 kJ/mol) revealed an entropy-driven process. Binding of esomeprazole affected the helical structure of human serum albumin. Molecular docking studies (theoretical) shows the binding pocket of ESM at site1(IIA), which is in accordance with the experimental result. Further, the interface residues involved in the binding were analysed from the 2D diagram and ligplot of the docked complex.

细胞过程依赖于药物分子与所需生物受体的特异性结合。生物分子受体与药物通过相互作用发挥其生物学功能。了解结合参数和结合的能量学提供了大量的信息，可能有助于药物设计和发现。此外，药物与载体蛋白的相互作用会影响其他外源性和内源性药物的药代动力学和动力学。在这项工作中，我们使用几种生物物理技术报道了埃索美拉唑与人血清白蛋白的结合行为。结合热力学参数和关键作用力的提取，从定性和定量两个方面进行了研究。Scatchard分析得到的结合常数（Kb）在298、303、308 K处分别为1.17 × 105、7.49 × 104和3.23 × 104 M-1。埃索美拉唑优先结合人血清白蛋白IIA亚结构域的1号位点，这一发现得到了位点特异性标记位移研究和对接模拟的证实。负值自由能的变化(∆G0) -32 焦每摩尔298 K显示热力学有利的互动和大于熵的因子(T∆S0 = 230.76 ± 3 kJ 298 T =  K)在向左反应贡献(∆H0 = -261.99 焦每摩尔)显示一个熵驱动过程。埃索美拉唑的结合影响了人血清白蛋白的螺旋结构。分子对接研究（理论）显示ESM的结合袋位于site1(IIA)，与实验结果一致。此外，通过对接配合物的二维图和光图分析了参与结合的界面残基。

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引用次数: 0

Multifunctionality analysis of serine hydroxymethyltransferases from human and Escherichia coli 人和大肠杆菌丝氨酸羟甲基转移酶的多功能分析

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-25 DOI: 10.1016/j.bbapap.2025.141107

Mahiro Hayashi , Kumiko Sakai-Kato , Tetsuya Miyamoto

Serine hydroxymethyltransferase (SHMT) catalyzes the conversion of l-serine and tetrahydrofolate (THF) to glycine and 5,10-methylenetetrahydrofolate, respectively. In a previous study, we found that human and Escherichia coli SHMTs possess THF-dependent d-serine dehydratase activity, which degrades d-serine to pyruvate and ammonia. Some activities including aldolase and racemase activities have also been reported for SHMTs. In the present study, we investigated the multifunctionality of E. coli SHMT and two human SHMTs. All three SHMTs displayed high aldolase activity toward l-allo-threonine and l-threo-phenylserine, and measurable activity toward l-threonine, but they did not act on d-allo-threonine and d-threonine. The catalytic efficiency (k_cat/K_m) for l-allo-threonine was higher than for l-threo-phenylserine. None of the SHMTs displayed racemase activity toward various amino acids, although slight alanine racemase activity was detected for E. coli SHMT. Likewise, none of the SHMTs showed lyase, aminotransferase, or aspartate decarboxylase activities, and none exhibited dehydratase activity toward other hydroxy amino acids except d-serine. SHMTs are multifunctional enzymes possessing canonical hydroxymethyltransferase, d-serine dehydratase, and low-specificity l-threonine aldolase activities.

丝氨酸羟甲基转移酶（SHMT）催化l-丝氨酸和四氢叶酸（THF）分别转化为甘氨酸和5,10-亚甲基四氢叶酸。在之前的研究中，我们发现人类和大肠杆菌的SHMTs具有thf依赖性d-丝氨酸脱水酶活性，可将d-丝氨酸降解为丙酮酸和氨。一些活性，包括醛缩酶和消旋酶活性也被报道为SHMTs。在本研究中，我们研究了大肠杆菌SHMT和两种人类SHMT的多功能性。所有三种shmt对l-异体苏氨酸和l-三苯基丝氨酸均表现出较高的醛缩酶活性，对l-苏氨酸具有可测量的活性，但对d-异体苏氨酸和d-苏氨酸没有作用。l-异丙苏氨酸的催化效率（kcat/Km）高于l-三苯基丝氨酸。虽然在大肠杆菌SHMT中检测到轻微的丙氨酸外消旋酶活性，但没有一种SHMT显示出对各种氨基酸的外消旋酶活性。同样，没有一个SHMTs显示裂解酶、转氨酶或天冬氨酸脱羧酶活性，也没有显示除d-丝氨酸外的其他羟基氨基酸的脱水酶活性。SHMTs是多功能酶，具有典型的羟甲基转移酶、d-丝氨酸脱水酶和低特异性的l-苏氨酸醛缩酶活性。

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引用次数: 0

Identification of new protein-coding potential in Leishmania braziliensis using a proteogenomics approach 利用蛋白质基因组学方法鉴定巴西利什曼原虫新的蛋白质编码潜力

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-25 DOI: 10.1016/j.bbapap.2025.141108

Aditi Shenoy , Soumi Chowdhury , Shubhankar Pawar , Nitin Tupperwar , Harsh Pawar

American tegumentary leishmaniasis (ATL) is primarily caused by Leishmania (Viannia) species such as Leishmania braziliensis, Leishmania panamensis, and Leishmania guyanensis, which show complex genomic organisation and stage-specific adaptations underlying their pathogenicity. Despite the availability of its reference genome, limitations in gene annotation persist due to the presence of hypothetical proteins, pseudogenes, and unrecognised coding regions. In this study, we used a proteogenomic approach integrating publicly available high-resolution mass spectrometry data with a custom six-frame translated genome database to refine the genome annotation of L. braziliensis strain MHOM/BR/75/M2904. Utilising stringent database-dependent searches with a 1 % false discovery rate, we identified many unique peptides, of which 1034 were genome search-specific peptides (GSSPs) mapping exclusively to unannotated genomic regions. These GSSPs facilitated the discovery of 56 novel protein-coding genes and the correction of 228 existing gene models, including N- and C-terminal extensions. Notably, several novel genes encode proteins with conserved domains such as membrane attack complex/perforin (MACPF), kinesin K39, and peptidase S9/S15, suggesting functional relevance in parasite biology. Our findings demonstrate the power of proteogenomics to uncover cryptic protein-coding regions and improve genome annotations beyond conventional predictions. This refined annotation enhances our understanding of L. braziliensis biology, providing a more accurate proteomic landscape that can inform studies on parasite virulence, host interaction, and potential therapeutic targets. The study underscores the importance of integrating proteomic evidence with genomic data to capture the full coding potential of kinetoplastid parasites, paving the way for improved diagnostics and interventions against leishmaniasis.

美洲土著利什曼病（ATL）主要由巴西利什曼原虫、巴拿马利什曼原虫和圭亚那利什曼原虫等利什曼原虫引起，它们表现出复杂的基因组组织和阶段特异性适应，是其致病性的基础。尽管有参考基因组的可用性，但由于存在假设的蛋白质、假基因和未识别的编码区，基因注释的局限性仍然存在。在这项研究中，我们使用蛋白质基因组学方法整合公开的高分辨率质谱数据和定制的六帧翻译基因组数据库来完善巴西乳杆菌菌株MHOM/BR/75/M2904的基因组注释。利用严格的数据库依赖搜索（错误发现率为1%），我们鉴定出许多独特的肽，其中1034个是基因组搜索特异性肽（gssp），仅映射到未注释的基因组区域。这些gssp促进了56个新的蛋白质编码基因的发现，并纠正了228个现有的基因模型，包括N端和c端扩展。值得注意的是，一些新基因编码具有保守结构域的蛋白质，如膜攻击复合物/穿孔素（MACPF）、激酶蛋白K39和肽酶S9/S15，这表明它们在寄生虫生物学中具有功能相关性。我们的研究结果证明了蛋白质基因组学在揭示隐蛋白编码区和改进基因组注释方面的能力，超出了传统的预测。这一改进的注释增强了我们对巴西乳杆菌生物学的理解，提供了一个更准确的蛋白质组学景观，可以为寄生虫毒力、宿主相互作用和潜在治疗靶点的研究提供信息。这项研究强调了将蛋白质组学证据与基因组数据结合起来的重要性，以捕获着丝质体寄生虫的全部编码潜力，为改进利什曼病的诊断和干预措施铺平道路。

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引用次数: 0

AttnSeq-PPI: Enhancing protein-protein interaction network prediction using transfer learning-driven hybrid attention AttnSeq-PPI：利用迁移学习驱动的混合注意增强蛋白质相互作用网络预测。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-24 DOI: 10.1016/j.bbapap.2025.141102

Dipayan Sarkar, Chiranjib Sarkar

Study of protein-protein interaction (PPI) network is fundamental to all cellular processes in living organisms. PPI study based on experimental techniques such as high-throughput assays, mass spectrometry is time-consuming and expensive. Computational techniques like molecular docking are restricted to availability of 3D protein structures and not suitable for large numbers of proteins. On the contrary Sequence-based PPI study is advantageous over the limitations of above techniques. Sequence-based PPI study has gained a broader scope with the help of deep learning techniques and large language model (LLM). In this study, we proposed AttnSeq-PPI, a deep learning framework based on two channels of hybrid attention mechanism. The protein sequences are embedded in high dimensional space using ProtT5 language model. In our model hybrid attention mechanism is designed by combining self-attention and cross-attention which enable the model to extract features from each protein with respect to the contextual features of both the proteins. The hybrid attention mechanism effectively captures long-range dependencies within protein sequences as well as interacting features of both proteins. The model was trained and evaluated based on 5-fold cross validation on intra-species and multi-species datasets. Additionally, four datasets of independent species and true PPI network datasets were used for validation. AttnSeq-PPI demonstrates superior generalization and outperforms existing models, achieving 99 % accuracy for both human and multi-species datasets. It can provide prediction of novel PPIs with fewer false negatives and higher precision. Additionally, we developed a web-based tool on AttnSeq-PPI accessible at https://compbiosysnbu.in/attnseqppi/ to provide PPI prediction based on protein sequences.

蛋白质-蛋白质相互作用（PPI）网络的研究是生物体中所有细胞过程的基础。基于高通量分析、质谱等实验技术的PPI研究耗时且昂贵。像分子对接这样的计算技术仅限于三维蛋白质结构的可用性，不适合大量蛋白质。相反，基于序列的PPI研究优于上述技术的局限性。在深度学习技术和大型语言模型（LLM）的帮助下，基于序列的PPI研究获得了更广泛的范围。在本研究中，我们提出了一种基于双通道混合注意机制的深度学习框架AttnSeq-PPI。利用ProtT5语言模型将蛋白质序列嵌入到高维空间中。在我们的模型中，混合注意机制通过结合自注意和交叉注意来设计，使模型能够根据两种蛋白质的上下文特征从每种蛋白质中提取特征。混合注意机制有效地捕获了蛋白质序列内的长期依赖关系以及两种蛋白质的相互作用特征。基于种内和多物种数据集的5倍交叉验证对模型进行了训练和评估。此外，使用4个独立物种数据集和真实PPI网络数据集进行验证。AttnSeq-PPI表现出卓越的泛化能力，优于现有模型，在人类和多物种数据集上都达到了99% %的准确率。该方法对新型ppi的预测具有较低的假阴性和较高的预测精度。此外，我们开发了一个基于web的AttnSeq-PPI工具，可访问https://compbiosysnbu.in/attnseqppi/，以提供基于蛋白质序列的PPI预测。

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引用次数: 0

Structure and analysis of a virulent chitinase from Listeria monocytogenes 单核增生李斯特菌毒力几丁质酶的结构与分析。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-16 DOI: 10.1016/j.bbapap.2025.141106

Saima Rehman , Maria Baczynska , Beichang Zhang , Christian.D. Lorenz , James A. Garnett

Listeria monocytogenes is the causative agent of Listeriosis, a serious foodborne illness that primarily affects pregnant women, new-borns, the elderly, and immunocompromised individuals. L. monocytogenes secretes proteins that bind and degrade chitin, a linear polysaccharide formed of β1,4-linked N-acetylglucosamine residues, and although humans do not produce chitin, these enzymes act as virulence factors that promote bacterial growth during host infection. The chitinase ChiA is a major contributor to virulence, and it can modulate host immunity through downregulating the expression of host inducible nitric oxide synthase (iNOS), although this precise mechanism has yet to be determined. Here we present the X-ray crystal structure of L. monocytogenes ChiA at 1.95 Å resolution, complemented by solution small angle X-ray scattering analysis and molecular dynamics simulations. Our comparative analyses reveal structural conservation with homologous bacterial chitinases and highlight potential alternative ligand-binding sites beyond the canonical chitin-binding channel. Molecular dynamics simulations of an N-glycopeptide model demonstrate stable interactions between LmChiA and the mannose-rich N-glycan core near these putative sites. These findings suggest that LmChiA may interact with branched host glycans rather than exclusively processing chitin-derived substrates, and this provides a potential explanation for its role in modulating host immune responses.

单核细胞增生李斯特菌是李斯特菌病的病原体，李斯特菌病是一种严重的食源性疾病，主要影响孕妇、新生儿、老年人和免疫功能低下的个体。单核增生乳杆菌分泌结合和降解几丁质的蛋白质，几丁质是一种由β1,4连接的n -乙酰氨基葡萄糖残基形成的线状多糖，尽管人类不产生几丁质，但这些酶在宿主感染期间作为毒力因子促进细菌生长。几丁质酶ChiA是毒力的主要贡献者，它可以通过下调宿主诱导型一氧化氮合酶（iNOS）的表达来调节宿主免疫，尽管其确切机制尚未确定。本文以1.95 Å分辨率展示了单核增生L. ChiA的x射线晶体结构，并辅以溶液小角x射线散射分析和分子动力学模拟。我们的比较分析揭示了与同源细菌几丁质酶的结构守恒，并强调了在典型几丁质结合通道之外的潜在替代配体结合位点。n -糖肽模型的分子动力学模拟表明，在这些假定位点附近，LmChiA与富含甘露糖的n -聚糖核之间存在稳定的相互作用。这些发现表明，LmChiA可能与分枝宿主聚糖相互作用，而不是专门处理几丁质衍生的底物，这可能解释了其在调节宿主免疫反应中的作用。

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引用次数: 0

Direct cryo-EM visualization of the β-sheet structure in curved amyloid protofibril 弯曲淀粉样原纤维β片结构的直接低温电镜可视化。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-16 DOI: 10.1016/j.bbapap.2025.141105

Naoki Yamamoto , Jin Inoue , Ritsumi Saito , Kei Nanatani , Ai Takahashi , Seizo Koshiba , Ryo Kanno

Protofibrils are key intermediates to explore effective therapeutic strategies for amyloid-related diseases; however, their structural features remain largely ambiguous. Here, we report a direct visualization of the intermolecular β-sheet structure of amyloid protofibrils using cryo-electron microscopy. We analyzed the protofibrils formed by an insulin-derived peptide and observed 4.7 Å regularly spaced lines at their centers surrounded by fuzzy regions, consistent with the hydrogen-bonded β-strand structure. We propose a model in which short β-strands form a β-sheet core in the center, whereas the outer fuzzy regions are composed of random coiled structures. This structure is different from that of mature amyloid fibrils, where β-sheets span the entire structure, suggesting that the partial β-sheet formation in protofibrils is responsible for their curvy noodle-like appearance. Overall, this study highlights cryo-electron microscopy as a powerful tool for visualizing seemingly flexible structures, such as protofibrils, and establishes a conceptual framework for the rational design of diagnostic and therapeutic agents targeting the protofibril β-sheet structure.

原原纤维是探索淀粉样蛋白相关疾病有效治疗策略的关键中间体；然而，它们的结构特征在很大程度上仍然是模糊的。在这里，我们报告了使用冷冻电子显微镜直接可视化淀粉样蛋白原纤维的分子间β-片结构。我们分析了由胰岛素衍生肽形成的原纤维，观察到4.7条 Å在它们的中心被模糊区域包围的规则间距线，与氢键β链结构一致。我们提出了一种模型，其中短β-链在中心形成β-片核，而外部模糊区域由随机卷曲结构组成。这种结构与成熟的淀粉样原纤维不同，成熟的淀粉样原纤维中β-薄片横跨整个结构，这表明原原纤维中部分β-薄片的形成是其弯曲面条状外观的原因。总的来说，本研究突出了低温电子显微镜作为一种强大的工具来可视化看似灵活的结构，如原原纤维，并建立了一个概念框架，为合理设计针对原原纤维β-片结构的诊断和治疗药物。

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引用次数: 0

Deciphering the structural attributes of PPAR-γ and SIRT1 to identify their dual activators using a combined molecular modeling approach 使用组合分子建模方法破译PPAR-γ和SIRT1的结构属性以识别它们的双激活剂。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-16 DOI: 10.1016/j.bbapap.2025.141104

Swati Dogra , Arijit Bhattacharya , Gera Narendra, Shraddha Gautam, Om Silakari

PPAR-γ and SIRT1 are the emerging targets that are vital in diabetes and diabetic complications. So, the development of dual activators for PPAR-γ and SIRT1 can be a good strategy in the treatment of diabetes and diabetic complications and in order to reduce the adverse effects that occur from the activation of these targets. The network analysis was applied to study the protein-protein interactions. Similarity-based virtual screening was done to screen Fisetin-based molecules, and docking analysis was performed for both targets. In addition, an ADME study and electrostatic complementarity analysis were conducted to study the role of binding energies between the ligands and the targets. The Molecular Dynamics (MD) simulation was performed to study the stable binding conformation. Different validation metrics from MD analysis, such as RMSD, RMSF, R_g, PCA and free energy landscape (FEL), were analysed to evaluate the stability of the compounds with the target proteins. Moreover, the WaterSwap and MMPBSA analyses were also done to calculate the binding free energy of the compounds. The findings from this extensive evaluation depicted that the selected three molecules can be used as potent and safe dual activators of PPAR-γ and SIRT1 to combat diabetes and several diabetic complications.

PPAR-γ和SIRT1是在糖尿病和糖尿病并发症中至关重要的新兴靶点。因此，PPAR-γ和SIRT1的双重激活剂的开发可能是治疗糖尿病和糖尿病并发症的一个很好的策略，并且为了减少这些靶点激活所产生的副作用。网络分析被应用于蛋白质-蛋白质相互作用的研究。采用基于相似性的虚拟筛选方法筛选非司汀类分子，并对两个靶点进行对接分析。此外，通过ADME研究和静电互补性分析来研究配体与靶标之间结合能的作用。通过分子动力学（MD）模拟研究了其稳定的结合构象。利用MD分析的RMSD、RMSF、Rg、PCA和自由能景观（FEL）等验证指标评价化合物与目标蛋白的稳定性。此外，还进行了WaterSwap和MMPBSA分析，计算了化合物的结合自由能。这项广泛评估的结果表明，所选的三种分子可以作为PPAR-γ和SIRT1的有效和安全的双重激活剂，用于对抗糖尿病和几种糖尿病并发症。

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引用次数: 0

Insights into key kinase regulatory network of LARP1 based on co-occurring phosphorylation events 基于共同发生的磷酸化事件的LARP1关键激酶调控网络的见解。

IF 2.3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-10-16 DOI: 10.1016/j.bbapap.2025.141103

Ashika Bangera, Nazah Naurah, Samseera Ummar, Poornima Ramesh, Rajesh Raju

LARP1 (La-related protein 1) is an important mediator of translation regulation that stabilizes terminal oligopyrimidine motif-containing mRNAs. LARP1, being a direct target of mechanistic Target of Rapamycin Complex 1 (mTORC1), undergoes phosphorylation in the presence of growth factors. Phosphorylation-dependent conformational changes in LARP1 dictate its ability to stabilize or repress mRNAs with 5′ terminal oligopyrimidine (TOP), which code for key proteins in ribosome biogenesis and translation. Due to this important role, LARP1 is involved in cancer cell survival, facilitating selective translation of oncogenic proteins with a tradeoff in cap-dependent translation. As the function of LARP1 is governed by phosphorylation, this review provides phosphoproteomics-based regulatory network of LARP1, identifying major phosphorylation sites, upstream kinases, and interactors, with mutual co-differential regulation events. Extensive literature synthesis identified 11 major phosphorylation sites of LARP1, and an understanding of interaction dynamics that contribute to functional plasticity of LARP1. Specially, this article synthesizes the co-regulatory network of LARP1 with other proteins, and the interactions central to mTOR signaling, phosphorylation of LARP1, and its functional role in disease manifestation. This approach focusing on the LARP1-kinase regulatory network is crucial in untangling its miscellaneous role in cancer, which provides novel therapeutic paths for malignancies.

LARP1 （la -相关蛋白1）是一种重要的翻译调节介质，它稳定末端含有寡聚嘧啶基序的mrna。LARP1是mechanistic target of Rapamycin Complex 1 （mTORC1）的直接靶点，在生长因子存在下发生磷酸化。LARP1磷酸化依赖的构象变化决定了它稳定或抑制含有5'端寡聚嘧啶（TOP）的mrna的能力，而TOP编码核糖体生物发生和翻译中的关键蛋白。由于这一重要作用，LARP1参与癌细胞存活，促进致癌蛋白的选择性翻译，并在帽依赖翻译中进行权衡。由于LARP1的功能受磷酸化控制，本综述提供了基于磷酸化蛋白质组学的LARP1调控网络，确定了主要的磷酸化位点、上游激酶和相互作用物，它们具有相互共差异的调控事件。广泛的文献综合鉴定了LARP1的11个主要磷酸化位点，并了解了LARP1功能可塑性的相互作用动力学。特别地，本文合成了LARP1与其他蛋白的共调控网络，以及与mTOR信号传导、LARP1磷酸化及其在疾病表现中的功能作用相关的相互作用。这种专注于larp1激酶调控网络的方法对于解开其在癌症中的复杂作用至关重要，这为恶性肿瘤提供了新的治疗途径。

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引用次数: 0