Biochimica et biophysica acta. General subjects最新文献_第5页

RFBGCpred: A Random forest based tool for prediction of biosynthetic gene clusters RFBGCpred：一个基于随机森林的生物合成基因簇预测工具。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-08 DOI: 10.1016/j.bbagen.2025.130859

Sharanbasappa D. Madival , Dwijesh Chandra Mishra , Krishna Kumar Chaturvedi , Neeraj Budhlakoti , Mohammad Samir Farooqi , Sudhir Srivastava , Anu Sharma , Shivadarshan S. Jirli , Alka Arora , Girish K. Jha , Shesh N. Rai

Biosynthetic gene clusters (BGCs) encode enzymatic pathways that produce diverse natural products with applications in pharmaceuticals, agriculture, and biotechnology. Broad-spectrum tools such as antiSMASH and DeepBGC cover many BGC classes but may face challenges in detecting atypical or hybrid architectures. Here we present RFBGCPred, an open-source machine learning classifier focused on five clinically and agriculturally important classes—PKS, NRPS, RiPPs, terpenes, and PKS–NRPS hybrids. Rather than replacing existing pipelines, RFBGCPred complements them by improving class-level discrimination within this subset.

Using curated data from the MiBIG database, we applied Word2Vec for feature extraction, supervised UMAP for dimensionality reduction, and SMOTE to address class imbalance. Multiple classifiers were benchmarked, with Random Forest identified as the top performer using the TOPSIS decision-making criterion. The final model achieved an accuracy of 98.0 % (MCC: 0.9752, AUC: 0.9928) on a balanced test set, and maintained strong generalization on an unbalanced validation set (accuracy: 94.8 %, MCC: 0.89, AUC: 0.96). Compared with antiSMASH and DeepBGC, RFBGCPred showed improved recall for hybrid PKS–NRPS clusters while sustaining competitive precision, thereby reducing misclassification of atypical arrangements.

RFBGCPred supports FASTA, GenBank, and CSV inputs, with full source code, curated datasets, and documentation available at: https://github.com/SHARANBASAPPA/RFBGCPred.git.

生物合成基因簇（BGCs）编码产生多种天然产物的酶途径，在制药、农业和生物技术中有广泛的应用。antiSMASH和DeepBGC等广谱工具涵盖了许多BGC类，但在检测非典型或混合架构方面可能面临挑战。在这里，我们提出了RFBGCPred，一个开源的机器学习分类器，专注于五个临床和农业上重要的类别- pks， NRPS, RiPPs，萜烯和PKS-NRPS杂交。RFBGCPred并没有取代现有的管道，而是通过改进这个子集内的类级别区分来补充它们。使用来自MiBIG数据库的精选数据，我们使用Word2Vec进行特征提取，使用监督UMAP进行降维，使用SMOTE来解决类别不平衡问题。对多个分类器进行基准测试，随机森林被确定为使用TOPSIS决策标准的最佳表演者。最终模型在平衡测试集上的准确率为98.0 % (MCC: 0.9752, AUC: 0.9928)，在不平衡验证集上保持了较强的泛化（准确率：94.8 %,MCC: 0.89, AUC: 0.96）。与antiSMASH和DeepBGC相比，RFBGCPred在保持竞争精度的同时，提高了pps - nrps混合簇的召回率，从而减少了非典型排列的错误分类。RFBGCPred支持FASTA， GenBank和CSV输入，完整的源代码，策划的数据集和文档可在：https://github.com/SHARANBASAPPA/RFBGCPred.git。

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引用次数: 0

Untargeted metabolomics and proteomics reveal the versatile effects of myeloperoxidase-oxidized LDL on endothelial cells 非靶向代谢组学和蛋白质组学揭示了髓过氧化物酶氧化LDL对内皮细胞的多种作用。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-07 DOI: 10.1016/j.bbagen.2025.130865

Cecilia Tangeten , Axelle Bourez , Alexandre Rousseau , Virginie Imbault , Jianru Stahl-Zeng , Florence Souard , Xavier Bisteau , Cedric Delporte , Karim Zouaoui Boudjeltia , Pierre Van Antwerpen

Background

Myeloperoxidase-oxidized LDLs (Mox-LDLs) trigger endothelial cells and contribute to the development of atherosclerosis. However, the mechanisms underlying Mox-LDL-induced stimulation remain elusive. In this study, we applied untargeted metabolomics and proteomics approaches to investigate human umbilical vein endothelial cells (HUVECs) following exposure to Mox-LDLs.

Methods

HUVECs were exposed for 24 h to Mox-LDLs (0 or 100 μg/ml) with or without native LDLs (0 or 1 mg/ml). Supernatants and cell lysates were analyzed by liquid chromatography coupled to mass spectrometry. Using Workflow4Metabolomics work environment, MZmine, SIRIUS and MetGem, we selected and identified key metabolites influenced by Mox-LDL treatment. For the proteomics analysis, we used DIA-NN and the FragPipe-Analyst application to detect proteins differentially expressed after Mox-LDL treatment.

Results

Metabolomics analysis revealed increased levels of sphingolipids, phospholipids and oxidized-cholesterol derived compounds in HUVECs following Mox-LDL exposure. We also detected an increase in small peptides, likely reflecting Mox-LDLs catabolism. Mox-LDL treatment of HUVECs also altered the expression of proteins involved in hemostasis, cell adhesion, angiogenesis, inflammation and stress responses. In addition, proteins from the mitochondrial respiratory chain were upregulated after Mox-LDL treatment. Finally, a trihydroxy-unsaturated fatty acid was secreted by HUVECs exposed to Mox-LDLs and could serve as a biomarker of Mox-LDL exposure.

Conclusions

Our findings suggest that Mox-LDLs are internalized and degraded by HUVECs. They seem to induce increased mitochondrial activity and oxidative stress, likely mediated by reactive oxygen species. We believe that HUVECs activate cytoprotective antioxidant coping mechanisms (glutathione synthesis, heme oxygenase-1…) to survive. Mox-LDLs may also modulate hemostasis and inflammatory responses.

背景：髓过氧化物酶氧化ldl （mox - ldl）触发内皮细胞并促进动脉粥样硬化的发展。然而，mox - ldl诱导刺激的机制仍然难以捉摸。在这项研究中，我们应用非靶向代谢组学和蛋白质组学方法来研究暴露于mox - ldl后的人脐静脉内皮细胞（HUVECs）。方法：将HUVECs暴露于含或不含天然ldl（0或1 mg/ml）的mox - ldl（0或100 μg/ml）中24 h。上清液和细胞裂解液采用液相色谱-质谱联用分析。利用Workflow4Metabolomics工作环境、MZmine、SIRIUS和MetGem，我们选择并鉴定了受Mox-LDL处理影响的关键代谢物。对于蛋白质组学分析，我们使用DIA-NN和FragPipe-Analyst应用程序来检测Mox-LDL处理后差异表达的蛋白质。结果：代谢组学分析显示，暴露于Mox-LDL后，HUVECs中鞘脂、磷脂和氧化胆固醇衍生化合物水平升高。我们还检测到小肽的增加，可能反映了mox - ldl的分解代谢。Mox-LDL处理HUVECs还改变了参与止血、细胞粘附、血管生成、炎症和应激反应的蛋白质的表达。此外，在Mox-LDL处理后，线粒体呼吸链蛋白上调。最后，暴露于Mox-LDL的huvec分泌一种三羟基不饱和脂肪酸，可以作为Mox-LDL暴露的生物标志物。结论：我们的研究结果表明，mox - ldl被HUVECs内化和降解。它们似乎诱导线粒体活性增加和氧化应激，可能是由活性氧介导的。我们认为HUVECs激活细胞保护性抗氧化应对机制（谷胱甘肽合成，血红素加氧酶-1…）来生存。mox - ldl也可能调节止血和炎症反应。

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引用次数: 0

Seasonal and COVID-19 lockdown variations in PM2.5 composition to apoptosis pathways and chemical toxicity in lung cells PM2.5成分对肺细胞凋亡途径和化学毒性的季节性和COVID-19封锁变化。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-04 DOI: 10.1016/j.bbagen.2025.130864

Ting-Hsuan Wu , Yu-Cheng Chen , Hong-Lin Chan , Hsiu-Chuan Chou

Objective

To investigate seasonal and COVID-19-lockdown variations in PM2.5 chemical composition in Taipei and the effects of those compositional differences on lung cell toxicity.

Methods

PM2.5 was collected in warm (2021/07–2021/08) and cold (2021/11–2022/02) seasons and during LV2/LV3 COVID-19 alert periods. Composition (metals, PAHs) was analyzed and A549 and PC9 lung cells were exposed to equal mass concentrations (0–100 μg/mL) of extracted PM2.5. Cell viability, ROS, apoptosis, mitochondrial membrane potential and GSH/GPX4 were measured.

Results

At equivalent mass concentrations (50 μg/mL), warm-season PM2.5 induced higher ROS and greater reduction in viability than cold-season PM2.5. LV2-period PM2.5 contained higher metal content and caused more severe cellular damage than LV3. Spearman correlation plus single-compound assays identified cadmium and Dibenzo[a,e]pyrene as components strongly associated with cytotoxicity.

Conclusions

Seasonal and human-activity driven compositional changes—rather than mass concentration alone—affect PM2.5 toxicity in vitro; these results underscore the importance of controlling specific chemical emissions.

目的：探讨台北市PM2.5化学成分的季节性变化及其对肺细胞毒性的影响。方法：在温暖季节（2021/07-2021/08）和寒冷季节（2021/11-2022/02）以及LV2/LV3 COVID-19预警期采集PM2.5。分析其组成（金属、多环芳烃），并将A549和PC9肺细胞暴露于等质量浓度（0-100 μg/mL）的提取PM2.5中。测定细胞活力、ROS、凋亡、线粒体膜电位和GSH/GPX4。结果：在同等质量浓度（50 μg/mL）下，暖季PM2.5比冷季PM2.5诱导更高的ROS和更大的活力降低。与LV3相比，lv2期PM2.5的金属含量更高，造成的细胞损伤更严重。Spearman相关性加单化合物测定鉴定出镉和二苯并[a，e]芘是与细胞毒性密切相关的成分。结论：季节性和人类活动驱动的成分变化，而不是质量浓度单独影响PM2.5的体外毒性；这些结果强调了控制特定化学物质排放的重要性。

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引用次数: 0

Midkine and TNFSF10 as downstream molecules of type I interferon are involved in the treatment of myelofibrosis Midkine和TNFSF10作为I型干扰素的下游分子参与骨髓纤维化的治疗。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-09-29 DOI: 10.1016/j.bbagen.2025.130863

Yaoyao Chen , Fanxiang Yin , Xiaoqian Wang , Huilin Zhang , Ping Tang , Mengjiao Xue , Nannan Sun , Jin Li , Chang Chen , Bingjie Wang , Qingxuan Xin , Juanxia Zhou , Yingmei Li , Shuya Wang , Shaohua Yan , Jiani Li , Yunling Zhu , Bo Qin , Baohong Yue , Yong Jiang , Rongqun Guo

Myelofibrosis (MF), a myeloproliferative neoplasm, remains incurable for most patients. Although some individuals are eligible for allogeneic hematopoietic stem cell transplantation, current therapies generally slow disease progression rather than achieve a cure. In this study, we found that type I interferon (IFN) treatment enhances midkine (MDK) expression, and MDK is involved in the differentiation and maturation of progenitor cells. Notably, MDK treatment drives tumor cells into the cell cycle, thereby increasing the therapeutic effect of busulfan. Furthermore, MDK promotes osteogenic differentiation of mesenchymal stem cells (MSC), contributing to the remodeling of the bone marrow microenvironment. In addition, type I IFN upregulates TNFSF10, leading to tumor cell death through mutual killing.

骨髓纤维化（MF）是一种骨髓增生性肿瘤，对大多数患者来说仍然是无法治愈的。虽然有些人适合异体造血干细胞移植，但目前的治疗方法通常会减缓疾病的进展，而不是实现治愈。在本研究中，我们发现I型干扰素（IFN）处理可增强midkine （MDK）的表达，而MDK参与了祖细胞的分化和成熟。值得注意的是，MDK治疗可使肿瘤细胞进入细胞周期，从而提高了布苏凡的治疗效果。此外，MDK促进间充质干细胞（MSC）的成骨分化，有助于骨髓微环境的重塑。此外，I型IFN上调TNFSF10，通过相互杀伤导致肿瘤细胞死亡。

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引用次数: 0

AMPK regulates BK-channel current in CA1 hippocampal neurons AMPK调节CA1海马神经元的bk通道电流。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-09-22 DOI: 10.1016/j.bbagen.2025.130862

Ricardo Esquivel-Garcia, Jorge Bravo-Martinez, Karina Bermeo, Isabel Arenas, David E. Garcia

AMP-activated protein kinase (AMPK) is a fundamental energy sensor fine-tuning cellular activity based on ATP availability. On the other hand, BK-channel current is tightly regulated by leptin, which in turn regulates neuronal excitability by modulating ion channels such as the BK-channel. However, this mechanism remains unclear to date. In this work we aimed to determine whether AMPK mediates the leptin regulation on BK-channel. We hypothesized that leptin regulation of BK-channel through AMPK underlies the modulating changes in neuronal excitability of CA1 hippocampal neurons. By using patch-clamping methods on CA1 pyramidal neurons in brain slices and biochemical reagents, we found that AMPK activation with AICAR inhibits BK-channel current, while AMPK inhibition with Compound C enhances BK-channel activity. Remarkably, AMPK activation reverses BK-channel current enhanced by leptin supporting an AMPK-dependent metabolic regulation of BK. Accordingly, current-clamp experiments revealed that AMPK manipulations significantly affect leptin responses on CA1 neuronal firing. These results support AMPK as a key mediator of the interplay between leptin and neuronal excitability, readily integrating metabolic signals with the computing state of firing outputs in CA1 hippocampal neurons.

ATP活化蛋白激酶（AMPK）是一种基于ATP可用性微调细胞活性的基本能量传感器。另一方面，bk通道电流受到瘦素的严格调节，瘦素反过来通过调节离子通道（如bk通道）来调节神经元的兴奋性。然而，这一机制至今仍不清楚。在这项工作中，我们旨在确定AMPK是否介导瘦素对bk通道的调节。我们假设瘦素通过AMPK调控bk通道是CA1海马神经元兴奋性调节变化的基础。通过脑切片CA1锥体神经元的膜片箝位方法和生化试剂，我们发现用AICAR激活AMPK可抑制bk通道电流，而用化合物C抑制AMPK可增强bk通道活性。值得注意的是，AMPK激活逆转了瘦素增强的BK通道电流，支持AMPK依赖性的BK代谢调节。因此，电流钳实验显示，AMPK操作显著影响瘦素对CA1神经元放电的反应。这些结果支持AMPK作为瘦素和神经元兴奋性之间相互作用的关键中介，容易将代谢信号与CA1海马神经元放电输出的计算状态整合起来。

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引用次数: 0

Evidence for singlet oxygen production from indocyanine green by electron paramagnetic resonance 电子顺磁共振证明吲哚菁绿产生单线态氧。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-09-22 DOI: 10.1016/j.bbagen.2025.130861

Magdalena Szpunar , David Aebisher , Bogumił Cieniek , Ireneusz Stefaniuk , Łukasz Dubiel , Andrzej Wal

Indocyanine green (ICG) is a well-known dye used for cardiovascular fluorescence imaging in medicine and a potential photosensitizer for photodynamic therapy. Using electron paramagnetic resonance (EPR), we have shown that illumination of aqueous solutions of ICG leads to the generation of singlet oxygen. The use of a selective spin trap allowed for the rate of singlet oxygen generation to be determined which provides evidence that ICG undergoes Type II photosensitization.

吲哚菁绿（ICG）是一种众所周知的用于心血管荧光成像的染料，也是一种潜在的光动力治疗光敏剂。利用电子顺磁共振（EPR），我们已经证明了ICG水溶液的照明导致单线态氧的产生。选择性自旋阱的使用使单线态氧生成速率得以确定，这提供了ICG经历II型光敏化的证据。

引用次数: 0

The F54L mutation of Thioredoxin shows protein instability and increased fluctuations of the catalytic center 硫氧还蛋白的F54L突变表现出蛋白质的不稳定性和催化中心的波动增加。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-09-13 DOI: 10.1016/j.bbagen.2025.130860

Takumi Baba , Go Ueno , Chika Ohe , Shuku Saji , Sachiko Yamamoto , Masaki Yamamoto , Hiroshi Nakagawa , Nobuo Okazaki , Mamoru Ouchida , Iori Kawasaki Ohmori , Kohei Takeshita

Thioredoxin is a ubiquitous redox protein that acts as an electron donor via its conserved dithiol motif (C32GPC35), catalyzing dithiol–disulfide exchange to regulate the redox state of target proteins. It supports antioxidant defense via peroxiredoxins, facilitates DNA synthesis by donating electrons to ribonucleotide reductase, and regulates redox-sensitive signaling pathways, including those controlling transcription and apoptosis. Neuronal degeneration and chronic kidney disease have been observed in Txn-F54L mutant rats; however, the details of why the Txn mutation causes these phenomena remain unknown. The present study aimed to elucidate the functional and structural changes caused by the F54L mutation. The Thioredoxin-F54L showed less insulin-reducing activity and more thermosensitivity to denaturation in the body temperature range compared to the wild type. The crystal structure revealed that F54 forms hydrophobic interactions with the surrounding hydrophobic amino acids. In addition, molecular dynamics simulation predicts increased fluctuations around the F54L mutation and a tendency for the distance between residues C32 and C35 at the catalytic center to be widened. The increased distance between residues C32 and C35 of the catalytic center may affect the reducing activity of the enzyme on the substrate. The finding that Thioredoxin-F54L is prone to denaturation at normal body temperature may reduce the normally functioning Thioredoxin. These molecular characteristics of Thioredoxin-F54L may be related to brain and kidney disease development in the Txn-F54L rats.

硫氧还蛋白是一种普遍存在的氧化还原蛋白，通过其保守的二硫醇基序（C32GPC35）作为电子供体，催化二硫醇-二硫交换，调节靶蛋白的氧化还原状态。它通过过氧化物还原素支持抗氧化防御，通过向核糖核苷酸还原酶提供电子促进DNA合成，并调节氧化还原敏感信号通路，包括控制转录和凋亡的信号通路。Txn-F54L突变大鼠出现神经元变性和慢性肾脏疾病；然而，为什么Txn突变导致这些现象的细节仍然未知。本研究旨在阐明F54L突变引起的功能和结构变化。与野生型相比，Thioredoxin-F54L在体温范围内表现出更低的胰岛素降低活性和更强的变性热敏性。晶体结构表明，F54与周围的疏水氨基酸形成疏水相互作用。此外，分子动力学模拟预测F54L突变周围的波动增加，催化中心残基C32和C35之间的距离有扩大的趋势。催化中心残基C32和C35之间距离的增加可能会影响酶对底物的还原活性。发现Thioredoxin- f54l在正常体温下容易变性，可能会降低正常功能的Thioredoxin。硫氧还蛋白- f54l的这些分子特征可能与Txn-F54L大鼠脑和肾脏疾病的发生有关。

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引用次数: 0

Rhipicephalus microplus triosephosphate isomerase dimer interface is stabilized by a key cysteine residue 微头猪三磷酸异构酶二聚体界面由一个关键的半胱氨酸残基稳定。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-09-12 DOI: 10.1016/j.bbagen.2025.130857

Luiz Saramago , Nallely Cabrera , Beatriz Aguirre , Helga Gomes , Bruno Moraes , Valdir Braz , Itabajara da Silva Vaz Jr. , Mayra A. Marques , Jerson L. Silva , Tomohiro Okagawa , Satoru Konnai , Ruy Pérez-Montfort , Carlos Logullo , Jorge Moraes

The functional significance of a non-conserved cysteine residue (C86) proximal to the interfacial region of Rhipicephalus microplus triosephosphate isomerase (RmTIM) was investigated through systematic substitution with aspartic acid (C86D), lysine (C86K), and alanine (C86A) via site-directed mutagenesis. Kinetic analyses revealed substantial perturbations in enzymatic parameters for the C86D and C86K variants, with marked alterations in maximal velocity (V_max), substrate affinity (K_m), catalytic turnover (k_cat), and catalytic efficiency (k_cat/K_m). Thermodynamic destabilization was universally observed across all mutants via Protein Thermal Shift assays, with reductions in melting temperature (T_m) ranging from 15.7 to 27.1 °C relative to the wild-type enzyme (Wt-TIM). Chemical denaturation studies employing guanidine hydrochloride demonstrated heightened susceptibility to unfolding in all mutants, with destabilization profiles following the order: C86K > C86D > C86A. Computational structural analyses elucidated molecular mechanisms underlying these perturbations. Disruption of a putative salt bridge between residues D49 and K18 was predicted in the C86K mutant, potentially destabilizing the dimeric interface. Comparative free energy calculations (ΔG) further corroborated these findings: Wt-TIM exhibited a ΔG of −21.2 kcal/mol and an interfacial contact area of 1604.8 Å², indicative of robust dimeric stabilization. In contrast, the C86K mutant displayed diminished stability (ΔG = −16.0 kcal/mol) despite an expanded interface (1615.6 Å²), suggesting compromised packing efficiency. These observations imply that C86, while not directly conserved, plays a critical structural role in maintaining interfacial integrity and catalytic competence. The pronounced destabilization and kinetic impairment observed in the C86K variant highlight the residue's significance in RmTIM functionality. This residue-specific destabilization strategy may aid in the rational design of acaricidal compounds targeting interfacial regions of RmTIM, taking advantage of structural vulnerabilities produced by non-conserved residues.

采用定点诱变的方法，系统替换了天冬氨酸（C86D）、赖氨酸（C86K）和丙氨酸（C86A），研究了微头猪三磷酸酯异构酶（RmTIM）界面附近的非保守半胱氨酸残基（C86）的功能意义。动力学分析显示，C86D和C86K变体的酶促参数发生了实质性的扰动，最大速度（Vmax）、底物亲和力（Km）、催化周转率（kcat）和催化效率（kcat/Km）发生了显著变化。通过蛋白质热移分析，所有突变体都普遍观察到热力学不稳定，相对于野生型酶（Wt-TIM），熔化温度（Tm）降低了15.7至27.1 °C。使用盐酸胍的化学变性研究表明，所有突变体对展开的敏感性都提高了，不稳定谱的顺序如下：C86K > C86D > C86A。计算结构分析阐明了这些扰动背后的分子机制。在C86K突变体中，预测残基D49和K18之间假定的盐桥断裂，可能破坏二聚体界面的稳定。比较自由能计算（ΔG）进一步证实了这些发现：Wt-TIM表现出-21.2 kcal/mol的ΔG和1604.8 Å2的界面接触面积，表明二聚体稳定。相比之下，C86K突变体表现出稳定性降低（ΔG = -16.0 kcal/mol），尽管扩大了界面（1615.6 Å2），表明包装效率降低。这些观察结果表明，C86虽然不是直接保守的，但在维持界面完整性和催化能力方面起着关键的结构作用。在C86K变体中观察到的明显的不稳定和动力学损伤突出了残基在RmTIM功能中的重要性。这种残基特异性不稳定策略可能有助于合理设计针对RmTIM界面区域的杀螨化合物，利用非保守残基产生的结构脆弱性。

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引用次数: 0

Circ-ATF7IP promotes IL13RA1 dependent M2 polarization of macrophage via sponging MiR-488-3p in papillary thyroid carcinoma Circ-ATF7IP通过海绵MiR-488-3p在甲状腺乳头状癌中促进IL13RA1依赖性巨噬细胞M2极化

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-09-11 DOI: 10.1016/j.bbagen.2025.130855

Yan Hu , Shujun Xia , Yanhua Yang , Weiwei Zhan

The preoperative assessment of lymph node metastasis (LNM) is of critical importance for the selection of appropriate surgical and therapeutic strategies for papillary thyroid carcinoma (PTC). However, the mechanisms underlying LNM in PTC remain unclear, and effective diagnostic tools are currently lacking. This study aims to identify circRNAs as diagnostic molecular markers for LNM and to investigate their molecular mechanisms in the occurrence of LNM in PTC. In this study, bioinformatics analysis and qPCR verification were used and identified that circ-ATF7IP was the key molecule in PTC progression and overexpressed in PTC patients with LNM. Mechanistically, circ-ATF7IP acts as a molecular sponge for miR-488-3p in PTC cells. PTC cell-derived miR-488-3p acts on macrophage (Mɸ) through exosome transfer. In Mɸ, miR-488-3p negatively regulates IL13RA1 at post transcription stage, facilitating M2 phenotype polarization. This reshapes the tumor microenvironment, enhancing tumor invasiveness. To be brief, circ-ATF7IP is a newly identified biomarker for PTC related LNM. Targeting circ-ATF7IP/miR-488-3p/IL13RA1 axis is a promising therapeutic strategy for PTC.

术前评估淋巴结转移（LNM）对甲状腺乳头状癌（PTC）选择合适的手术和治疗策略至关重要。然而，PTC中LNM的机制尚不清楚，目前缺乏有效的诊断工具。本研究旨在鉴定环状rna作为LNM的诊断分子标记物，并探讨其在PTC中发生LNM的分子机制。本研究通过生物信息学分析和qPCR验证，发现circ-ATF7IP是PTC进展的关键分子，在LNM的PTC患者中过表达。在机制上，circ-ATF7IP在PTC细胞中充当miR-488-3p的分子海绵。PTC细胞来源的miR-488-3p通过外泌体转移作用于巨噬细胞。在M， miR-488-3p在转录后阶段负调控IL13RA1，促进M2表型极化。这重塑了肿瘤微环境，增强了肿瘤的侵袭性。简而言之，circ-ATF7IP是一种新发现的PTC相关LNM的生物标志物。靶向circ-ATF7IP/miR-488-3p/IL13RA1轴是一种很有前景的PTC治疗策略。

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引用次数: 0

Rapid kinase activity detection and kinetic analysis using a convenient EGFR FRET-based detection probe 使用方便的EGFR fret检测探针快速检测激酶活性和动力学分析。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-09-08 DOI: 10.1016/j.bbagen.2025.130854

Kittitat Jaengwang , Suleeporn Pommayon , Chanikan Sonklin , Kiattawee Choowongkomon , Dujdaun Waraho-Zhmayev , Lueacha Tabtimmai

In modern drug discovery, there is a pressing need for rapid, cost-effective, and accessible methods to evaluate the biological activities of newly synthesized compounds. Traditional kinase assay platforms are often labor-intensive, time-consuming, and require specialized equipment or expertise. To address these limitations, we developed and validated a convenient in vitro kinase assay based on a recombinant biosensor, Picchu-B, constructed using a bacterial expression system. Picchu-B, derived from the live-cell EGFR FRET biosensor Picchu, was successfully expressed as a highly soluble, fluorescent protein. It served as a direct Probe for EGFR kinase, enabling real-time FRET-based detection of kinase activity. Optimization of Picchu-B concentration revealed a linear correlation between FRET signal intensity and EGFR-TK levels. The biosensor demonstrated high selectivity for EGFR and its clinically relevant mutants (e.g., T790M/L858R), with minimal cross-reactivity to unrelated kinases such as JAK-2. Enzyme kinetic studies confirmed nucleotide specificity of EGFR-TK in the presence of Picchu-B. This study highlights Picchu-B as a practical and scalable tool for EGFR-targeted drug screening, offering significant advantages in speed, and simplicity over conventional approaches.

在现代药物发现中，迫切需要快速、经济、可及的方法来评价新合成化合物的生物活性。传统的激酶检测平台通常是劳动密集型的，耗时的，并且需要专门的设备或专业知识。为了解决这些局限性，我们开发并验证了一种基于重组生物传感器Picchu-B的便捷的体外激酶测定方法，该方法使用细菌表达系统构建。Picchu- b来源于活细胞EGFR FRET生物传感器Picchu，成功表达为高可溶性荧光蛋白。它作为EGFR激酶的直接探针，能够实时检测基于fret的激酶活性。Picchu-B浓度优化显示FRET信号强度与EGFR-TK水平呈线性相关。该生物传感器对EGFR及其临床相关突变体（如T790M/L858R）具有高选择性，对无关激酶（如JAK-2）具有极小的交叉反应性。酶动力学研究证实了EGFR-TK在Picchu-B存在下的核苷酸特异性。这项研究强调了Picchu-B作为一种实用且可扩展的egfr靶向药物筛选工具，与传统方法相比，在速度和简单性方面具有显著优势。

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