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Phenolic fractions of Heliotropium Bacciferum inhibit human insulin aggregation and protect against amyloid-induced cytotoxicity: Structural and biophysical analysis Heliotropium Bacciferum的酚类组分抑制人胰岛素聚集和防止淀粉样蛋白诱导的细胞毒性:结构和生物物理分析
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-27 DOI: 10.1016/j.bpc.2025.107437
Moneera Saud Al-Bagmi , Majed S. Alokail , Nasser M. Al-Daghri , Nojood Altwaijry , Ibrahim M. Aziz , Fahad N. Almajhdi , Mohd Shahnawaz Khan
In humans, more than 50 diseases are related to protein fibrillation, including Alzheimer's and Parkinson's diseases. Inhibition of amyloid fibril formation using natural products is one of the main therapeutic strategies for preventing the progression of these diseases. In this context, phenolic extract fractions from Heliotropium bacciferum leaves were evaluated for their ability to inhibit the aggregation of human insulin (HI), an appropriate model protein for fibrillation under physiological conditions and agitation at 600 rpm. Our results exhibited HI fibrillation under studied conditions, with aggregation kinetic fitting a sigmoidal curve with tlag and kapp values of 44.4 h and 0.16 h−1, respectively. Structural changes preceding the onset of fibril formation were detected by 8-Anilino-1-naphthalene-sulphonic acid (ANS) probe, revealed the exposure of hydrophobic regions in the HI peptide to the solvent, with tlag and kapp values of 18.2 h 0.12 h−1, respectively. CD spectroscopy calculated the formed fibrils comprised of 51.6 % β-sheet structure and 43.0 % unordered structure. In vitro studies demonstrated a dose-dependent inhibitory effect of H. bacciferum extracts on HI fibrillation. The free phenolic fraction (FPF) at 200 μg/mL exhibited nearly complete inhibition, whereas the bound phenolic fraction (BPF) demonstrated a 52 % reduction in fibrillation. These findings were further validated using Rayleigh light scattering (RLS) and circular dichroism analyses. Transmission electron microscopy (TEM) validated the formation of insulin fibrillation and its inhibition by extract fractions. Moreover, MTT assay results on SH-SY5Y cells showed that both extract fractions attenuated HI fibril-induced neuronal toxicity in a dose-dependent manner. Furthermore, RT-PCR analysis revealed that co-treatment with a low concentration (7.8 μg/mL) of H. bacciferum extracts led to a significant reduction in the expression levels of pro-apoptotic genes (Casp3 and Bax) and an increase in the anti-apoptotic gene Bcl-2 in SH-SY5Y cells treated with fibrillated HI. This study highlights the potential of H. bacciferum extracts as therapeutic agents against protein fibrillation-related diseases and underscores the importance of polyphenols in preventing amyloid fibril formation.
在人类中,有50多种疾病与蛋白质纤颤有关,包括阿尔茨海默病和帕金森病。使用天然产物抑制淀粉样蛋白纤维的形成是预防这些疾病进展的主要治疗策略之一。在这种情况下,从Heliotropium bacciferum叶片中提取的酚类提取物被评估其抑制人胰岛素(HI)聚集的能力,HI是生理条件下纤维性颤动的合适模型蛋白,在600转/分的搅拌下。我们的研究结果显示,在研究条件下,HI纤颤的聚集动力学符合s型曲线,其标志和kapp值分别为44.4 h和0.16 h−1。通过8-苯胺-1-萘磺酸(ANS)探针检测纤维形成前的结构变化,发现HI肽中的疏水区暴露于溶剂中,其标记值和kapp值分别为18.2 h 0.12 h−1。CD谱计算出形成的原纤维由51.6%的β片结构和43.0%的无序结构组成。体外研究表明,芽孢杆菌提取物对HI纤颤有剂量依赖性的抑制作用。200 μg/mL的游离酚组分(FPF)表现出几乎完全的抑制作用,而结合酚组分(BPF)显示出52%的纤颤减少。使用瑞利光散射(RLS)和圆二色性分析进一步验证了这些发现。透射电镜(TEM)证实了胰岛素纤颤的形成及其提取物的抑制作用。此外,SH-SY5Y细胞的MTT实验结果显示,两种提取物都以剂量依赖的方式减弱了HI原纤维诱导的神经元毒性。此外,RT-PCR分析显示,低浓度(7.8 μg/mL) H. bacciferum提取物共处理SH-SY5Y细胞后,促凋亡基因Casp3和Bax的表达水平显著降低,抗凋亡基因Bcl-2的表达水平显著升高。本研究强调了芽孢杆菌提取物作为治疗蛋白纤颤相关疾病的潜力,并强调了多酚在预防淀粉样纤维形成中的重要性。
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引用次数: 0
The amyloidogenic peptide stretch in human tau, tau306–311 is a promising injectable hydrogelator 人tau蛋白中的淀粉样蛋白肽片段tau306-311是一种很有前途的注射用凝胶剂
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-24 DOI: 10.1016/j.bpc.2025.107438
Shubhangini Singh Verma, Shinjini Bhattacharya, Sachin Kumar, Nitin Chaudhary
A vast majority of peptide hydrogelators harbor a bulky, non-native aromatic moiety. Such foreign moieties raise safety concerns as far as biomedical applications of hydrogels are concerned. The hydrogel research, therefore, has branched to another dimension – to identify native or native-like short peptide stretches that could cause the gelation of biological fluids. Using well-defined criteria to identify native peptide stretches that could form a viscous solution in water but cause gelation of phosphate-buffered saline (PBS), we identified the hexapeptide stretch from human tau, viz. tau306–311, as a promising injectable hydrogelator. The peptide causes instant gelation of PBS and the cell culture media. Such hydrogels find applications as drug delivery vehicles, scaffolds for mammalian cell culture, wound-dressing material, etc.
绝大多数肽凝胶都含有大量非天然的芳香基团。就水凝胶的生物医学应用而言,这些外国成分引起了安全问题。因此,水凝胶研究已经扩展到另一个维度——识别可能导致生物液体凝胶化的天然或类似于天然的短肽延伸。使用定义明确的标准来鉴定天然肽段,这些肽段可以在水中形成粘性溶液,但会导致磷酸盐缓冲盐水(PBS)凝胶化,我们鉴定了来自人类tau蛋白的六肽段,即tau306-311,作为一种有前途的可注射凝胶剂。肽使PBS和细胞培养基瞬间凝胶化。这种水凝胶可以应用于药物输送载体、哺乳动物细胞培养支架、伤口敷料等。
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引用次数: 0
Characterization of metabolism associated with outcomes in severe acute pancreatitis: Insights from serum metabolomic analysis 代谢与重症急性胰腺炎预后相关的特征:来自血清代谢组学分析的见解
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-15 DOI: 10.1016/j.bpc.2025.107436
Mohd Adnan Siddiqui , Anamika Singh , Swarnima Pandey , Mohammed Haris Siddiqui , Afzal Azim , Neeraj Sinha
Severe Acute Pancreatitis (SAP) is characterized by an abrupt onset of pancreatic inflammation, which may induce damage to other organs, and is associated with significant morbidity and mortality. Despite the considerable disease burden, specific treatments to stop progression or prevent occurrence are limited. Currently, there is a paucity of comprehensive studies that thoroughly explore metabolic dysregulation in SAP, particularly those that emphasize changes in outcomes. Nuclear magnetic resonance (NMR) based metabolomics coupled with multivariate analysis was applied to serum samples of 20 survivors and 30 non-survivors of SAP to identify metabolic changes linked to different outcomes. The discriminant analysis of serum samples of SAP survivors and non-survivors revealed isoleucine, leucine, valine, arginine, lactate, and 3-hydroxybutyrate as significant metabolites elevated in the non-survivors. These identified metabolites had shown a significant positive correlation with clinical severity scores in the Pearson correlation analysis. Pathway analysis revealed disruptions in amino acid metabolism, driven by protein catabolism to fulfill the patient's energy requirements. This study highlights the importance of metabolomics in unraveling the molecular and physiological mechanisms underlying SAP. These findings offer valuable insights for clinicians to develop treatment strategies that target metabolic pathways in SAP, potentially for improving patient outcomes.
严重急性胰腺炎(SAP)的特点是胰腺炎症的突然发作,可引起其他器官的损害,并与显著的发病率和死亡率相关。尽管有相当大的疾病负担,但阻止进展或预防发生的特定治疗是有限的。目前,缺乏全面深入探讨SAP代谢失调的研究,特别是那些强调结果变化的研究。基于核磁共振(NMR)的代谢组学结合多变量分析应用于20名SAP幸存者和30名非SAP幸存者的血清样本,以确定与不同结果相关的代谢变化。SAP幸存者和非幸存者的血清样本的判别分析显示,异亮氨酸、亮氨酸、缬氨酸、精氨酸、乳酸和3-羟基丁酸盐是非幸存者显著升高的代谢物。在Pearson相关分析中,这些鉴定出的代谢物与临床严重程度评分显示出显著的正相关。通路分析揭示了氨基酸代谢的中断,由蛋白质分解代谢驱动,以满足患者的能量需求。这项研究强调了代谢组学在揭示SAP的分子和生理机制方面的重要性。这些发现为临床医生制定针对SAP代谢途径的治疗策略提供了有价值的见解,有可能改善患者的预后。
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引用次数: 0
A detailed review of genetically encodable RFPs and far-RFPs and their applications in advanced super-resolution imaging techniques 综述了遗传可编码rfp和远编码rfp及其在先进超分辨率成像技术中的应用。
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-15 DOI: 10.1016/j.bpc.2025.107432
Jianshu Dong , Bilal Tayyab , Jiangyun Wang
The red fluorescent proteins (RFPs) and far-red fluorescent proteins (far-RFPs) that are encoded genetically can emit fluorescence within the spectral ranges of 580–680 nm when exposed to the light of appropriate wavelengths. Unlike many RFPs derived from coral species, numerous far-RFPs are optimized synthetic constructs engineered from different orange or red-emitting progenitors. Various categories have been established for the available RFPs and far-red fluorescent proteins based on their photo-chemical profile, fluorescence mechanism, and switching kinetics. Fluorescent probes (FPs) derived from these classes are extensively utilized for labelling and visualizing in vivo and in vitro specimens. Traditional optical microscopy methods generate diffraction-limited, indistinct images owing to the restricted resolution capability of light ranging from 200 to 300 nm. Since 2005, super-resolution microscopy has been a topic of great interest due to its ability to achieve imaging at spatial resolutions of less than 100 nm. The 2014 Nobel Prize in Chemistry was awarded to Eric Betzig, Stefan Hell, and William E. Moerner for their contributions to demonstrating the effectiveness of genetically encodable fluorescent proteins in visualizing biological systems through super-resolution fluorescence microscopy. This review provides a concise overview of RFPs and far-RFPs, including the involvement of surrounding residues in chromophore intactness, stability, autocatalytic maturation and switching kinetics. All the chemical pathways proposed for photoactivation, photoconversion and photoswitching mechanisms are concisely reviewed. Subsequently, a comprehensive summary was provided regarding the various types of super-resolution techniques that are commonly employed, elucidating their underlying principles of operation, as well as the potential future applications of RFPs/far-RFPs in the field of biological imaging.
基因编码的红色荧光蛋白(rfp)和远红色荧光蛋白(far- rfp)在适当波长的光照射下可发出580-680 nm光谱范围内的荧光。与许多来自珊瑚物种的rfp不同,许多远rfp是由不同的橙色或红色发光祖细胞工程化的优化合成结构。基于它们的光化学特征、荧光机制和开关动力学,已经为可用的rfp和远红色荧光蛋白建立了各种类别。来自这些类别的荧光探针(FPs)广泛用于体内和体外标本的标记和可视化。传统的光学显微镜方法产生衍射有限,模糊的图像,由于有限的分辨率的光范围从200到300纳米。自2005年以来,超分辨率显微镜一直是一个非常感兴趣的话题,因为它能够在小于100纳米的空间分辨率下实现成像。2014年诺贝尔化学奖被授予Eric Betzig, Stefan Hell和William E. Moerner,以表彰他们通过超分辨率荧光显微镜展示遗传可编码荧光蛋白在可视化生物系统中的有效性。本文简要介绍了rfp和远rfp的研究进展,包括周围残基对发色团完整性、稳定性、自催化成熟和开关动力学的影响。简要介绍了光激活、光转化和光开关机制的所有化学途径。随后,对各种常用的超分辨率技术进行了全面的总结,阐明了其基本的工作原理,以及rfp /far- rfp在生物成像领域的潜在应用前景。
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引用次数: 0
Interaction of native and aggregated albumin with DMPC bilayers 天然白蛋白和聚集白蛋白与DMPC双层的相互作用
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-14 DOI: 10.1016/j.bpc.2025.107431
Brigitte Magdalena Merino , Rosa Bartucci , Rita Guzzi
The study of protein-lipid interaction offers interesting insights into the mutual alterations determined in the formation of the supramolecular complex. It gains even more interest, not only in basic research but also in biomedical and biomaterial applications, when protein aggregation and fibril formation are involved. In this study, the reciprocal influence of human serum albumin (HSA), in both the native and the thermally aggregated state, and dimyristoylphosphatidylcholine (DMPC) bilayers is investigated by combining UV–Vis scattering, attenuated total reflection Fourier transform infrared (ATR-FTIR), and spin-label electron paramagnetic resonance (EPR) spectroscopies. Temperature-dependent optical density at fixed wavelength reveals the pre- and the main phase transitions in DMPC bilayers as well as the onset of protein aggregation at Tagg ≈ 70 °C. In native protein/lipid complexes, the protein adsorption on the membrane surfaces suppresses the pre-transition and downshifts the temperature of the main phase transitions of DMPC, whereas the presence of DMPC increases Tagg without affecting the thermal profile. Kinetics experiments reveal that lipid bilayers reduce the thermally-induced aggregation of the protein. ATR-FTIR data indicate that albumin weakens the hydrogen bonding network at the carbonyl groups of the membrane. Conversely, lipid bilayers in any physical state do not alter the structural features of both native and aggregated HSA. In protein/lipid complexes, spin-label EPR of the lipid component reveals that the proteins reduce the packing density of the first chain segments and stabilize the fluid state, the effect being more evident for the native protein.
蛋白质-脂质相互作用的研究为超分子复合物形成过程中确定的相互改变提供了有趣的见解。当涉及蛋白质聚集和纤维形成时,不仅在基础研究中,而且在生物医学和生物材料应用中,它获得了更多的兴趣。本研究通过紫外-可见散射、衰减全反射傅立叶变换红外(ATR-FTIR)和自旋标记电子顺磁共振(EPR)光谱,研究了天然和热聚集状态下的人血清白蛋白(HSA)和二酰基磷脂酰胆碱(DMPC)双分子层的相互影响。固定波长下温度相关的光密度揭示了DMPC双分子层的前相变和主相变以及tag≈70°C时蛋白质聚集的开始。在天然蛋白/脂质复合物中,膜表面的蛋白质吸附抑制了DMPC的预转变并降低了DMPC的主要相变温度,而DMPC的存在增加了Tagg,但不影响热剖面。动力学实验表明,脂质双分子层减少了热诱导的蛋白质聚集。ATR-FTIR数据表明,白蛋白削弱了膜羰基上的氢键网络。相反,任何物理状态下的脂质双分子层都不会改变天然和聚集的HSA的结构特征。在蛋白/脂质复合物中,脂质组分的自旋标记EPR表明,蛋白质降低了第一链段的堆积密度,稳定了流体状态,对天然蛋白的作用更为明显。
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引用次数: 0
Decoding the interaction of an imidazo-pyrimidine derivative with serum proteins: Spectroscopic, computational and structure-activity relationship analysis 解码咪唑嘧啶衍生物与血清蛋白的相互作用:光谱,计算和构效关系分析
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-13 DOI: 10.1016/j.bpc.2025.107435
Bishwayan Chakraborty , Asmit Santra , Debangana Tah , Koushik Goswami , Anupam Jana , Agnishwar Girigoswami , Debosreeta Bose
In the present article, we have tried to theoretically analyze the structure-function relationship of a novel imidazo pyrimidine derivative, IPD, and decipher its interactions with two serum proteins, BSA and HSA, spectroscopically. IPD is almost non-fluorescent in a polar environment, but its fluorescence enhancement is significant in non-polar mediums like proteins. Steady-state fluorometric investigations indicate a strong binding interaction between the probe, IPD, and serum proteins, with HSA being more strongly bound to IPD. This stronger binding affinity of the IPD–HSA complex than compared to the IPD–BSA complex was corroborated through denaturation and quenching studies, too. In silico molecular docking interactions also reveal a similar stronger binding affinity in HSA than BSA. This is attributed to the probe residing in a more hydrophobic region in HSA; thus, the π and alkyl interactions are stronger in HSA than in BSA.
在本文中,我们试图从理论上分析一种新的咪唑嘧啶衍生物IPD的结构-功能关系,并从光谱上解释它与两种血清蛋白(BSA和HSA)的相互作用。IPD在极性环境中几乎是无荧光的,但在蛋白质等非极性介质中其荧光增强是显著的。稳态荧光研究表明,探针、IPD和血清蛋白之间存在很强的结合相互作用,HSA与IPD的结合更强。通过变性和猝灭研究也证实了IPD-HSA复合物比IPD-BSA复合物更强的结合亲和力。在硅分子对接相互作用中,HSA也显示出与BSA相似的更强的结合亲和力。这是由于探针驻留在HSA中更疏水的区域;因此,π和烷基的相互作用在HSA中比在BSA中更强。
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引用次数: 0
Equilibrium solubility, solvent effect, solvation and thermodynamic modeling of 1, 3-dinitropyrazole in solutions of methyl alcohol /ethyl alcohol + water 1,3 -二硝基吡唑在甲醇/乙醇+水溶液中的平衡溶解度、溶剂效应、溶剂化和热力学模型
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-10 DOI: 10.1016/j.bpc.2025.107430
Adel Noubigh , Manef Abderrabba
1,3-dinitropyrazole's (DNP) solubility was studied by utilizing the gravimetric method across temperatures ranging 278.15 to 318.15 K and a pressure of 101.2 kPa. In the study, two solvent mixtures were investigated: aqueous methyl alcohol and aqueous ethyl alcohol. Based on the findings, higher temperatures favorably influenced solute dissolution in both solvent systems. To relate the solubility of DNP in two binary solvents mixture, the KAT-LSER model was used. This implies that the polarity of the solvents, as well as the cavity term and hydrogen bonding interactions were pivotal to DNP's solubility. By utilizing the Jouyban-Acree, van't Hoff-Jouyban-Acree, Apelblat-Jouyban-Acree and Ma models, the derived results were compiled. The experimental results prove that the Apelblat-Jouyban-Acree model could give the best correlation results with the experimental data, with the overall relative average deviation values (RAD) of 2.05 %, 2.51 % and the root mean-square deviation (RMSD) of 0.415 × 10−4, 0.492 × 10−4 in aqueous methyl alcohol and aqueous ethyl alcohol, respectively. Using the inverse Kirkwood–Buff integrals method, the preferential solvation parameters for the solute DNP determined. The obtained results show that DNP exhibited a preference for solvation in methyl alcohol and ethyl alcohol at all mole fractions of alcohol.
用重量法研究了1,3-二硝基吡唑(DNP)在278.15 ~ 318.15 K温度和101.2 kPa压力下的溶解度。在研究中,研究了两种溶剂混合物:含水甲醇和含水乙醇。根据研究结果,较高的温度有利于两种溶剂体系中的溶质溶解。为了研究DNP在两种二元溶剂混合物中的溶解度,采用了KAT-LSER模型。这意味着溶剂的极性,以及空腔期和氢键相互作用对DNP的溶解度至关重要。利用Jouyban-Acree、van't Hoff-Jouyban-Acree、Apelblat-Jouyban-Acree和Ma模型,对推导结果进行了编译。实验结果表明,apelblat - jouybana - acree模型与实验数据的相关性最好,在甲醇水溶液和乙醇水溶液中,其总体相对平均偏差(RAD)分别为2.05%、2.51%,均方根偏差(RMSD)分别为0.415 × 10−4、0.492 × 10−4。利用逆Kirkwood-Buff积分法,确定了溶质DNP的首选溶剂化参数。结果表明,DNP在乙醇的所有摩尔分数中均表现出对甲醇和乙醇溶剂化的偏好。
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引用次数: 0
Autoencoder-based drug-virus association prediction with reliable negative sample selection: A case study with COVID-19 基于自编码器的药物-病毒关联预测与可靠的阴性样本选择:COVID-19病例研究
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-10 DOI: 10.1016/j.bpc.2025.107434
A.S. Aruna , K.R. Remesh Babu , K. Deepthi
Emergence of viruses cause unprecedented challenges and thus leading to wide-ranging consequences today. The world has faced massive disruptions like COVID-19 and continues to suffer in terms of public health and world economy. Fighting with this emergence of viruses and its reemergence plays a critical role in the health care industry. Identification of novel virus-drug associations is a vital step in drug discovery. Prediction and prioritization of novel virus-drug associations through computational approaches is an alternative and best choice considering the cost and risk of biological experiments. This study proposes a method, KR-AEVDA that relies on k-nearest neighbor based reliable negative sample selection and autoencoder based feature extraction to explore promising virus-drug associations for further experimental validation. The method analyzes complex relationships among drugs and viruses by investigating similarity and association data between drugs and viruses. It generates feature vectors from the similarity data, and reliable negative samples are extracted through an effective distance-based algorithm from the unlabeled samples in the dataset. Then high level features are extracted via an autoencoder and is fed to an ensemble classifier for inferring novel associations. Experimental results on three different datasets showed that KR-AEVDA reliably attained better performance than other state-of-the-art methods. Molecular docking is carried out between the top-predicted drugs and the crystal structure of the SARS-CoV-2's main protease to further validate the predictions. Case studies for SARS-CoV-2 illustrate the effectiveness of KR-AEVDA in identifying potential virus-drug associations.
病毒的出现带来了前所未有的挑战,从而导致了今天广泛的后果。世界已经面临了像 COVID-19 这样的大规模破坏,在公共卫生和世界经济方面继续遭受损失。应对这种病毒的出现和再次出现在医疗保健行业中起着至关重要的作用。鉴定新型病毒与药物的关联是药物发现的重要一步。考虑到生物实验的成本和风险,通过计算方法预测新型病毒与药物的关联并确定其优先次序是一种可供选择的最佳方法。本研究提出了一种名为 KR-AEVDA 的方法,它依赖于基于 k 近邻的可靠负样本选择和基于自动编码器的特征提取来探索有前景的病毒-药物关联,以便进一步进行实验验证。该方法通过研究药物和病毒之间的相似性和关联数据,分析药物和病毒之间的复杂关系。它从相似性数据中生成特征向量,并通过有效的基于距离的算法从数据集中的未标记样本中提取可靠的阴性样本。然后通过自动编码器提取高级特征,并将其输入集合分类器以推断新的关联。在三个不同数据集上的实验结果表明,KR-AEVDA 能可靠地获得比其他先进方法更好的性能。为了进一步验证预测结果,KR-AEVDA 将预测结果最好的药物与 SARS-CoV-2 主要蛋白酶的晶体结构进行了分子对接。针对 SARS-CoV-2 的案例研究说明了 KR-AEVDA 在识别潜在病毒-药物关联方面的有效性。
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引用次数: 0
Relevance of ceramide 1-phosphate domain formation in activation of cytosolic phospholipase A2 神经酰胺1-磷酸结构域形成与胞质磷脂酶A2激活的相关性
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-09 DOI: 10.1016/j.bpc.2025.107433
Tomokazu Yasuda , Daiki Ueura , Madoka Nakagomi , Shinya Hanashima , Michio Murata
Ceramide 1-phosphate (C1P), as a lipid mediator, specifically binds and activates cytosolic phospholipase A2α (cPLA2α). Previous findings revealed that modification of the specific hydrophobic moiety decreases the affinity with cPLA2α. However, the possible biological role of the temporal C1P-enriched domains formed in biomembranes for the molecular recognition of cPLA2α has not been fully elucidated. In this study we elucidated the properties of segregated domains formed by C1P (and its analogs) and the affinity of cPLA2α for C1P in different co-lipid environments by fluorescence spectroscopy using trans-parinaric acid and surface plasmon resonance (SPR). Fluorescence measurements suggested that the formation of C1P ordered domains is strongly influenced by interfacial 3-OH and phosphate groups of C1P, such as hydrogen-bonding and electrostatic interactions, and depends on the co-lipid composition of the host bilayer. SPR indicated that C1P under the lipid environment favorable for the formation of C1P clusters has higher affinity for cPLA2α. Thus, we speculate that C1P clusters formed under certain membrane conditions are important in specific binding with cPLA2α by increasing the interaction between the C1P headgroup and basic residues of cPLA2α. In conclusion, this study revealed that the local formation of lipid mediator-rich clusters in biomembranes likely has a significant effect on the interaction between the mediator and its receptor protein.
神经酰胺1-磷酸(C1P)作为一种脂质介质,特异性结合并激活胞质磷脂酶A2α (cPLA2α)。先前的研究结果表明,特定疏水片段的修饰降低了与cPLA2α的亲和力。然而,生物膜中形成的时间型c1p富集结构域在cPLA2α分子识别中的可能生物学作用尚未完全阐明。本研究利用反式粒子酸和表面等离子体共振(SPR)荧光光谱分析了C1P(及其类似物)形成的分离结构域的性质,以及cPLA2α在不同共脂环境下对C1P的亲和力。荧光测量表明,C1P有序结构域的形成受到C1P的界面3-OH和磷酸基团(如氢键和静电相互作用)的强烈影响,并取决于宿主双分子层的共脂质组成。SPR结果表明,在有利于形成C1P簇的脂质环境下,C1P对cPLA2α具有较高的亲和力。因此,我们推测在一定的膜条件下形成的C1P簇通过增加C1P头基与cPLA2α基本残基之间的相互作用,在与cPLA2α的特异性结合中起重要作用。综上所述,本研究揭示了生物膜中富含脂质介质簇的局部形成可能对介质与其受体蛋白的相互作用有重要影响。
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引用次数: 0
Unveiling theranostic potential: Insights into cell-free microRNA-protein interactions 揭示治疗潜力:洞察无细胞microrna -蛋白相互作用
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-03-03 DOI: 10.1016/j.bpc.2025.107421
Vishal Kumar Sahu , Subhayan Sur , Sanjana Agarwal , Harishkumar Madhyastha , Amit Ranjan , Soumya Basu
MicroRNAs (miRNAs) belong to a short endogenous class of non-coding RNAs which have been well studied for their crucial role in regulating cellular homeostasis. Their role in the modulation of diverse biological pathways by interacting with cellular proteins, genes, and RNAs through cellular communication projects them as promising biomarkers and therapeutic targets. However, studying miRNA-protein interactions specific to disease in the extracellular or cell-free environments for drug discovery and biomarker establishment is challenging and resource-intensive due to their structural complexities. In this study, we present a computational approach to uncover patterns in miRNA-protein interactions in the cell-free milieu leveraging existing experimental data. We employed motif discovery tools, extracted motifs from 3D protein and miRNA structures, and conducted molecular docking analyses to identify and rank these interactions. This in silico-based approach reveals 204 and 2874 consensus sequences in miRNAs and proteins, respectively, within the interactome highlighting their potential roles in the cardiovascular diseases, neurological disorders, and cancers. The role of proteins like METTL3 and AGO2 and miRNAs such as hsa-miR-484 and hsa-miR-30 families, hsa-mir-126-5p has been discussed contextually. Additionally, we discovered simple sequence repeats in the consensus patterns having unexplored functional roles. Our observations provide new insights into the extracellular miRNA-protein interactions that may drive disease initiation and progression offering potential avenues for overcoming challenges like therapy relapse and drug inefficacy. The results of our analysis are available in the miRPin database (https://www.mirna.in/miRPin).
MicroRNAs (miRNAs)是一类短的内源性非编码rna,因其在调节细胞稳态中的重要作用而被广泛研究。它们通过细胞通讯与细胞蛋白、基因和rna相互作用,调节多种生物途径,使它们成为有前途的生物标志物和治疗靶点。然而,研究细胞外或无细胞环境中特异性疾病的mirna -蛋白相互作用,用于药物发现和生物标志物的建立,由于其结构的复杂性,是具有挑战性和资源密集型的。在这项研究中,我们提出了一种利用现有实验数据揭示无细胞环境中mirna -蛋白相互作用模式的计算方法。我们使用基序发现工具,从3D蛋白和miRNA结构中提取基序,并进行分子对接分析,以识别和排序这些相互作用。这种基于硅的方法分别揭示了相互作用组内mirna和蛋白质中的204和2874个共识序列,突出了它们在心血管疾病、神经系统疾病和癌症中的潜在作用。蛋白如METTL3和AGO2以及mirna如hsa-miR-484和hsa-miR-30家族,hsa-mir-126-5p的作用已经在背景下进行了讨论。此外,我们发现共识模式中简单的序列重复具有未探索的功能作用。我们的观察结果为细胞外mirna -蛋白相互作用提供了新的见解,这种相互作用可能驱动疾病的发生和进展,为克服治疗复发和药物无效等挑战提供了潜在的途径。我们的分析结果可在miRPin数据库(https://www.mirna.in/miRPin)中找到。
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Biophysical chemistry
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