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Recent Advancements in Biosensors for the Detection and Characterization of Amyloids: A Review 用于检测和表征淀粉样蛋白的生物传感器的最新进展:综述。
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-02 DOI: 10.1007/s10930-024-10205-0
Md Harun Rashid, Priyankar sen

Modern medicine has increased the human lifespan. However, with an increase in average lifespan risk of amyloidosis increases. Amyloidosis is a condition characterized by protein misfolding and aggregation. Early detection of amyloidosis is crucial, yet conventional diagnostic methods are costly and lack precision, necessitating innovative tools. This review explores recent advancements in diverse amyloid detection methodologies, highlighting the need for interdisciplinary research to develop a miniaturized electrochemical biosensor leveraging nanotechnology. However, the diagnostics industry faces obstacles such as skilled labor shortages, standardized selection processes, and concurrent multi-analyte identification challenges. Research efforts are focused on integrating electrochemical techniques into clinical applications and diagnostics, with the successful transition of miniaturized technologies from development to testing posing a significant hurdle. Label-free transduction techniques like voltammetry and electrochemical impedance spectroscopy (EIS) have gained traction due to their rapid, cost-effective, and user-friendly nature.

现代医学延长了人类的寿命。然而,随着平均寿命的延长,患淀粉样变性病的风险也随之增加。淀粉样变性是一种以蛋白质错误折叠和聚集为特征的疾病。早期检测淀粉样变性至关重要,但传统诊断方法成本高昂且缺乏精确性,因此需要创新工具。本综述探讨了各种淀粉样蛋白检测方法的最新进展,强调了利用纳米技术开发微型电化学生物传感器的跨学科研究的必要性。然而,诊断行业面临着各种障碍,如熟练劳动力短缺、标准化选择流程以及同时进行多种分析鉴定的挑战。研究工作的重点是将电化学技术整合到临床应用和诊断中,而微型化技术从开发到测试的成功过渡则是一个重大障碍。伏安法和电化学阻抗光谱法(EIS)等无标记传导技术因其快速、成本效益高和用户友好的特性而备受青睐。
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引用次数: 0
Bioinformatics Analysis of Actin Interactome: Characterization of the Nuclear and Cytoplasmic Actin-Binding Proteins 肌动蛋白相互作用组的生物信息学分析:核与细胞质肌动蛋白结合蛋白的特征描述
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-02 DOI: 10.1007/s10930-024-10207-y
Yakov I. Mokin, Olga I. Povarova, Iuliia A. Antifeeva, Alexey V. Artemov, Vladimir N. Uversky, Konstantin K. Turoverov, Irina M. Kuznetsova, Alexander V. Fonin

Actin is present in the cytoplasm and nucleus of every eukaryotic cell. In the cytoplasm, framework and motor functions of actin are associated with its ability to polymerize to form F-actin. In the nucleus, globular actin plays a significant functional role. For a globular protein, actin has a uniquely large number of proteins with which it interacts. Bioinformatics analysis of the actin interactome showed that only a part of actin-binding proteins are both cytoplasmic and nuclear. There are proteins that interact only with cytoplasmic, or only with nuclear actin. The first pool includes proteins associated with the formation, regulation, and functioning of the actin cytoskeleton predominate, while nuclear actin-binding proteins are involved in the majority of key nuclear processes, from regulation of transcription to DNA damage response. Bioinformatics analysis of the structure of actin-binding proteins showed that these are mainly intrinsically disordered proteins, many of which are part of membrane-less organelles. Interestingly, although the number of intrinsically disordered actin-binding proteins in the nucleus is greater than in the cytoplasm, the drivers for the formation of the membrane-less organelles in the cytoplasm are significantly (four times) greater than in the nucleus.

肌动蛋白存在于每一个真核细胞的细胞质和细胞核中。在细胞质中,肌动蛋白的框架和运动功能与其聚合形成 F-肌动蛋白的能力有关。在细胞核中,球状肌动蛋白发挥着重要的功能作用。对于球状蛋白质来说,肌动蛋白与之相互作用的蛋白质数量之多是独一无二的。对肌动蛋白相互作用组的生物信息学分析表明,只有一部分肌动蛋白结合蛋白既与细胞质结合,又与细胞核结合。有些蛋白质只与细胞质肌动蛋白相互作用,有些则只与核肌动蛋白相互作用。第一类蛋白主要包括与肌动蛋白细胞骨架的形成、调节和功能有关的蛋白,而核肌动蛋白结合蛋白则参与了从转录调节到 DNA 损伤反应等大多数关键的核过程。对肌动蛋白结合蛋白结构的生物信息学分析表明,这些蛋白主要是内在无序蛋白,其中许多是无膜细胞器的一部分。有趣的是,虽然细胞核中本质无序的肌动蛋白结合蛋白的数量比细胞质中的多,但细胞质中形成无膜细胞器的驱动力却比细胞核中的大得多(四倍)。
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引用次数: 0
Exploring the Potential of Arginine to Increase Coelenterazine-Renilla Luciferase Affinity and Enzyme Stability: Kinetic and Molecular Dynamics Studies 探索精氨酸提高腔肠素-瑞尼拉荧光素酶亲和力和酶稳定性的潜力:动力学和分子动力学研究。
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-02 DOI: 10.1007/s10930-024-10208-x
Maryam Salehian, Rahman Emamzadeh, Mahboobeh Nazari

Renilla luciferase catalyzes the oxidation of coelenterazine to coelenteramide and results in the emission of a photon of light. Although Renilla luciferase has various applications in biotechnology, its low thermal stability limits the development of its applications. Arginine is a well-known stabilizing amino acid that plays a key role in protein stabilization against inactivation. However, its impact on enzyme properties is unpredictable. This study investigates the impact of arginine on the kinetics and thermal stability of Renilla luciferase. The enzyme's performance was significantly enhanced in the presence of arginine, with catalytic efficiency increasing by 3.31-fold and 3.08-fold when exposed to 0.2 M and 0.3 M arginine, respectively. Additionally, arginine improved the thermal stability of Renilla luciferase. Molecular dynamics simulation showed that the addition of 0.2 M arginine reduced the binding of coelenteramide, the reaction product and an enzyme inhibitor, to the active site of the Renilla luciferase. Therefore, the release of the product was accelerated, and the affinity of Renilla luciferase for coelenterazine increased. Furthermore, Molecular dynamics studies indicated an increased network of water molecules surrounding Renilla luciferase in the presence of 0.2 M arginine. This network potentially enhances the hydrophobic effect on the protein structure, ultimately improving enzyme stability. The findings of this study hold promise for the development of commercial kits incorporating Renilla luciferase.

瑞宁拉荧光素酶催化腔肠素氧化成腔肠酰胺,从而发出光子。尽管瑞宁拉荧光素酶在生物技术中有多种应用,但其热稳定性较低,限制了其应用的发展。精氨酸是一种众所周知的稳定氨基酸,在稳定蛋白质防止失活方面起着关键作用。然而,精氨酸对酶特性的影响却难以预测。本研究探讨了精氨酸对雷尼拉荧光素酶动力学和热稳定性的影响。在精氨酸存在的情况下,酶的性能显著提高,当暴露于 0.2 M 和 0.3 M 精氨酸时,催化效率分别提高了 3.31 倍和 3.08 倍。此外,精氨酸还提高了雷尼拉荧光素酶的热稳定性。分子动力学模拟显示,加入 0.2 M 精氨酸后,反应产物和酶抑制剂腔肠酰胺与雷尼拉荧光素酶活性位点的结合减少。因此,产物的释放速度加快,而雷尼拉荧光素酶对腔肠素的亲和力增加。此外,分子动力学研究表明,在 0.2 M 精氨酸存在的情况下,Renilla 荧光素酶周围的水分子网络增加。这种网络可能会增强蛋白质结构的疏水效应,最终提高酶的稳定性。这项研究的结果为开发含有雷尼拉荧光素酶的商业试剂盒带来了希望。
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引用次数: 0
Molecular Insights of an Avian Species with Low Oxygen Affinity, the Crystal Structure of Duck T-State Methemoglobin 对低氧亲和力禽类物种的分子认识--鸭 T 态高铁血红蛋白的晶体结构。
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-05-20 DOI: 10.1007/s10930-024-10206-z
Sathya Moorthy Ponnuraj, Neelagandan Kamariah, Balasubramanian Moovarkumudalvan, Ramya Ramadoss, M. N. Ponnuswamy

Hemoglobin (Hb) is the key metalloprotein within red blood cells involved in oxygen transportation from lungs to body cells. The heme-iron atom inherent within Hb effectuates the mechanism of oxygen transportation and carbon dioxide removal. Structural investigations on avian Hb are limited when compared with the enormous work has been carried out on mammalian Hb. Here, the crystal structure of T-state methemoglobin (T-metHb) from domestic duck (Anas platyrhynchos), a low oxygen affinity avian species, determined to 2.1Å resolution is presented. Duck T-metHb crystallized in the orthorhombic space group C2221 with unit cell parameters a = 59.89, b = 109.42 and c = 92.07Å. The final refined model with R-factor: 19.5% and Rfree: 25.2% was obtained. The structural analysis reveals that duck T-metHb adopts a unique quaternary structure that is distinct from any of the avian liganded Hb structures. Moreover, it closely resembles the deoxy Hb of bar-headed goose, a high oxygen-affinity species. Besides the amino acid αPro119 located in the α1β1 interface, a unique quaternary structure with a constrained heme environment is attributed for the intrinsic low oxygen-affinity of duck Hb. This study reports the first protein crystal structure of low oxygen-affinity avian T-metHb from Anas platyrhynchos.

血红蛋白(Hb)是红细胞内的关键金属蛋白,参与从肺到身体细胞的氧气运输。Hb 中固有的血红素-铁原子实现了氧气运输和二氧化碳清除的机制。与哺乳动物 Hb 的大量研究工作相比,对鸟类 Hb 的结构研究十分有限。本文展示了家鸭(Anas platyrhynchos)这种低氧亲和力禽类的 T 态高铁血红蛋白(T-metHb)的晶体结构,其分辨率为 2.1 Å。鸭 T-metHb 在正交空间群 C2221 中结晶,单胞参数 a = 59.89、b = 109.42 和 c = 92.07 Å。最终得到的精炼模型的 R 因子为 19.5%,Rfree 为 25.2%:25.2%。结构分析表明,鸭 T-metHb 采用了独特的四元结构,不同于任何禽类配体 Hb 结构。此外,它与棒头鹅的脱氧 Hb(一种高氧亲和性物种)非常相似。除了位于α1β1界面的氨基酸αPro119外,鸭血红蛋白具有独特的四元结构和受约束的血红素环境,这也是鸭血红蛋白固有的低氧亲和性的原因。本研究首次报道了鸭血红蛋白(Anas platyrhynchos)的低亲氧性禽 T-metHb 蛋白晶体结构。
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引用次数: 0
Expression of Recombinant Stonustoxin Alpha Subunit and Preparation of polyclonal antiserum for Stonustoxin Neutralization Studies 重组石蒜毒素α亚基的表达和用于石蒜毒素中和研究的多克隆抗血清的制备。
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-05-17 DOI: 10.1007/s10930-024-10203-2
Amir Sajjad Hojjati-Razgi, Shahram Nazarian, Hossein Samiei-Abianeh, Amir Vazirizadeh, Emad kordbacheh, Seyed Mojtaba Aghaie

Stonustoxin (SNTX) is a lethal protein found in stonefish venom, responsible for many of the symptoms associated with stonefish envenomation. To counter stonefish venom challenges, antivenom is a well-established and effective solution. In this study, we aimed to produce the recombinant alpha subunit protein of Stonustoxin from Synanceia horrida and prepare antibodies against it The SNTXα gene sequence was optimized for E. coli BL21 (DE3) expression and cloned into the pET17b vector. Following purification, the recombinant protein was subcutaneously injected into rabbits, and antibodies were extracted from rabbit´s serum using a G protein column As a result of codon optimization, the codon adaptation index for the SNTXα cassette increased to 0.94. SDS-PAGE analysis validated the expression of SNTXα, with a band observed at 73.5 kDa with a yield of 60 mg/l. ELISA results demonstrated rabbits antibody titers were detectable up to a 1:256,000 dilution. The isolated antibody from rabbit´s serum exhibited a concentration of 1.5 mg/ml, and its sensitivity allowed the detection of a minimum protein concentration of 9.7 ng. In the neutralization assay the purified antibody against SNTXα protected mice challenged with 2 LD50. In conclusion, our study successfully expressed the alpha subunit of Stonustoxin in a prokaryotic host, enabling the production of antibodies for potential use in developing stonefish antivenom.

Graphical Abstract

石首鱼毒素(SNTX)是一种存在于石首鱼毒液中的致命蛋白质,是造成许多与石首鱼中毒相关症状的原因。为应对石首鱼毒液的挑战,抗蛇毒血清是一种行之有效的解决方案。在这项研究中,我们的目标是生产石首鱼毒素的重组α亚基蛋白,并制备针对它的抗体。 SNTXα 基因序列经过优化,可在大肠杆菌 BL21 (DE3) 中表达,并克隆到 pET17b 载体中。纯化后,将重组蛋白注射到兔子皮下,用 G 蛋白柱从兔子血清中提取抗体。SDS-PAGE 分析验证了 SNTXα 的表达,观察到一条 73.5 kDa 的条带,产量为 60 mg/l。酶联免疫吸附试验(ELISA)结果表明,兔子的抗体滴度在 1:256,000 稀释度时仍可检测到。从兔血清中分离出的抗体浓度为 1.5 毫克/毫升,其灵敏度可检测到最小浓度为 9.7 纳克的蛋白质。在中和试验中,纯化的 SNTXα 抗体能保护受到 2 LD50 病毒挑战的小鼠。总之,我们的研究成功地在原核宿主中表达了石首毒蛋白的α亚基,从而生产出了可能用于开发石首鱼抗蛇毒血清的抗体。 图文摘要
{"title":"Expression of Recombinant Stonustoxin Alpha Subunit and Preparation of polyclonal antiserum for Stonustoxin Neutralization Studies","authors":"Amir Sajjad Hojjati-Razgi,&nbsp;Shahram Nazarian,&nbsp;Hossein Samiei-Abianeh,&nbsp;Amir Vazirizadeh,&nbsp;Emad kordbacheh,&nbsp;Seyed Mojtaba Aghaie","doi":"10.1007/s10930-024-10203-2","DOIUrl":"10.1007/s10930-024-10203-2","url":null,"abstract":"<div><p>Stonustoxin (SNTX) is a lethal protein found in stonefish venom, responsible for many of the symptoms associated with stonefish envenomation. To counter stonefish venom challenges, antivenom is a well-established and effective solution. In this study, we aimed to produce the recombinant alpha subunit protein of Stonustoxin from <i>Synanceia horrida</i> and prepare antibodies against it The SNTXα gene sequence was optimized for <i>E. coli</i> BL21 (DE3) expression and cloned into the pET17b vector. Following purification, the recombinant protein was subcutaneously injected into rabbits, and antibodies were extracted from rabbit´s serum using a G protein column As a result of codon optimization, the codon adaptation index for the SNTXα cassette increased to 0.94. SDS-PAGE analysis validated the expression of SNTXα, with a band observed at 73.5 kDa with a yield of 60 mg/l. ELISA results demonstrated rabbits antibody titers were detectable up to a 1:256,000 dilution. The isolated antibody from rabbit´s serum exhibited a concentration of 1.5 mg/ml, and its sensitivity allowed the detection of a minimum protein concentration of 9.7 ng. In the neutralization assay the purified antibody against SNTXα protected mice challenged with 2 LD50. In conclusion, our study successfully expressed the alpha subunit of Stonustoxin in a prokaryotic host, enabling the production of antibodies for potential use in developing stonefish antivenom.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140963370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular Cloning, Expression and Enzymatic Characterization of Tetrahymena thermophila Glutathione-S-Transferase Mu 34 嗜热四膜虫谷胱甘肽-S-转移酶 Mu 34 的分子克隆、表达和酶学特征。
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-05-14 DOI: 10.1007/s10930-024-10204-1
Handan Açelya Kapkaç, Muhittin Arslanyolu

Glutathione-S-transferase enzymes (GSTs) are essential components of the phase II detoxification system and protect organisms from oxidative stress induced by xenobiotics and harmful toxins such as 1-chloro-2,4-dinitrobenzene (CDNB). In Tetrahymena thermophila, the TtGSTm34 gene was previously reported to be one of the most responsive GST genes to CDNB treatment (LD50 = 0.079 mM). This study aimed to determine the kinetic features of recombinantly expressed and purified TtGSTm34 with CDNB and glutathione (GSH). TtGSTm34-8xHis was recombinantly produced in T. thermophila as a 25-kDa protein after the cloning of the 660-bp full-length ORF of TtGSTm34 into the pIGF-1 vector. A three-dimensional model of the TtGSTm34 protein constructed by the AlphaFold and PyMOL programs confirmed that it has structurally conserved and folded GST domains. The recombinant production of TtGSTm34-8xHis was confirmed by SDS‒PAGE and Western blot analysis. A dual-affinity chromatography strategy helped to purify TtGSTm34-8xHis approximately 3166-fold. The purified recombinant TtGSTm34-8xHis exhibited significantly high enzyme activity with CDNB (190 µmol/min/mg) as substrate. Enzyme kinetic analysis revealed Km values of 0.68 mM with GSH and 0.40 mM with CDNB as substrates, confirming its expected high affinity for CDNB. The optimum pH and temperature were determined to be 7.0 and 25 °C, respectively. Ethacrynic acid inhibited fully TtGSTm34-8xHis enzyme activity. These results imply that TtGSTm34 of T. thermophila plays a major role in the detoxification of xenobiotics, such as CDNB, as a first line of defense in aquatic protists against oxidative damage.

谷胱甘肽-S-转移酶(GST)是第二阶段解毒系统的重要组成部分,能保护生物免受异生物体和有害毒素(如 1-氯-2,4-二硝基苯(CDNB))引起的氧化应激。据报道,在嗜热四膜虫中,TtGSTm34 基因是对 CDNB 处理反应最灵敏的 GST 基因之一(LD50 = 0.079 mM)。本研究旨在确定重组表达和纯化的 TtGSTm34 与 CDNB 和谷胱甘肽(GSH)的动力学特征。将 TtGSTm34 的 660-bp 全长 ORF 克隆到 pIGF-1 载体后,在嗜热菌中重组产生了 25-kDa 的 TtGSTm34-8xHis 蛋白。利用 AlphaFold 和 PyMOL 程序构建的 TtGSTm34 蛋白三维模型证实,该蛋白具有结构保守的折叠 GST 结构域。SDS-PAGE 和 Western 印迹分析证实了 TtGSTm34-8xHis 的重组产物。双亲和层析策略帮助纯化了 TtGSTm34-8xHis 约 3166 倍。纯化的重组 TtGSTm34-8xHis 以 CDNB(190 µmol/min/mg)为底物,表现出极高的酶活性。酶动力学分析表明,以 GSH 和 CDNB 为底物时,Km 值分别为 0.68 mM 和 0.40 mM,证实了其对 CDNB 的预期高亲和力。最佳 pH 值和温度分别为 7.0 和 25 °C。乙草胺完全抑制了 TtGSTm34-8xHis 的酶活性。这些结果表明,嗜热菌的 TtGSTm34 在 CDNB 等异种生物的解毒过程中发挥着重要作用,是水生原生动物抵御氧化损伤的第一道防线。
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引用次数: 0
Expression, Purification and Characterization of Recombinant Disintegrin from Gloydius Brevicaudus Venom in Escherichia Coli 在大肠杆菌中表达、纯化和表征来自 Gloydius Brevicaudus 毒液的重组崩解素。
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-05-11 DOI: 10.1007/s10930-024-10198-w
Yinxiang Lan, Xiuliang Qiu, Yunlu Xu

Disintegrins, a family of snake venom protein, which are capable of modulating the activity of integrins that play a fundamental role in the regulation of many physiological and pathological processes. The main purpose of this study is to obtain the recombinant disintegrin (r-DI) and evaluate its biological activity. In this study, we explored a high-level expression prokaryotic system and purification strategy for r-DI. Then, r-DI was treated to assay effects on cell growth, migration, and invasion. The affinity for the interactions of r-DI with integrin was determined using Surface plasmon resonance (SPR) analyses. The r-DI can be expressed in Escherichia coli and purified by one-step chromatography. The r-DI can inhibit B16F10 cells proliferation, migration, and invasion. Also, we found that r-DI could interact with the integrin αIIbβ3 (GPIIb/IIIa). The r-DI can be expressed, purified, characterized through functional assays, and can also maintain strong biological activities. Thus, this study showed potential therapeutic effects of r-DI for further functional and structural studies.

崩解素是蛇毒蛋白的一个家族,能够调节整合素的活性,而整合素在许多生理和病理过程的调节中发挥着重要作用。本研究的主要目的是获得重组崩解素(r-DI)并评估其生物活性。在这项研究中,我们探索了一种高水平的原核表达系统和 r-DI 的纯化策略。然后,对 r-DI 进行处理,检测其对细胞生长、迁移和侵袭的影响。利用表面等离子体共振(SPR)分析确定了 r-DI 与整合素相互作用的亲和力。r-DI 可以在大肠杆菌中表达,并通过一步色谱法纯化。r-DI 可抑制 B16F10 细胞的增殖、迁移和侵袭。此外,我们还发现 r-DI 可与整合素 αIIbβ3 (GPIIb/IIIa)相互作用。r-DI 可以表达、纯化,并通过功能测试进行表征,还能保持很强的生物活性。因此,这项研究显示了 r-DI 的潜在治疗作用,可用于进一步的功能和结构研究。
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引用次数: 0
The Impact of Terminal Peptide Extensions of Retinal Inosine 5´Monophosphate Dehydrogenase 1 Isoforms on their DNA-binding Activities 视网膜肌苷-5´单磷酸脱氢酶 1 异构体的末端肽延伸对其 DNA 结合活性的影响
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-05-11 DOI: 10.1007/s10930-024-10202-3
Mohsen Nabi Afjadi, Razieh Yazdanparast, Ebrahim Barzegari

The main structural difference between the mutation-susceptible retinal isoforms of inosine 5´-monophosphate dehydrogenase-1 (IMPDH-1) with the canonical form resides in the C- and N-terminal peptide extensions with unknown structural/functional impacts. In this report, we aimed to experimentally evaluate the functional impact of these extensions on the specific/non-specific single-stranded DNA (ssDNA)-binding activities relative to those of the canonical form. Our in silico findings indicated the possible contribution of the C-terminal segment to the reduced flexibility of the Bateman domain of the enzyme. In addition, the in silico data indicated that the N-terminal tail acts by altering the distance between the tetramers in the concave octamer complex (the native form) of the enzyme. The overall impact of these predicted structural variations became evident, first, through higher Km values with respect to either of the substrates relative to the canonical isoform, as reported previously (Andashti et al. in Mol Cell Biochem 465(1):155-164, 2020). Secondary, the binding of the recombinant mouse retinal isoform IMPDH1 (603) to its specific Rhodopsin target gene was significantly augmented while its binding to non-specific ssDNA was lower than that of the canonical isoform. The DNA-binding activity of the other mouse retinal isoform, IMPDH1(546), to specific and non-specific ssDNA was lower than that of the canonical form most probably due to the in silico predicted rigidity created in the Bateman domain by the C-terminal peptide extension. Furthermore, the DNA binding to the Rhodopsin target gene by each of the IMPDH isoforms influenced in the presence of GTP (Guanosine triphosphate) and ATP (Adenosine triphosphate).

肌苷-5´-单磷酸脱氢酶-1(IMPDH-1)的易突变视网膜异构体与标准形式之间的主要结构差异在于 C 端和 N 端肽延伸部分,其结构/功能影响尚不清楚。在本报告中,我们旨在通过实验评估这些扩展肽对特异性/非特异性单链 DNA(ssDNA)结合活性的功能影响。我们的硅学研究结果表明,C-末端片段可能导致酶的贝特曼结构域灵活性降低。此外,硅学数据还表明,N 端尾部的作用是改变酶的凹八聚体复合物(原生形式)中四聚体之间的距离。这些预测的结构变化的总体影响显而易见,首先,与标准同工型相比,与任何一种底物的 Km 值都更高,这在以前的报告中已有报道(Andashti 等人,发表于《细胞生物化学分子》465(1):155-164, 2020 年)。其次,重组小鼠视网膜异构体 IMPDH1 (603) 与特异性视网膜蛋白靶基因的结合明显增强,而与非特异性 ssDNA 的结合则低于典型异构体。另一种小鼠视网膜异构体 IMPDH1(546)与特异性和非特异性 ssDNA 的 DNA 结合活性均低于同源异构体,这很可能是由于 C 端多肽延伸在 Bateman 结构域中产生了硅学预测的刚性。此外,在 GTP(三磷酸腺苷)和 ATP(三磷酸腺苷)存在的情况下,每种 IMPDH 异构体都会影响 DNA 与黄体素靶基因的结合。
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引用次数: 0
Understanding the Specific Implications of Amino Acids in the Antibody Development 了解氨基酸在抗体发展中的具体影响。
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-05-09 DOI: 10.1007/s10930-024-10201-4
Akshata Gavade, Anil Kumar Nagraj, Riya Patel, Roylan Pais, Pratiksha Dhanure, Juergen Scheele, Werner Seiz, Jaspal Patil

As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody’s architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.

随着治疗和控制癌症、传染病和其他疾病的免疫疗法需求的增长,全面了解氨基酸及其在抗体工程中的复杂作用已成为首要要求。天然生产的抗体在互补决定区(CDR)和框架区可能没有最适合治疗目的的氨基酸。因此,为了提高抗体的结合亲和力和治疗特性,必须深入研究某些氨基酸对抗体结构的具体影响。在抗体工程中,找出对改善抗体特性有重大贡献的关键氨基酸残基至关重要。通过修饰或替换非常合适的氨基酸残基,可以获得具有更高的结合亲和力和更好的功能性的治疗性抗体。在此,我们指出了 CDR 中氨基酸的频率及其与结合自由能的关系。综述还分析了揭示 CDR 中氨基酸频率的两项研究的实验结果,并提供了结果之间的显著相关性。此外,它还讨论了抗体结构和抗原结合中的各种键相互作用。详细了解这些氨基酸的特性有助于分析设计和提高治疗性抗体整体性能所需的抗体序列和结构。
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引用次数: 0
Mechanism of Peptide Self-assembly and Its Study in Biomedicine 多肽自组装机制及其在生物医学中的研究
IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-27 DOI: 10.1007/s10930-024-10200-5
Xinyue Yang, Li Ma, Kui Lu, Dongxin Zhao

The development of peptide-based materials is one of the most challenging aspects of biomaterials research in recent years. The assembly of peptides is mainly controlled by forces such as hydrogen bonding, hydrophobic interaction, electrostatic interaction, and π-π accumulation. Peptides have unique advantages such as simple structure, easy synthesis, good biocompatibility, non-toxicity, easy modification, etc. These factors make peptides turn into ideal biomedical materials, and they have a broad application prospect in biomedical materials, and thus have received wide attention. In this review, the mechanism and classification of peptide self-assembly and its applications in biomedicine and hydrogels were introduced.

肽基材料的开发是近年来生物材料研究领域最具挑战性的课题之一。肽的组装主要受氢键作用、疏水作用、静电作用和π-π堆积等力的控制。多肽具有结构简单、易于合成、生物相容性好、无毒、易修饰等独特优势。这些因素使多肽成为理想的生物医学材料,在生物医学材料领域具有广阔的应用前景,因而受到广泛关注。本综述介绍了多肽自组装的机理、分类及其在生物医学和水凝胶中的应用。
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The Protein Journal
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