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Handheld portable device for delivering capped silver nanoparticles for antimicrobial applications. 手持式便携式设备,用于提供用于抗菌应用的盖银纳米颗粒。
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-12-03 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.9
Kumar Naveen, Sandeep Bose, Chanbasha Basheer, Richard N Zare, Elumalai Gnanamani

We describe a simple, cost-effective, green method for producing capped silver nanoparticles (Ag NPs) using a handheld portable mesh nebulizer. The precursor solution containing a 1:1 mixture of silver nitrate (AgNO3) and ligand (glycerol or sodium alginate) was sprayed using the nebulizer. The Ag NPs were generated in the water microdroplets within a few milliseconds under ambient conditions without any external reducing agent or action of a radiation source. The synthesized nanoparticles were characterized by using high-resolution transmission electron microscopy (HR-TEM), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction analysis (XRD), which validated the formation of Ag NPs. The synthesized glycerate-capped silver nanoparticles (Ag-gly NPs) were used as a catalyst to show the oxidative coupling of aniline to form azobenzene products with a yield of up to 61%. Experiments conducted using Ag NPs produced in the droplets demonstrated more than 99% antibacterial activity when contacting Escherichia Coli. Our in-situ synthesis-cum-fabrication technique using a portable sprayer represents a viable alternative to the existing fiber or hydrogel-based antimicrobial wound healing.

我们介绍了一种利用手持便携式网状雾化器生产封端银纳米粒子(Ag NPs)的简单、经济、绿色方法。使用雾化器喷洒含有硝酸银(AgNO3)和配体(甘油或海藻酸钠)1:1 混合物的前体溶液。在环境条件下,无需任何外部还原剂或辐射源作用,Ag NPs 在几毫秒内就在水微滴中生成。利用高分辨率透射电子显微镜(HR-TEM)、X 射线光电子能谱(XPS)和 X 射线衍射分析(XRD)对合成的纳米粒子进行了表征,验证了 Ag NPs 的形成。合成的甘油酸脂封端银纳米粒子(Ag-gly NPs)被用作催化剂,用于苯胺的氧化偶联生成偶氮苯产品,产率高达 61%。使用液滴中产生的 Ag NPs 进行的实验表明,在与大肠杆菌接触时,Ag NPs 的抗菌活性超过 99%。我们使用便携式喷雾器进行原位合成和制造的技术是现有纤维或水凝胶抗菌伤口愈合技术的一种可行替代方案。
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引用次数: 0
The potential of fluorogenicity for single molecule FRET and DyeCycling. 单分子FRET和染料循环的致氟性潜力。
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-12-03 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.11
Srijayee Ghosh, Sonja Schmid

Single Molecule Förster Resonance Energy Transfer (smFRET) is a popular technique to directly observe biomolecular dynamics in real time, offering unique mechanistic insight into proteins, ribozymes, and so forth. However, inevitable photobleaching of the fluorophores puts a stringent limit on the total time a surface-tethered molecule can be monitored, fundamentally limiting the information gain through conventional smFRET measurements. DyeCycling addresses this problem by using reversibly - instead of covalently - coupled FRET fluorophores, through which it can break the photobleaching limit and theoretically provide unlimited observation time. In this perspective paper, we discuss the potential of various fluorogenic strategies to suppress the background fluorescence caused by unbound, freely diffusing fluorophores inherent to the DyeCycling approach. In comparison to nanophotonic background suppression using zero-mode waveguides, the fluorogenic approach would enable DyeCycling experiments on regular glass slides with fluorogenic FRET probes that are quenched in solution and only fluoresce upon target binding. We review a number of fluorogenic approaches and conclude, among other things, that short-range quenching appears promising for realising fluorogenic DyeCycling on regular glass slides. We anticipate that our discussion will be relevant for all single-molecule fluorescence techniques that use reversible fluorophore binding.

单分子Förster共振能量转移(smFRET)是一种流行的技术,直接观察生物分子动力学的实时,提供独特的机制洞察蛋白质,核酶,等等。然而,不可避免的荧光团的光漂白对表面拴系分子的总时间进行了严格的限制,从根本上限制了通过传统smFRET测量获得的信息。dyecycle通过使用可逆而不是共价耦合的FRET荧光团来解决这个问题,通过它可以打破光漂白限制,理论上提供无限的观察时间。在这篇前瞻性的论文中,我们讨论了各种荧光策略的潜力,以抑制由未结合的、自由扩散的染料循环方法固有的荧光团引起的背景荧光。与使用零模波导的纳米光子背景抑制相比,荧光方法可以在常规玻片上使用荧光FRET探针进行dyrecycle实验,荧光探针在溶液中淬灭,仅在目标结合时发出荧光。我们回顾了一些荧光方法,并得出结论,除其他外,短程猝灭似乎有希望在常规玻片上实现荧光染料循环。我们预计,我们的讨论将适用于所有使用可逆荧光基团结合的单分子荧光技术。
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引用次数: 0
The Future of Chemistry is through Computations. 化学的未来在于计算。
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-10-22 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.16
Giulia Palermo, Bengt Nordén
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引用次数: 0
As air relative humidity increases, infectivity of SARS-CoV-2 decreases within water droplets. 随着空气相对湿度的增加,SARS-CoV-2在水滴中的传染性降低。
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-08-29 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.7
Yu Liu, Lei Cao, Yu Xia, Pan Pan, Lang Rao, Bolei Chen, Richard N Zare

Water droplets containing the SARS-CoV-2 virus, responsible for coronavirus 2019 transmission, were introduced into a controlled-temperature and -humidity chamber. The SARS-CoV-2 virus with green fluorescent protein tag in droplets was used to infect Caco-2 cells, with viability assessed through flow cytometry and microscopic counting. Whereas temperature fluctuations within typical indoor ranges (20°C-30°C) had minimal impact, we observed a notable decrease in infection rate as the surrounding air's relative humidity increased. By investigating humidity levels between 20% and 70%, we identified a threshold of ≥40% relative humidity as most effective in diminishing SARS-CoV-2 infectivity. We also found that damage of the viral proteins under high relative humidity may be responsible for the decrease in their activity. This outcome supports previous research demonstrating a rise in the concentration of reactive oxygen species within water droplets with elevated relative humidity.

将含有导致 2019 年冠状病毒传播的 SARS-CoV-2 病毒的水滴引入控温控湿室。水滴中带有绿色荧光蛋白标签的 SARS-CoV-2 病毒被用来感染 Caco-2 细胞,通过流式细胞仪和显微镜计数评估其存活率。在典型的室内温度范围(20°C-30°C)内,温度波动的影响微乎其微,但随着周围空气相对湿度的增加,我们观察到感染率明显下降。通过研究 20% 到 70% 之间的湿度水平,我们发现相对湿度≥40% 的阈值对降低 SARS-CoV-2 感染率最有效。我们还发现,病毒蛋白质在高相对湿度下受损可能是其活性降低的原因。这一结果支持了以前的研究,即随着相对湿度的升高,水滴中活性氧的浓度也会升高。
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引用次数: 0
Titratable residues that drive RND efflux: insights from molecular simulations 驱动 RND 外流的可滴定残基:分子模拟的启示
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-01 DOI: 10.1017/qrd.2024.6
Robert Clark, Kahlan E. Newman, S. Khalid
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引用次数: 0
Editorial. 社论
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-06 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.5
Bengt Nordén
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引用次数: 0
“Druggability” of the PAS domains of human PASK kinase, a therapeutic target for metabolic and liver disorders 人类 PASK 激酶 PAS 结构域的 "可药性"--新陈代谢和肝脏疾病的治疗靶标
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-02 DOI: 10.1017/qrd.2024.1
Shangze Xu, Lanyu Fan, Piotr Zaborniak, Ruidi Zhu, Haoyuan Ji, Katrina S Madden, J. V. de Souza, Agnieszka K. Bronowska
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引用次数: 0
“Druggability” of the PAS domains of human PASK kinase, a therapeutic target for metabolic and liver disorders 人类 PASK 激酶 PAS 结构域的 "可药性"--新陈代谢和肝脏疾病的治疗靶标
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-02 DOI: 10.1017/qrd.2024.1
Shangze Xu, Lanyu Fan, Piotr Zaborniak, Ruidi Zhu, Haoyuan Ji, Katrina S Madden, J. V. de Souza, Agnieszka K. Bronowska
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引用次数: 0
Protein structures unravel the signatures and patterns of deep time evolution 蛋白质结构揭示了深层进化的特征和模式
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-29 DOI: 10.1017/qrd.2024.4
Ajith Harish
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引用次数: 0
Sequence – Dynamics – Function Relationships in Protein Tyrosine Phosphatases 蛋白酪氨酸磷酸酶的序列-动力学-功能关系
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-24 DOI: 10.1017/qrd.2024.3
Rory M. Crean, Marina Corbella, A. R. Calixto, A. Hengge, S. C. Kamerlin
Protein tyrosine phosphatases are crucial regulators of cellular signaling. Their activity is regulated by the motion of a conserved loop, the WPD-loop, from a catalytically inactive open to a catalytically active closed conformation. WPD-loop motion optimally positions a catalytically critical residue into the active site, and is directly linked to the turnover number of these enzymes. Crystal structures of chimeric PTPs constructed by grafting parts of the WPD-loop sequence of PTP1B onto the scaffold of YopH showed WPD-loops in a wide-open conformation never previously observed in either parent enzyme. This wide-open conformation has, however, been observed upon binding of small molecule inhibitors to other PTPs, suggesting the potential of targeting it for drug discovery efforts. Here, we have performed simulations of both enzymes and show that there are negligible energetic differences in the chemical step of catalysis, but significant differences in the dynamical properties of the WPD-loop. Detailed interaction network analysis provides insight into the molecular basis for this population shift to a wide-open conformation. Taken together, our study provides insight into the links between loop dynamics and chemistry in these YopH variants specifically, and how WPD-loop dynamic can be engineered through modification of the internal protein interaction network.
蛋白酪氨酸磷酸酶是细胞信号传导的关键调节因子。它们的活性受一个保守的环--WPD-环--从无催化活性的开放构象运动到有催化活性的封闭构象的调节。WPD 环的运动能将催化关键残基最佳地定位到活性位点,并与这些酶的周转次数直接相关。通过将 PTP1B 的部分 WPD-环序列嫁接到 YopH 的支架上而构建的嵌合 PTP 的晶体结构显示,WPD-环呈宽开放构象,这是以前从未在这两种母酶中观察到的。不过,在小分子抑制剂与其他 PTPs 结合时,也观察到了这种宽开口构象,这表明有可能将其作为药物发现的靶点。在这里,我们对这两种酶进行了模拟,结果表明,在催化的化学步骤中,能量差异可以忽略不计,但在 WPD 环的动态特性上却存在显著差异。详细的相互作用网络分析深入揭示了这种向宽开放构象转变的分子基础。综上所述,我们的研究深入揭示了这些 YopH 变体的环路动力学与化学之间的联系,以及如何通过改变内部蛋白质相互作用网络来设计 WPD-环路动力学。
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引用次数: 0
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QRB Discovery
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