Pub Date : 2024-12-03eCollection Date: 2024-01-01DOI: 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。
{"title":"Handheld portable device for delivering capped silver nanoparticles for antimicrobial applications.","authors":"Kumar Naveen, Sandeep Bose, Chanbasha Basheer, Richard N Zare, Elumalai Gnanamani","doi":"10.1017/qrd.2024.9","DOIUrl":"10.1017/qrd.2024.9","url":null,"abstract":"<p><p>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 (AgNO<sub>3</sub>) 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 <i>Escherichia Coli.</i> 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.</p>","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e9"},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-03eCollection Date: 2024-01-01DOI: 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.
{"title":"The potential of fluorogenicity for single molecule FRET and DyeCycling.","authors":"Srijayee Ghosh, Sonja Schmid","doi":"10.1017/qrd.2024.11","DOIUrl":"10.1017/qrd.2024.11","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e8"},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-22eCollection Date: 2024-01-01DOI: 10.1017/qrd.2024.16
Giulia Palermo, Bengt Nordén
{"title":"The Future of Chemistry is through Computations.","authors":"Giulia Palermo, Bengt Nordén","doi":"10.1017/qrd.2024.16","DOIUrl":"10.1017/qrd.2024.16","url":null,"abstract":"","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e7"},"PeriodicalIF":0.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-29eCollection Date: 2024-01-01DOI: 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.
{"title":"As air relative humidity increases, infectivity of SARS-CoV-2 decreases within water droplets.","authors":"Yu Liu, Lei Cao, Yu Xia, Pan Pan, Lang Rao, Bolei Chen, Richard N Zare","doi":"10.1017/qrd.2024.7","DOIUrl":"10.1017/qrd.2024.7","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e6"},"PeriodicalIF":0.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Titratable residues that drive RND efflux: insights from molecular simulations","authors":"Robert Clark, Kahlan E. Newman, S. Khalid","doi":"10.1017/qrd.2024.6","DOIUrl":"https://doi.org/10.1017/qrd.2024.6","url":null,"abstract":"","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"828 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140782010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shangze Xu, Lanyu Fan, Piotr Zaborniak, Ruidi Zhu, Haoyuan Ji, Katrina S Madden, J. V. de Souza, Agnieszka K. Bronowska
{"title":"“Druggability” of the PAS domains of human PASK kinase, a therapeutic target for metabolic and liver disorders","authors":"Shangze Xu, Lanyu Fan, Piotr Zaborniak, Ruidi Zhu, Haoyuan Ji, Katrina S Madden, J. V. de Souza, Agnieszka K. Bronowska","doi":"10.1017/qrd.2024.1","DOIUrl":"https://doi.org/10.1017/qrd.2024.1","url":null,"abstract":"","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"28 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139870955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shangze Xu, Lanyu Fan, Piotr Zaborniak, Ruidi Zhu, Haoyuan Ji, Katrina S Madden, J. V. de Souza, Agnieszka K. Bronowska
{"title":"“Druggability” of the PAS domains of human PASK kinase, a therapeutic target for metabolic and liver disorders","authors":"Shangze Xu, Lanyu Fan, Piotr Zaborniak, Ruidi Zhu, Haoyuan Ji, Katrina S Madden, J. V. de Souza, Agnieszka K. Bronowska","doi":"10.1017/qrd.2024.1","DOIUrl":"https://doi.org/10.1017/qrd.2024.1","url":null,"abstract":"","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"46 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139810852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Protein structures unravel the signatures and patterns of deep time evolution","authors":"Ajith Harish","doi":"10.1017/qrd.2024.4","DOIUrl":"https://doi.org/10.1017/qrd.2024.4","url":null,"abstract":"","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"231 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140489886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Sequence – Dynamics – Function Relationships in Protein Tyrosine Phosphatases","authors":"Rory M. Crean, Marina Corbella, A. R. Calixto, A. Hengge, S. C. Kamerlin","doi":"10.1017/qrd.2024.3","DOIUrl":"https://doi.org/10.1017/qrd.2024.3","url":null,"abstract":"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.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"27 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139599982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}