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Calcium-binding site in AA10 LPMO from Vibrio cholerae suggests modulating effects during environmental survival and infection. 霍乱弧菌AA10 LPMO中的钙结合位点提示在环境存活和感染过程中具有调节作用。
QRB Discovery Pub Date : 2024-12-26 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.14
Mateu Montserrat-Canals, Kaare Bjerregaard-Andersen, Henrik Vinther Sørensen, Eirik Kommedal, Gabriele Cordara, Gustav Vaaje-Kolstad, Ute Krengel
{"title":"Calcium-binding site in AA10 LPMO from <i>Vibrio cholerae</i> suggests modulating effects during environmental survival and infection.","authors":"Mateu Montserrat-Canals, Kaare Bjerregaard-Andersen, Henrik Vinther Sørensen, Eirik Kommedal, Gabriele Cordara, Gustav Vaaje-Kolstad, Ute Krengel","doi":"10.1017/qrd.2024.14","DOIUrl":"10.1017/qrd.2024.14","url":null,"abstract":"<p><p>Despite major efforts toward its eradication, cholera remains a major health threat and economic burden in many low- and middle-income countries. Between outbreaks, the bacterium responsible for the disease, <i>Vibrio cholerae</i>, survives in aquatic environmental reservoirs, where it commonly forms biofilms, for example, on zooplankton. <i>N</i>-acetyl glucosamine-binding protein A (GbpA) is an adhesin that binds to the chitinaceous surface of zooplankton and breaks its dense crystalline packing thanks to its lytic polysaccharide monooxygenase (LPMO) activity, which provides <i>V. cholerae</i> with nutrients. In addition, GbpA is an important colonization factor associated with bacterial pathogenicity, allowing the binding to mucins in the host intestine. Here, we report the discovery of a cation-binding site in proximity of the GbpA active site, which allows Ca<sup>2+</sup>, Mg<sup>2+</sup>, or K<sup>+</sup> binding close to its carbohydrate-binding surface. In addition to the X-ray crystal structures of cation-LPMO complexes (to 1.5 Å resolution), we explored how the presence of ions affects the stability and activity of the protein. Calcium and magnesium ions were found to bind to GbpA specifically, with calcium ions - abundant in natural sources of chitin - having the strongest effect on protein stability. When the cation-binding site was rendered non-functional, a decrease in activity was observed, highlighting the importance of the structural elements stabilized by calcium. Our findings suggest a cation-binding site specific to GbpA and related LPMOs that may fine-tune binding and activity for its substrates during environmental survival and host infection.</p>","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e12"},"PeriodicalIF":0.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984103","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}
引用次数: 0
An integrated approach using proximity labelling and chemical crosslinking to probe in situ host-virus protein-protein interactions. 使用接近标记和化学交联的综合方法来原位探测宿主-病毒蛋白质-蛋白质相互作用。
QRB Discovery Pub Date : 2024-12-16 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.19
Jiaqi Li, Zhewang Lin
{"title":"An integrated approach using proximity labelling and chemical crosslinking to probe <i>in situ</i> host-virus protein-protein interactions.","authors":"Jiaqi Li, Zhewang Lin","doi":"10.1017/qrd.2024.19","DOIUrl":"10.1017/qrd.2024.19","url":null,"abstract":"<p><p>Host-virus interactions are critically important for various stages of the viral replication cycle. The reliance of viruses on the host factors for their entry, replication, and maturation processes can be exploited for the development of antiviral therapeutics. Thus, the identification and characterization of such viral-host dependency factors has been an attractive area of research to provide novel antiviral targets. Traditional proteomic efforts based on affinity purification of protein complexes from cell lysates are limited to detecting strong and stable interactions. In this perspective, we discuss the integration of two latest proteomic techniques, based on <i>in situ</i> proximity labelling and chemical crosslinking methods, to uncover host-virus protein-protein interactions in living cells.</p>","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e11"},"PeriodicalIF":0.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839831","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}
引用次数: 0
The big chill: Growth of in situ structural biology with cryo-electron tomography. 大寒意：低温电子断层扫描原位结构生物学的生长。
QRB Discovery Pub Date : 2024-12-13 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.10
Mikhail Kudryashev
{"title":"The big chill: Growth of <i>in situ</i> structural biology with cryo-electron tomography.","authors":"Mikhail Kudryashev","doi":"10.1017/qrd.2024.10","DOIUrl":"10.1017/qrd.2024.10","url":null,"abstract":"<p><p><i>In situ</i> structural biology with cryo-electron tomography (cryo-ET) and subtomogram averaging (StA) is evolving as a major method to understand the structure, function, and interactions of biological molecules in cells in a single experiment. Since its inception, the method has matured with some stellar highlights and with further opportunities to broaden its applications. In this short review, I want to provide a personal perspective on the developments in cryo-ET as I have seen it for the last ~20 years and outline the major steps that led to its success. This perspective highlights cryo-ET with my eyes as a junior researcher and my view on the present and past developments in hardware and software for <i>in situ</i> structural biology with cryo-ET.</p>","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e10"},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839852","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}
引用次数: 0
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。
QRB Discovery 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
{"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}
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。
QRB Discovery Pub Date : 2024-12-03 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.11
Srijayee Ghosh, Sonja Schmid
{"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}
引用次数: 0
The Future of Chemistry is through Computations. 化学的未来在于计算。
QRB Discovery Pub Date : 2024-10-22 eCollection Date: 2024-01-01 DOI: 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}
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。
QRB Discovery 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
{"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}
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
QRB Discovery Pub Date : 2024-04-01 DOI: 10.1017/qrd.2024.6
Robert Clark, Kahlan E. Newman, S. Khalid
{"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}
引用次数: 0
Editorial. 社论
QRB Discovery Pub Date : 2024-02-06 eCollection Date: 2024-01-01 DOI: 10.1017/qrd.2024.5
Bengt Nordén
{"title":"Editorial.","authors":"Bengt Nordén","doi":"10.1017/qrd.2024.5","DOIUrl":"https://doi.org/10.1017/qrd.2024.5","url":null,"abstract":"","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"5 ","pages":"e2"},"PeriodicalIF":0.0,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10988142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874816","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}
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
QRB Discovery 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
{"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}
引用次数: 0
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