QRB Discovery最新文献

The dawn of biophysical representations in computational immunology. 计算免疫学中生物物理表征的曙光。

QRB Discovery Pub Date : 2025-05-28 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.7

Eric Wilson, Akshansh Kaushik, Soumya Dutta, Abhishek Singharoy

引用次数: 0

High-throughput single-molecule nanofluidic studies on B. subtilis Rok protein interaction with DNA. 枯草芽孢杆菌Rok蛋白与DNA相互作用的高通量单分子纳米流体研究。

QRB Discovery Pub Date : 2025-05-19 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.10007

Evgeniya Pavlova, Radhika Nambannor Kunnath, Bert van Erp, Albertas Dvirnas, Sriram Kk, Remus T Dame, Fredrik Westerlund

{"title":"High-throughput single-molecule nanofluidic studies on B. subtilis Rok protein interaction with DNA.","authors":"Evgeniya Pavlova, Radhika Nambannor Kunnath, Bert van Erp, Albertas Dvirnas, Sriram Kk, Remus T Dame, Fredrik Westerlund","doi":"10.1017/qrd.2025.10007","DOIUrl":"10.1017/qrd.2025.10007","url":null,"abstract":"Single-molecule methods offer powerful insights into DNA-protein interactions at the individual DNA molecule level. We developed an automated, high-throughput nanofluidic imaging platform to characterize DNA-protein complexes in solution. The platform uses a nanofluidic chip with 10 sets of nanochannels where thousands of DNA molecules can be simultaneously analyzed in different conditions. Using this approach, we investigate Rok, a multifunctional Bacillus subtilis protein involved in genome organization and transcription regulation. Our findings confirm the DNA-condensing activity of Rok, likely attributed to its ability to bridge distant DNA segments. Additionally, Rok promotes the hybridization of 12 base complementary single-stranded DNA overhangs, suggesting a potential role in homology search during recombination. Rok also displays sequence-selective binding, preferentially associating with adenine and thymine-rich (AT-rich) DNA regions. To explore the structural features of Rok underlying these activities and test our nanofluidic system further, we compare wild-type Rok with two variants: ∆Rok, lacking the neutral part of the internal linker, and sRok, a naturally occurring variant without the linker. This comparison highlights the role of the linker in hybridization, i.e., interaction with single-stranded DNA. Together, these findings enhance our understanding of Rok-mediated DNA dynamics and establish single-molecule nanofluidics as a powerful tool for high-throughput studies of DNA-protein interactions.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e17"},"PeriodicalIF":0.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12231313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585062","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

Insights on the effect of macromolecular crowding on transcription and its regulation. 大分子拥挤对转录及其调控的影响。

QRB Discovery Pub Date : 2025-04-03 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.8

Wenxuan Xu, Dylan Collette, Jin Qian, Laura Finzi, David Dunlap

{"title":"Insights on the effect of macromolecular crowding on transcription and its regulation.","authors":"Wenxuan Xu, Dylan Collette, Jin Qian, Laura Finzi, David Dunlap","doi":"10.1017/qrd.2025.8","DOIUrl":"10.1017/qrd.2025.8","url":null,"abstract":"Transcription of DNA into RNA is a fundamental cellular process upon which life depends. It is tightly regulated in several different ways, and among the most important mechanisms are protein-induced topological changes in DNA such as looping. In vivo neither transcription, nor protein-induced looping dynamics exhibited by individual molecules are easily monitored. In vitro single-molecule approaches do offer that possibility, but assays are conducted in rarefied, saline buffer conditions which greatly differ from the crowded intracellular environment. In the following, we describe monitoring both transcription and lac repressor-mediated DNA looping of single DNA molecules in the presence of different concentrations of crowders to bridge the gap between in vitro and in vivo experimentation. We found that crowding shifts the preferred orientation of DNA strands in the looped complex. Crowding also attenuates the rate of transcript elongation and enhances readthrough at the terminator. Clearly, the activities of proteins involved in gene regulation are modified in surprising ways by crowding.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e16"},"PeriodicalIF":0.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112048","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

Unleashing virus structural biology: Probing protein and membrane intermediates in the dynamic process of membrane fusion. 释放病毒结构生物学：探索膜融合动态过程中的蛋白质和膜中间体。

QRB Discovery Pub Date : 2025-03-31 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.3

Kelly K Lee

{"title":"Unleashing virus structural biology: Probing protein and membrane intermediates in the dynamic process of membrane fusion.","authors":"Kelly K Lee","doi":"10.1017/qrd.2025.3","DOIUrl":"10.1017/qrd.2025.3","url":null,"abstract":"Viruses are highly dynamic macromolecular assemblies. They undergo large-scale changes in structure and organization at nearly every stage of their infectious cycles from virion assembly to maturation, receptor docking, cell entry, uncoating and genome delivery. Understanding structural transformations and dynamics across the virus infectious cycle is an expansive area for research that that can also provide insight into mechanisms for blocking infection, replication, and transmission. Additionally, the processes viruses carry out serve as excellent model systems for analogous cellular processes, but in more accessible form. Capturing and analyzing these dynamic events poses a major challenge for many structural biological approaches due to the size and complexity of the assemblies and the heterogeneity and transience of the functional states that are populated. Here we examine the process of protein-mediated membrane fusion, which is carried out by specialized machinery on enveloped virus surfaces leading to delivery of the viral genome. Application of two complementary methods, cryo-electron tomography and structural mass spectrometry enable dynamic intermediate states in intact fusion systems to be imaged and probed, providing a new understanding of the mechanisms and machinery that drive this fundamental biological process.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e14"},"PeriodicalIF":0.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144080015","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 structural and biophysical approach to study carbon metabolism in Mycobacterium tuberculosis. 综合结构和生物物理方法研究结核分枝杆菌的碳代谢。

QRB Discovery Pub Date : 2025-03-12 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.6

Evelyn Y-W Huang, Francis Kuang, Haozhe Wu, Chai Xin Yu, Xiaoxu Chen, Glenda Vasku, Le Thao Anh Nguyen, Katherine J Jeppe, Anna K Coussens, Brooke X C Kwai, Ivanhoe K H Leung

{"title":"An integrated structural and biophysical approach to study carbon metabolism in Mycobacterium tuberculosis.","authors":"Evelyn Y-W Huang, Francis Kuang, Haozhe Wu, Chai Xin Yu, Xiaoxu Chen, Glenda Vasku, Le Thao Anh Nguyen, Katherine J Jeppe, Anna K Coussens, Brooke X C Kwai, Ivanhoe K H Leung","doi":"10.1017/qrd.2025.6","DOIUrl":"10.1017/qrd.2025.6","url":null,"abstract":"Metabolic enzymes are the catalysts that drive the biochemical reactions essential for sustaining life. Many of these enzymes are tightly regulated by feedback mechanisms. To fully understand their roles and modulation, it is crucial to investigate the relationship between their structure, catalytic mechanism, and function. In this perspective, by using three examples from our studies on Mycobacterium tuberculosis (Mtb) isocitrate lyase and related proteins, we highlight how an integrated approach combining structural, activity, and biophysical data provides insights into their biological functions. These examples underscore the importance of employing fast-fail experiments at the early stages of a research project, emphasise the value of complementary techniques in validating findings, and demonstrate how in vitro data combined with chemical, biochemical, and physiological knowledge can lead to a broader understanding of metabolic adaptations in pathogenic bacteria. Finally, we address the unexplored questions in Mtb metabolism and discuss how we expand our approach to include microbiological and bioanalytical techniques to further our understanding. Such an integrated and interdisciplinary strategy has the potential to uncover novel regulatory mechanisms and identify new therapeutic opportunities for the eradication of tuberculosis. The approach can also be broadly applied to investigate other biochemical networks and complex biological systems.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e15"},"PeriodicalIF":0.0,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112025","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

Probing DNA melting behaviour under vibrational strong coupling. 探测DNA在振动强耦合下的熔化行为。

QRB Discovery Pub Date : 2025-03-10 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.5

Weijian Tao, Fatma Mihoubi, Bianca Patrahau, Claudia Bonfio, Bengt Nordén, Thomas W Ebbesen

引用次数: 0

Modeling for understanding and engineering metabolism. 为理解和工程代谢建模。

QRB Discovery Pub Date : 2025-02-18 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.1

Jens Nielsen, Dina Petranovic

{"title":"Modeling for understanding and engineering metabolism.","authors":"Jens Nielsen, Dina Petranovic","doi":"10.1017/qrd.2025.1","DOIUrl":"10.1017/qrd.2025.1","url":null,"abstract":"Metabolism is at the core of all functions of living cells as it provides Gibbs free energy and building blocks for synthesis of macromolecules, which are necessary for structures, growth, and proliferation. Metabolism is a complex network composed of thousands of reactions catalyzed by enzymes involving many co-factors and metabolites. Traditionally it has been difficult to study metabolism as a whole network and most traditional efforts were therefore focused on specific metabolic pathways, enzymes, and metabolites. By using engineering principles of mathematical modeling to analyze and study metabolism, as well as engineer it, that is, design and build, new metabolic features, it is possible to gain many new fundamental insights as well as applications in biotechnology. Here, we present the history and basic principles of engineering metabolism, as well as the newest developments in the field. We are using examples of applications in: (1) production of protein pharmaceuticals and chemicals; (2) basic studies of metabolism; and (3) impacting health care. We will end by discussing how engineering metabolism can benefit from advances in artificial intelligence (AI)-based models.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e11"},"PeriodicalIF":0.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606214","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

Reduced protein solubility - cause or consequence in amyloid disease? 蛋白溶解度降低——淀粉样蛋白病的原因或后果？

QRB Discovery Pub Date : 2025-02-17 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2024.12

Max Lindberg, Jing Hu, Emma Sparr, Sara Linse

引用次数: 0

Structural bioinformatic study of human mitochondrial respiratory integral membrane megacomplex and its AlphaFold3 predicted water-soluble QTY megacomplex analog. 人线粒体呼吸整体膜巨复合物的结构生物信息学研究及其AlphaFold3预测水溶性QTY巨复合物类似物。

QRB Discovery Pub Date : 2025-02-05 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.2

Edward Chen, Shuguang Zhang

{"title":"Structural bioinformatic study of human mitochondrial respiratory integral membrane megacomplex and its AlphaFold3 predicted water-soluble QTY megacomplex analog.","authors":"Edward Chen, Shuguang Zhang","doi":"10.1017/qrd.2025.2","DOIUrl":"10.1017/qrd.2025.2","url":null,"abstract":"Human mitochondrial Complex I is one of the largest multi-subunit membrane protein megacomplexes, which plays a critical role in oxidative phosphorylation and ATP production. It is also involved in many neurodegenerative diseases. However, studying its structure and the mechanisms underlying proton translocation remains challenging due to the hydrophobic nature of its transmembrane parts. In this structural bioinformatic study, we used the QTY code to reduce the hydrophobicity of megacomplex I, while preserving its structure and function. We carried out the structural bioinformatics analysis of 20 key enzymes in the integral membrane parts. We compare their native structure, experimentally determined using Cryo-electron microscopy (CryoEM), with their water-soluble QTY analogs predicted using AlphaFold 3. Leveraging AlphaFold 3's advanced capabilities in predicting protein-protein complex interactions, we further explore whether the QTY-code integral membrane proteins maintain their protein-protein interactions necessary to form the functional megacomplex. Our structural bioinformatics analysis not only demonstrates the feasibility of engineering water-soluble integral membrane proteins using the QTY code, but also highlights the potential to use the water-soluble membrane protein QTY analogs as soluble antigens for discovery of therapeutic monoclonal antibodies, thus offering promising implications for the treatment of various neurodegenerative diseases.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e12"},"PeriodicalIF":0.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754854","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

Protein secondary structure determined from independent and integrated infra-red absorbance and circular dichroism data using the algorithm SELCON. 利用SELCON算法从独立和集成的红外吸光度和圆二色性数据确定蛋白质二级结构。

QRB Discovery Pub Date : 2025-02-03 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2025.4

Søren Vrønning Hoffmann, Nykola C Jones, Alison Rodger

引用次数: 0