QRB Discovery最新文献

Modeling for understanding and engineering metabolism.

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":"https://doi.org/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?

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

Frontiers in integrative structural modeling of macromolecular assemblies.

QRB Discovery Pub Date : 2025-01-22 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2024.15

Kartik Majila, Shreyas Arvindekar, Muskaan Jindal, Shruthi Viswanath

{"title":"Frontiers in integrative structural modeling of macromolecular assemblies.","authors":"Kartik Majila, Shreyas Arvindekar, Muskaan Jindal, Shruthi Viswanath","doi":"10.1017/qrd.2024.15","DOIUrl":"10.1017/qrd.2024.15","url":null,"abstract":"Integrative modeling enables structure determination for large macromolecular assemblies by combining data from multiple experiments with theoretical and computational predictions. Recent advancements in AI-based structure prediction and cryo electron-microscopy have sparked renewed enthusiasm for integrative modeling; structures from AI-based methods can be integrated with in situ maps to characterize large assemblies. This approach previously allowed us and others to determine the architectures of diverse macromolecular assemblies, such as nuclear pore complexes, chromatin remodelers, and cell-cell junctions. Experimental data spanning several scales was used in these studies, ranging from high-resolution data, such as X-ray crystallography and AlphaFold structure, to low-resolution data, such as cryo-electron tomography maps and data from co-immunoprecipitation experiments. Two recurrent modeling challenges emerged across a range of studies. First, these assemblies contained significant fractions of disordered regions, necessitating the development of new methods for modeling disordered regions in the context of ordered regions. Second, methods needed to be developed to utilize the information from cryo-electron tomography, a timely challenge as structural biology is increasingly moving towards in situ characterization. Here, we recapitulate recent developments in the modeling of disordered proteins and the analysis of cryo-electron tomography data and highlight other opportunities for method development in the context of integrative modeling.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e3"},"PeriodicalIF":0.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411147","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

Diverse single-stranded nucleic acid binding proteins enable both stable protection and rapid exchange required for biological function.

QRB Discovery Pub Date : 2025-01-14 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2024.21

Michael Morse, Ben A Cashen, Ioulia Rouzina, Mark C Williams

{"title":"Diverse single-stranded nucleic acid binding proteins enable both stable protection and rapid exchange required for biological function.","authors":"Michael Morse, Ben A Cashen, Ioulia Rouzina, Mark C Williams","doi":"10.1017/qrd.2024.21","DOIUrl":"10.1017/qrd.2024.21","url":null,"abstract":"Single-stranded nucleic acid (ssNA) binding proteins must both stably protect ssNA transiently exposed during replication and other NA transactions, and also rapidly reorganize and dissociate to allow further NA processing. How these seemingly opposing functions can coexist has been recently elucidated by optical tweezers (OT) experiments that isolate and manipulate single long ssNA molecules to measure conformation in real time. The effective length of an ssNA substrate held at fixed tension is altered upon protein binding, enabling quantification of both the structure and kinetics of protein-NA interactions. When proteins exhibit multiple binding states, however, OT measurements may produce difficult to analyze signals including non-monotonic response to free protein concentration and convolution of multiple fundamental rates. In this review we compare single-molecule experiments with three proteins of vastly different structure and origin that exhibit similar ssNA interactions. These results are consistent with a general model in which protein oligomers containing multiple binding interfaces switch conformations to adjust protein:NA stoichiometry. These characteristics allow a finite number of proteins to protect long ssNA regions by maximizing protein-ssNA contacts while also providing a pathway with reduced energetic barriers to reorganization and eventual protein displacement when these ssNA regions are diminished.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e1"},"PeriodicalIF":0.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411145","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

Unzipping of knotted DNA via nanopore translocation.

QRB Discovery Pub Date : 2025-01-09 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2024.26

Antonio Suma, Cristian Micheletti

{"title":"Unzipping of knotted DNA via nanopore translocation.","authors":"Antonio Suma, Cristian Micheletti","doi":"10.1017/qrd.2024.26","DOIUrl":"10.1017/qrd.2024.26","url":null,"abstract":"DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a coarse-grained model of DNA to address the nanopore unzipping of DNA filaments that are knotted. This previously unaddressed problem is motivated by the fact that DNA knots inevitably occur in isolated equilibrated filaments and in vivo. We study how different types of tight knots in the DNA segment just outside the pore impact unzipping at different driving forces. We establish three main results. First, knots do not significantly affect the unzipping process at low forces. However, knotted DNAs unzip more slowly and heterogeneously than unknotted ones at high forces. Finally, we observe that the microscopic origin of the hindrance typically involves two concurrent causes: the topological friction of the DNA chain sliding along its knotted contour and the additional friction originating from the entanglement with the newly unzipped DNA. The results reveal a previously unsuspected complexity of the interplay of DNA topology and unzipping, which should be relevant for interpreting nanopore-based single-molecule unzipping experiments and improving the modeling of DNA transactions in vivo.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e4"},"PeriodicalIF":0.0,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143410754","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

Challenges in observing transcription-translation for bottom-up synthetic biology.

QRB Discovery Pub Date : 2025-01-03 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2024.27

Vadim G Bogatyr, Gijs J L Wuite

{"title":"Challenges in observing transcription-translation for bottom-up synthetic biology.","authors":"Vadim G Bogatyr, Gijs J L Wuite","doi":"10.1017/qrd.2024.27","DOIUrl":"10.1017/qrd.2024.27","url":null,"abstract":"Synthetic biology aims to create a viable synthetic cell. However, to achieve this goal, it is essential first to gain a profound understanding of the cellular systems used to build that cell, how to reconstitute those systems in the compartments, and how to track their function. Transcription and translation are two vital cellular systems responsible for the production of RNA and, consequently, proteins, without which the cell would not be able to maintain itself or fulfill its functions. This review discusses in detail how the Protein synthesis Using Recombinant Element (PURE) system and cell lysate are used to reconstitute transcription-translation in vitro. Furthermore, it examines how these systems can be encapsulated in GUVs using the existing methods. It also assesses approaches available to image transcription and translation with a diverse arsenal of fluorescence microscopy techniques and a broad collection of probes developed in recent decades. Finally, it highlights solutions for the challenge ahead, namely the decoupling of the two systems in PURE, and discusses the prospects of synthetic biology in the modern world.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e5"},"PeriodicalIF":0.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411085","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

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 Vibrio cholerae 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":"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, Vibrio cholerae, survives in aquatic environmental reservoirs, where it commonly forms biofilms, for example, on zooplankton. N-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 V. cholerae 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 Ca2+, Mg2+, or K+ 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.","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

引用次数: 0

The conformational landscape of TRiC ring-opening and its underlying stepwise mechanism revealed by cryo-EM.

QRB Discovery Pub Date : 2024-12-16 eCollection Date: 2025-01-01 DOI: 10.1017/qrd.2024.17

Mingliang Jin, Yunxiang Zang, Huping Wang, Yao Cong

{"title":"The conformational landscape of TRiC ring-opening and its underlying stepwise mechanism revealed by cryo-EM.","authors":"Mingliang Jin, Yunxiang Zang, Huping Wang, Yao Cong","doi":"10.1017/qrd.2024.17","DOIUrl":"https://doi.org/10.1017/qrd.2024.17","url":null,"abstract":"The TRiC/CCT complex assists in the folding of approximately 10% of cytosolic proteins through an ATP-driven conformational cycle, playing a crucial role in maintaining protein homeostasis. Despite our understanding of ATP-driven TRiC ring closing and substrate folding, the process and mechanisms underlying TRiC ring-opening and substrate release remain largely unexplored. In this study, by determining an ensemble of cryo-EM structures of yeast TRiC in the presence of ADP, including three intermediate transition states, we present a comprehensive picture of the TRiC ring-opening process. During this process, CCT3 detects the loss of γ-phosphate and initiates with the dynamics of its apical protrusion, and expands to the outward leaning of the consecutive CCT6/8/7/5 subunits. This is followed by significant movements of CCT2, CCT4, and especially CCT1 subunits, resulting in the opening of the TRiC rings. We also observed an unforeseen temporary separation between the two rings in the CCT2 side, coordinating the release of the originally locked CCT4 N-terminus, which potentially participates in the ring-opening process. Collectively, our study reveals a stepwise TRiC ring-opening mechanism, provides a comprehensive view of the TRiC conformational landscape, and sheds lights on its subunit specificity in sensing nucleotide status and substrate release. Our findings deepen our understanding of protein folding assisted by TRiC and may inspire new strategies for the diagnosis and treatment of related diseases.","PeriodicalId":34636,"journal":{"name":"QRB Discovery","volume":"6 ","pages":"e7"},"PeriodicalIF":0.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606391","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

引用次数: 0