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Dynamic integration of feature- and template-based methods improves the prediction of conformational B cell epitopes

IF 5.7 2区生物学

Structure Pub Date : 2025-02-11 DOI: 10.1016/j.str.2025.01.018

Yueyue Shen, Zheng Jiang, Rong Liu

{"title":"Dynamic integration of feature- and template-based methods improves the prediction of conformational B cell epitopes","authors":"Yueyue Shen, Zheng Jiang, Rong Liu","doi":"10.1016/j.str.2025.01.018","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.018","url":null,"abstract":"The accurate prediction of conformational epitopes promotes our understanding of antigen-antibody interactions. All existing algorithms depend on a feature-based strategy, which limits their performance. A template-based strategy can provide complementary information, and the interplay between these two strategies could improve the prediction of epitopes. Here, we present DynaBCE, a dynamic ensemble algorithm to effectively identify conformational B cell epitopes (BCEs). Using novel handcrafted structural descriptors and embeddings from protein language models, we developed machine learning and deep learning modules based on boosting algorithms and geometric graph neural networks, respectively. Furthermore, we built a template module by leveraging known structural template information and transformer-based algorithms to capture binding signatures. Finally, we integrated the three modules using a dynamic weighting approach to maximize the strength of each module for different samples. DynaBCE achieved promising results for both native and predicted structures and outperformed previous methods as demonstrated in various evaluation scenarios.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"28 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering

IF 5.7 2区生物学

Structure Pub Date : 2025-02-10 DOI: 10.1016/j.str.2025.01.017

Aldrex Munsayac, Wellington C. Leite, Jesse B. Hopkins, Ian Hall, Hugh M. O’Neill, Sarah C. Keane

引用次数: 0

Transcription termination—Some like it hot

IF 5.7 2区生物学

Structure Pub Date : 2025-02-06 DOI: 10.1016/j.str.2025.01.016

Kristine Bourke Arnvig, Finn Werner

引用次数: 0

Illuminating cholesterol-mTORC1 signaling: LYCHOS in focus

IF 5.7 2区生物学

Structure Pub Date : 2025-02-06 DOI: 10.1016/j.str.2025.01.009

Hijai R. Shin, Roberto Zoncu

引用次数: 0

CryoVIA: An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs

IF 5.7 2区生物学

Structure Pub Date : 2025-02-06 DOI: 10.1016/j.str.2025.01.013

Philipp Schönnenbeck, Benedikt Junglas, Carsten Sachse

引用次数: 0

The Anti-TB Structural Center at ShanghaiTech University

IF 5.7 2区生物学

Structure Pub Date : 2025-02-06 DOI: 10.1016/j.str.2025.01.006

Haitao Yang, Lu Zhang, Quan Wang, Jun Li, Xiuna Yang, Yan Gao, Bing Zhang

引用次数: 0

Epithelial sodium channels assemble in an orderly manner: Biology does not play dice

IF 5.7 2区生物学

Structure Pub Date : 2025-02-06 DOI: 10.1016/j.str.2025.01.015

Sarah Pellizzari, Erhu Cao

引用次数: 0

The mechanosensitive channel YbiO has a conductance equivalent to the largest gated-pore

IF 5.7 2区生物学

Structure Pub Date : 2025-02-06 DOI: 10.1016/j.str.2025.01.014

Benjamin J. Lane, Mariangela Dionysopoulou, Nana Yan, Jonathan D. Lippiat, Stephen P. Muench, Christos Pliotas

引用次数: 0

Structures of a T1-like siphophage reveal capsid stabilization mechanisms and high structural similarities with a myophage

IF 5.7 2区生物学

Structure Pub Date : 2025-02-05 DOI: 10.1016/j.str.2025.01.012

Can Cai, Yueting Wang, Yunshu Liu, Qianqian Shao, Aohan Wang, Lin Li, Yaqi Zheng, Tianyi Zhang, Ziwen Luo, Chongguang Yang, Qianglin Fang

引用次数: 0

Direct effect of membrane environment on the activation of mGluR2 revealed by single-molecule FRET

IF 5.7 2区生物学

Structure Pub Date : 2025-02-04 DOI: 10.1016/j.str.2025.01.011

Chiranjib Banerjee, Brandon Wey-Hung Liauw, Reza Vafabakhsh

{"title":"Direct effect of membrane environment on the activation of mGluR2 revealed by single-molecule FRET","authors":"Chiranjib Banerjee, Brandon Wey-Hung Liauw, Reza Vafabakhsh","doi":"10.1016/j.str.2025.01.011","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.011","url":null,"abstract":"The microenvironment of membrane receptors controls their mobility, structure, interactions, and dynamics, but a systematic understanding of how it modulates receptor function is often lacking. Using single-molecule Förster resonance energy transfer (smFRET), we characterized how detergents and cholesterol modulate the conformational dynamics of metabotropic glutamate receptor 2 (mGluR2), a class C G protein-coupled receptor (GPCR). We found that, within the resolution of our measurements, all tested detergents stabilize the same overall active and inactive structure of different domains of mGluR2. However, the degree of stabilization and the equilibrium between active and inactive conformations depended on the detergent. Detergents with a single hydrophobic tail increased the active state occupancy compared to those with long, branched tails. Adding cholesterol to micelles with branched hydrophobic tails shifted the equilibrium toward the inactive state. Mutagenesis identified residues potentially involved in cholesterol interaction with mGluR2. Targeting the cholesterol-binding site with synthetic molecules could be a viable therapeutic approach.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"6 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0