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Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike 协同删除消除了 SARS-CoV-2 BA.2.87.1 穗状病毒中的中和超位点

IF 5.7 2区生物学

Structure Pub Date : 2024-08-21 DOI: 10.1016/j.str.2024.07.020

Helen M.E. Duyvesteyn, Aiste Dijokaite-Guraliuc, Chang Liu, Piyada Supasa, Barbara Kronsteiner, Katie Jeffery, Lizzie Stafford, Paul Klenerman, Susanna J. Dunachie, Juthathip Mongkolsapaya, Elizabeth E. Fry, Jingshan Ren, David I. Stuart, Gavin R. Screaton

{"title":"Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike","authors":"Helen M.E. Duyvesteyn, Aiste Dijokaite-Guraliuc, Chang Liu, Piyada Supasa, Barbara Kronsteiner, Katie Jeffery, Lizzie Stafford, Paul Klenerman, Susanna J. Dunachie, Juthathip Mongkolsapaya, Elizabeth E. Fry, Jingshan Ren, David I. Stuart, Gavin R. Screaton","doi":"10.1016/j.str.2024.07.020","DOIUrl":"https://doi.org/10.1016/j.str.2024.07.020","url":null,"abstract":"BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an “all-down” conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142023034","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

Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations Ca2+依赖性脂质偏好决定突触表敏-1 C2A和C2B的动态：实验和模拟的启示

IF 5.7 2区生物学

Structure Pub Date : 2024-08-21 DOI: 10.1016/j.str.2024.07.017

Julian Bender, Til Kundlacz, Lucas S.P. Rudden, Melissa Frick, Julia Bieber, Matteo T. Degiacomi, Carla Schmidt

{"title":"Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations","authors":"Julian Bender, Til Kundlacz, Lucas S.P. Rudden, Melissa Frick, Julia Bieber, Matteo T. Degiacomi, Carla Schmidt","doi":"10.1016/j.str.2024.07.017","DOIUrl":"https://doi.org/10.1016/j.str.2024.07.017","url":null,"abstract":"Signal transmission between neurons requires exocytosis of neurotransmitters from the lumen of synaptic vesicles into the synaptic cleft. Following an influx of Ca2+, this process is facilitated by the Ca2+ sensor synaptotagmin-1. The underlying mechanisms involve electrostatic and hydrophobic interactions tuning the lipid preferences of the two C2 domains of synaptotagmin-1; however, the details are still controversially discussed. We, therefore, follow a multidisciplinary approach and characterize lipid and membrane binding of the isolated C2A and C2B domains. We first target interactions with individual lipid species, and then study interactions with model membranes of liposomes. Finally, we perform molecular dynamics simulations to unravel differences in membrane binding. We found that both C2 domains, as a response to Ca2+, insert into the lipid membrane; however, C2A adopts a more perpendicular orientation while C2B remains parallel. These findings allow us to propose a mechanism for synaptotagmin-1 during membrane fusion.","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142023079","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

PB-GPT: An innovative GPT-based model for protein backbone generation PB-GPT：基于 GPT 的创新型蛋白质骨架生成模型

IF 5.7 2区生物学

Structure Pub Date : 2024-08-21 DOI: 10.1016/j.str.2024.07.016

Xiaoping Min, Yiyang Liao, Xiao Chen, Qianli Yang, Junjie Ying, Jiajun Zou, Chongzhou Yang, Jun Zhang, Shengxiang Ge, Ningshao Xia

引用次数: 0

Structural basis for FN3K-mediated protein deglycation FN3K 介导蛋白质降解的结构基础

IF 5.7 2区生物学

Structure Pub Date : 2024-08-21 DOI: 10.1016/j.str.2024.07.018

Jameela Lokhandwala, Jenet K. Matlack, Tracess B. Smalley, Robert E. Miner, Timothy H. Tran, Jennifer M. Binning

引用次数: 0

Engineering of pH-dependent antigen binding properties for toxin-targeting IgG1 antibodies using light-chain shuffling 利用轻链洗牌技术为毒素靶向 IgG1 抗体设计 pH 依赖性抗原结合特性