Structure最新文献_第6页

Exploiting a rational β-strand insertion strategy and disulfide locking to mechanically manipulate domain-swapped protein structures 利用合理的β链插入策略和二硫锁来机械地操纵结构域交换的蛋白质结构

IF 5.7 2区生物学

Structure Pub Date : 2025-07-22 DOI: 10.1016/j.str.2025.06.012

Alireza Ghanbarpour, Nikolas Kenaya, Courtney Bingham, Miah Turke, Cody Pinger, Chris Kemp, Ellen Studzinski, Chrysoula Vasileiou, Babak Borhan, James H. Geiger

引用次数: 0

SeaMoon: From protein language models to continuous structural heterogeneity 从蛋白质语言模型到连续结构异质性

IF 5.7 2区生物学

Structure Pub Date : 2025-07-18 DOI: 10.1016/j.str.2025.06.010

Valentin Lombard, Dan Timsit, Sergei Grudinin, Elodie Laine

{"title":"SeaMoon: From protein language models to continuous structural heterogeneity","authors":"Valentin Lombard, Dan Timsit, Sergei Grudinin, Elodie Laine","doi":"10.1016/j.str.2025.06.010","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.010","url":null,"abstract":"How proteins move and deform determines their interactions with the environment and is thus of the utmost importance for cellular functioning. Following the revolution in single protein 3D structure prediction, researchers have focused on repurposing or developing deep learning models for sampling alternative protein conformations. In this work, we explored whether continuous compact representations of protein motions could be predicted directly from sequences, without exploiting 3D structures. SeaMoon leverages protein language model (pLM) embeddings as input to a lightweight convolutional neural network. We assessed SeaMoon against <math><mrow is=\"true\"><mo is=\"true\">∼</mo></mrow></math><script type=\"math/mml\"><math><mrow is=\"true\"><mo is=\"true\">∼</mo></mrow></math></script>1,000 collections of experimental conformations exhibiting diverse motions. It predicts at least one ground-truth motion with reasonable accuracy for 40% of the test proteins. SeaMoon captures motions inaccessible to normal mode analysis, an unsupervised physics-based method relying solely on 3D geometry, and generalizes to proteins without detectable sequence similarity to the training set. SeaMoon is easily retrainable with novel or updated pLMs.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144652610","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

A structure-guided approach to predict MHC-I restriction of T cell receptors for public antigens 一种结构导向的方法来预测MHC-I限制T细胞受体的公共抗原

IF 5.7 2区生物学

Structure Pub Date : 2025-07-18 DOI: 10.1016/j.str.2025.06.011

Sagar Gupta, Nikolaos G. Sgourakis

引用次数: 0

Accurate helical parameter estimation based on cylindrical unrolling 基于圆柱展开的螺旋参数精确估计

IF 5.7 2区生物学

Structure Pub Date : 2025-07-17 DOI: 10.1016/j.str.2025.06.008

Mingtao Huang, Jinying Ma, Xiaoyu Fu, Hongwei Wang, Yuan Shen, Xueming Li

{"title":"Accurate helical parameter estimation based on cylindrical unrolling","authors":"Mingtao Huang, Jinying Ma, Xiaoyu Fu, Hongwei Wang, Yuan Shen, Xueming Li","doi":"10.1016/j.str.2025.06.008","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.008","url":null,"abstract":"Helical structure is fundamental for filamentous and tubular macromolecular assemblies that play crucial roles in structural scaffolding and signaling processes. Structure determination of these assemblies relies on the precise estimation of their helical parameters. Although layer-line-based methods are widely used, their application is often challenging due to structural flexibility and heterogeneity. Herein, we report a method for helical parameter estimation based on cylindrical unrolling, called helix is simple (HELIS), which is implemented in a software package with the same name. HELIS treats helical structures as rolled two-dimensional (2D) crystals. Estimation of the helical parameters of structures visualized by cryo-electron tomography (cryo-ET) is derived from simplified 2D reciprocal-lattice measurements. HELIS also incorporates auxiliary algorithms to trace and unbend curved filaments, determine relative polarity, and perform in situ helical reconstruction. HELIS is a comprehensive helical structure determination tool with high accuracy for helical parameter estimation that is applicable to various helical assemblies.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"12 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144645284","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

Geometry-aware template matching for cryo-electron tomograms in Dynamo 基于几何感知的低温电子层析图模板匹配

IF 5.7 2区生物学

Structure Pub Date : 2025-07-17 DOI: 10.1016/j.str.2025.06.009

Raffaele Coray, Daniel Castaño-Díez

引用次数: 0

CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes 冷冻电镜下的视觉蛋白质组学揭示了寡聚蛋白复合物的新结构

IF 5.7 2区生物学

Structure Pub Date : 2025-07-14 DOI: 10.1016/j.str.2025.06.007

Yuanbo Shen, Ailiena O. Maggiolo, Tianzheng Zhang, Rebeccah A. Warmack

引用次数: 0

Structural basis for no retinal binding in flotillin-associated rhodopsins 游离蛋白相关视紫红质无视网膜结合的结构基础

IF 5.7 2区生物学

Structure Pub Date : 2025-07-11 DOI: 10.1016/j.str.2025.06.006

Kirill Kovalev, Artem Stetsenko, Florian Trunk, Egor Marin, Jose M. Haro-Moreno, Gerrit H.U. Lamm, Alexey Alekseev, Francisco Rodriguez-Valera, Thomas R. Schneider, Josef Wachtveitl, Albert Guskov

{"title":"Structural basis for no retinal binding in flotillin-associated rhodopsins","authors":"Kirill Kovalev, Artem Stetsenko, Florian Trunk, Egor Marin, Jose M. Haro-Moreno, Gerrit H.U. Lamm, Alexey Alekseev, Francisco Rodriguez-Valera, Thomas R. Schneider, Josef Wachtveitl, Albert Guskov","doi":"10.1016/j.str.2025.06.006","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.006","url":null,"abstract":"Rhodopsins are light-sensitive membrane proteins capturing solar energy via a retinal cofactor covalently attached to a lysine residue. Several groups of rhodopsins lack the conserved lysine and showed no retinal binding. Recently, flotillin-associated rhodopsins (FArhodopsins or FARs) were identified and suggested to lack the retinal-binding pocket despite preserving the lysine residue in many members of the group. Here, we present cryoelectron microscopic (cryo-EM) structures of paralog FArhodopsin and proteorhodopsin from marine bacterium Pseudothioglobus, both forming pentamers similar to those of other microbial rhodopsins. We demonstrate no binding of retinal to the FArhodopsin despite preservation of the lysine residue and overall similarity of the protein fold and internal organization to those of the retinal-binding paralog. Mutational analysis confirmed that two amino acids, H84 and E120, prevent retinal binding within the FArhodopsin. Our work provides insights into the natural retinal loss in microbial rhodopsins and might contribute to the further understanding of FArhodopsins.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"35 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144602982","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

Structures of USP7 in active and inactive states bound to DNMT1 revealed by cryo-EM 低温电镜显示USP7与DNMT1结合的活性和非活性结构

IF 5.7 2区生物学

Structure Pub Date : 2025-07-10 DOI: 10.1016/j.str.2025.06.005

Nao Nakamura, Sae Yoshimi, Amika Kikuchi, Hiroki Onoda, Satomi Kori, Makoto Nakanishi, Atsuya Nishiyama, Kyohei Arita

{"title":"Structures of USP7 in active and inactive states bound to DNMT1 revealed by cryo-EM","authors":"Nao Nakamura, Sae Yoshimi, Amika Kikuchi, Hiroki Onoda, Satomi Kori, Makoto Nakanishi, Atsuya Nishiyama, Kyohei Arita","doi":"10.1016/j.str.2025.06.005","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.005","url":null,"abstract":"The ubiquitin signal generated by UHRF1 is essential for DNA methylation maintenance by recruiting DNA methyltransferase 1 (DNMT1) to hemimethylated DNA through strong binding of its replication foci targeting sequence (RFTS) domain to ubiquitinated histone H3. The ubiquitin-specific protease 7 (USP7) forms a complex with DNMT1 and removes ubiquitin from H3. However, it remains unknown how USP7 deubiquitinates ubiquitinated H3 upon strong binding of the DNMT1 RFTS domain. Here, we show the activation mechanism of USP7 by combining biochemical and structural studies. USP7 is inactive toward ubiquitinated H3 in complex with the RFTS domain. However, when complexed with DNMT1, USP7 efficiently deubiquitinates ubiquitinated H3. Cryogenic electron microscopy (cryo-EM) single particle analysis revealed that USP7 bound to DNMT1 undergoes an open (inactive) and closed (active) conformational transition. Our findings provide mechanistic insights into the activation of USP7 upon binding to DNMT1 and contribute to a better understanding of the deubiquitination process in DNA methylation maintenance.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"11 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594756","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

Structure of a type II SMC Wadjet complex from Neobacillus vireti 病毒新杆菌II型SMC Wadjet复合物的结构

IF 5.7 2区生物学

Structure Pub Date : 2025-07-07 DOI: 10.1016/j.str.2025.06.004

Florian Roisné-Hamelin, Hon Wing Liu, Stephan Gruber

引用次数: 0

Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction 通过综合建模和突变预测阐明PTEN构象动力学和磷酸酶调控

IF 5.7 2区生物学

Structure Pub Date : 2025-07-03 DOI: 10.1016/j.str.2025.06.002

Jennifer Erin Dawson, Iris Nira Smith, Ann Marie Tushar, Charis Eng

引用次数: 0