Proteins-Structure Function and Bioinformatics最新文献

Protein Target Highlights in CASP16: Insights From the Structure Providers. CASP16蛋白靶点亮点：来自结构提供者的见解。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-09 DOI: 10.1002/prot.70025

Leila T Alexander, Océane M Follonier, Andriy Kryshtafovych, Kim Abesamis, Sabrina Bibi-Triki, Henry G Box, Cécile Breyton, Françoise Bringel, Loic Carrique, Alessio d'Acapito, Gang Dong, Rebecca DuBois, Deborah Fass, Juliana Martinez Fiesco, Daniel R Fox, Jonathan M Grimes, Rhys Grinter, Matthew Jenkins, Roman Kamyshinsky, Jeremy R Keown, Gerald Lackner, Michael Lammers, Shiheng Liu, Andrew L Lovering, Tomas Malinauskas, Benoît Masquida, Gottfried J Palm, Christian Siebold, Tiantian Su, Ping Zhang, Z Hong Zhou, Krzysztof Fidelis, Maya Topf, John Moult, Torsten Schwede

{"title":"Protein Target Highlights in CASP16: Insights From the Structure Providers.","authors":"Leila T Alexander, Océane M Follonier, Andriy Kryshtafovych, Kim Abesamis, Sabrina Bibi-Triki, Henry G Box, Cécile Breyton, Françoise Bringel, Loic Carrique, Alessio d'Acapito, Gang Dong, Rebecca DuBois, Deborah Fass, Juliana Martinez Fiesco, Daniel R Fox, Jonathan M Grimes, Rhys Grinter, Matthew Jenkins, Roman Kamyshinsky, Jeremy R Keown, Gerald Lackner, Michael Lammers, Shiheng Liu, Andrew L Lovering, Tomas Malinauskas, Benoît Masquida, Gottfried J Palm, Christian Siebold, Tiantian Su, Ping Zhang, Z Hong Zhou, Krzysztof Fidelis, Maya Topf, John Moult, Torsten Schwede","doi":"10.1002/prot.70025","DOIUrl":"https://doi.org/10.1002/prot.70025","url":null,"abstract":"This article presents an in-depth analysis of selected CASP16 targets, with a focus on their biological and functional significance. The authors highlight the most relevant features of the target proteins and discuss how well these were reproduced in the submitted predictions. While the overall performance of structure prediction methods remains impressive, challenges persist, particularly in modeling rare structural motifs, flexible regions, small molecule interactions, posttranslational modifications, and biologically important interfaces. Addressing these limitations can strengthen the role of structure prediction in complementing experimental efforts and advancing both basic research and biomedical applications.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145253956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Protein-Ligand Structure Prediction by Template-Guided Ensemble Docking Strategy. 基于模板引导集成对接策略的蛋白质配体结构预测。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-06 DOI: 10.1002/prot.70063

Keqiong Zhang, Qilong Wu, Sheng-You Huang

{"title":"Protein-Ligand Structure Prediction by Template-Guided Ensemble Docking Strategy.","authors":"Keqiong Zhang, Qilong Wu, Sheng-You Huang","doi":"10.1002/prot.70063","DOIUrl":"https://doi.org/10.1002/prot.70063","url":null,"abstract":"In the 15th Critical Assessment of Techniques for Structure Prediction (CASP15), the category of protein-ligand complexes was introduced to advance the development of protein-ligand structure prediction techniques. CASP16 further expanded this category by introducing four sets of pharmaceutical targets as super-targets. Each super-target consists of multiple protein-ligand complexes involving the same protein but different ligands. Given the outstanding performance of template-based methods in CASP15, we employed a template-guided ensemble docking strategy for ligand (LG) tasks in CASP16. MODELER, AlphaFold3, and AlphaFold-Multimer were used to generate structural ensembles for each target protein. Then, we searched the Protein Data Bank (PDB) for reliable template complexes based on sequence identity, ligand similarity, and maximum common substructure (MCS) coverage score. If templates were identified, we used LSalign to perform ligand 3D alignment. For targets without a template, XDock and MDock were used to predict the binding poses. Finally, a knowledge-based scoring function, ITScore, was employed for energy evaluation. It is shown that our method performed well in the CASP16's LG tasks, ranking 4th out of 38 participating teams.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145234256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction. 基于深度学习的多肽结构预测算法比较分析。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-05 DOI: 10.1002/prot.70049

Clément Sauvestre, Jean-François Zagury, Florent Langenfeld

{"title":"Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction.","authors":"Clément Sauvestre, Jean-François Zagury, Florent Langenfeld","doi":"10.1002/prot.70049","DOIUrl":"https://doi.org/10.1002/prot.70049","url":null,"abstract":"While of primary importance in both the biomedical and therapeutic fields, peptides suffer from a relative lack of dedicated tools to predict efficiently and accurately their 3D structures despite being a crucial step in understanding their physio-pathological function or designing new drugs. In recent years, deep-learning methods have enabled a major breakthrough for the protein 3D structure prediction approaches, allowing to predict protein 3D structures with a near-experimental accuracy for nearly any protein sequence. This present study aims at confronting some of these new methods (AlphaFold2, RoseTTAFold2, and ESMFold) for the peptides' 3D structure prediction problem and evaluating their performance. All methods produced high-quality results, but their overall performance is lower as compared to the prediction of protein 3D structures. We also identified a few structural features that impede the ability to produce high-quality peptide structure predictions. These findings point out the discrepancy that still exists between the protein and peptide 3D structure prediction methods and underline a few cases where the generated peptide structures should be used very cautiously.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145234154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Distinctive Properties of Mla Proteins Differentiate Them From Classical ABC Transporter Components. Mla蛋白的独特特性使其区别于经典的ABC转运蛋白组分。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-05 DOI: 10.1002/prot.70064

Angshu Dutta, Smit Patel, Shankar Prasad Kanaujia

{"title":"Distinctive Properties of Mla Proteins Differentiate Them From Classical ABC Transporter Components.","authors":"Angshu Dutta, Smit Patel, Shankar Prasad Kanaujia","doi":"10.1002/prot.70064","DOIUrl":"https://doi.org/10.1002/prot.70064","url":null,"abstract":"In Gram-negative bacteria, the non-canonical ABC transporter, namely, maintenance of lipid asymmetry (Mla) system, ferries phospholipids (PLs) between the inner (IM) and outer (OM) membranes to preserve the PL asymmetry of the OM. The system utilizes three sub-cellular complexes-lipoprotein MlaA-OmpC/F (OM), MlaC (periplasmic), and MlaFEDB complex (IM). The structural studies on the Mla system have primarily been dedicated to its organization in IM and transport mechanisms. The characteristics of the individual components of the Mla system are lacking in the literature. In this study, individual components, namely MlaA, MlaB, MlaE, and MlaF were analyzed using computational tools. This has resulted in the identification of unique features and their characterization, including understanding the dynamicity of the C-terminal extension (CTE) of MlaA, which protrudes into the periplasm and the orientation of the protein, as well as binding patterns. Utilization of artificial intelligence has led to the understanding of the conformational landscape of MlaA and the validation of the macromolecular arrangement of Mla systems. Based on the results obtained, we were able to propose a fascinating mechanism of ligand transport, namely, bait-capture-pull. Our results reveal the poorly understood interfaces of the MlaB-MlaF complex. Furthermore, the results also suggest that MlaE possesses an EQ loop, which helps maintain a unique orientation. Overall, the findings of this study provide a new perspective on non-vesicular PL transport mediated by the enigmatic Mla system, thereby providing a holistic understanding.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145234279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Assessment of Pharmaceutical Protein-Ligand Pose and Affinity Predictions in CASP16. CASP16中药物蛋白-配体位姿和亲和力预测的评估。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-04 DOI: 10.1002/prot.70061

Michael K Gilson, Jerome Eberhardt, Peter Škrinjar, Janani Durairaj, Xavier Robin, Andriy Kryshtafovych

{"title":"Assessment of Pharmaceutical Protein-Ligand Pose and Affinity Predictions in CASP16.","authors":"Michael K Gilson, Jerome Eberhardt, Peter Škrinjar, Janani Durairaj, Xavier Robin, Andriy Kryshtafovych","doi":"10.1002/prot.70061","DOIUrl":"https://doi.org/10.1002/prot.70061","url":null,"abstract":"The protein-ligand component of the 16th Critical Assessment of Structure Prediction (CASP16) challenged participants to predict both binding poses and affinities of small molecules to protein targets, with a focus on drug-like compounds from pharmaceutical discovery projects. Thirty research groups submitted predictions for 229 protein-ligand pose targets and 140 affinity targets across five protein systems. Among the submitted predictions, template-based pose-prediction methods did particularly well, with the best groups achieving mean LDDT-PLI values of 0.69 (scale of 0-1 with 1 best). For comparison, we also ran a set of automated baseline pose-prediction methods, including ones using deep neural networks. Of these, AlphaFold 3 did particularly well, with a mean LDDT-PLI of 0.8, thus outscoring the best CASP16 predictor. The CASP affinity predictions showed modest correlation with experimental data (maximum Kendall's τ = 0.42), well below the theoretical maximum possible given experimental uncertainty (~0.73). As seen in prior challenges, providing experimental structures did not improve affinity predictions in the second stage of the challenge, suggesting that the scoring functions used here are a key limiting factor. Overall, the accuracy achieved by CASP participants is similar to that observed in the prior Drug Design Data Resource (D3R) blinded prediction challenges. The present results highlight the progress and persistent challenges in computational protein-ligand modeling and provide valuable benchmarks for the field of computer-aided drug design.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

The CASP 16 Experimental Protein-Ligand Datasets. casp16实验蛋白配体数据集。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-03 DOI: 10.1002/prot.70053

Andreas Tosstorff, Markus G Rudolph, Jörg Benz, Bernd Kuhn, Christian Kramer, May Sharpe, Chia-Ying Huang, Alexander Metz, Julien Hazemann, Daniel Ritz, Aengus Mac Sweeney, Michael K Gilson

{"title":"The CASP 16 Experimental Protein-Ligand Datasets.","authors":"Andreas Tosstorff, Markus G Rudolph, Jörg Benz, Bernd Kuhn, Christian Kramer, May Sharpe, Chia-Ying Huang, Alexander Metz, Julien Hazemann, Daniel Ritz, Aengus Mac Sweeney, Michael K Gilson","doi":"10.1002/prot.70053","DOIUrl":"https://doi.org/10.1002/prot.70053","url":null,"abstract":"This paper presents the experimental protein-ligand datasets used as benchmarks in the CASP 16 blind prediction experiment-the first CASP round to incorporate targets from pharmaceutical discovery projects. We have assembled and characterized protein-ligand complexes for four proteins that are known or candidate drug targets: human chymase, human cathepsin G, human autotaxin, and the SARS-CoV-2 main protease. The collection encompasses over 200 co-crystal structures at resolutions better than 2.7 Å, paired with binding affinity measurements for approximately 160 compounds covering a broad affinity range (nanomolar to high micromolar). These data enabled the CASP16 pose-prediction and affinity-prediction challenges. Many systems feature potentially challenging characteristics, including chymase's electropositive surface and acidic ligands, which require proper handling of titratable ligand groups; autotaxin complexes with and without zinc coordination; and a SARS-CoV-2 protease crystal form exhibiting an unusually open active site conformation. We describe the experimental approaches-from protein production and crystallization to binding assay development-that yielded these reference data. Contributed by scientists at F. Hoffmann-La Roche and Idorsia Pharmaceuticals, these datasets represent actual drug discovery projects and therefore provide a realistic testbed for assessing how computational methods perform on pharmaceutically relevant targets. An accompanying paper in the present special journal issue provides a comprehensive assessment of the pose and affinity predictions for these pharmaceutical protein-ligand systems.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

In Silico Analysis of Human NEK10 Reveals Novel Domain Architecture and Protein-Protein Interactions. 人类NEK10的计算机分析揭示了新的结构域结构和蛋白质-蛋白质相互作用。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-03 DOI: 10.1002/prot.70067

Andriele S Eichner, Nathaniel Zimmerman, Avdar San, Shaneen Singh

{"title":"In Silico Analysis of Human NEK10 Reveals Novel Domain Architecture and Protein-Protein Interactions.","authors":"Andriele S Eichner, Nathaniel Zimmerman, Avdar San, Shaneen Singh","doi":"10.1002/prot.70067","DOIUrl":"https://doi.org/10.1002/prot.70067","url":null,"abstract":"Cancer is the second leading cause of death worldwide, with an estimated 27.5 million new cases projected by 2040. Disruptions in cell cycle control cause DNA replication errors to accumulate during cell growth, leading to genomic instability and tumor development. Proteins that regulate cell cycle progression and checkpoint mechanisms are crucial targets for cancer therapy. NIMA-related kinases (NEKs) are a family of serine/threonine kinases involved in regulating various aspects of the cell cycle and mitotic checkpoints in humans. Among these, NEK10 is the most divergent member and has been associated with both cancer and ciliopathies, a group of disorders caused by defects in cilia structure or function. Despite its biological significance and distinctive domain architecture, the structural details of NEK10 remain largely unknown. To address this gap, we employed computational modeling techniques to predict the complete structure of the NEK10 protein. Our analysis revealed a catalytic domain flanked by two coiled-coil domains, armadillo repeats (ARM repeats), an ATP binding site, two putative ubiquitin-associated (UBA) domains, and a PEST sequence known to regulate protein degradation. Furthermore, we mapped a comprehensive interactome of NEK10, uncovering previously unreported interactions with the cancer-related proteins MAP3K1 and HSPB1. MAP3K1, a serine/threonine kinase and E3 ubiquitin ligase frequently mutated in cancers, interacts with the catalytic region of NEK10. The interaction with HSPB1, a molecular chaperone associated with poor cancer prognosis, is mediated by NEK10's ARM repeats. Our findings highlight a potential connection between NEK10, ciliogenesis, and cancer, suggesting an important role in cancer development and progression.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

The RNA-Puzzles Assessments of RNA-Only Targets in CASP16. CASP16中仅rna靶点的rna谜题评估。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-03 DOI: 10.1002/prot.70052

Eric Westhof, Hao Sun, Fan Bu, Zhichao Miao

引用次数: 0

Probing Enzymatic Acetylation Events in Real Time With NMR Spectroscopy: Insights Into Acyl-Cofactor Dependent p300 Modification of Histone H4. 用核磁共振光谱实时探测酶乙酰化事件：对酰基辅助因子依赖的p300修饰组蛋白H4的见解。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-01 Epub Date: 2025-06-01 DOI: 10.1002/prot.26848

Sophia M Dewing, Scott A Showalter

{"title":"Probing Enzymatic Acetylation Events in Real Time With NMR Spectroscopy: Insights Into Acyl-Cofactor Dependent p300 Modification of Histone H4.","authors":"Sophia M Dewing, Scott A Showalter","doi":"10.1002/prot.26848","DOIUrl":"10.1002/prot.26848","url":null,"abstract":"Lysine acylation is a rapidly expanding class of post-translational modifications with largely unexplored functional roles; the study of acylations beyond acetylation is especially impeded by limited methods for their preparation, detection, and characterization in vitro. We previously reported a nuclear magnetic resonance (NMR)-based approach to monitor Nε-lysine acetylation following Ada2/Gcn5-catalyzed installation of a 13C-acetyl probe on the histone H3 tail. Building on this foundation, here we expand those techniques by demonstrating the installation and 1H, 13C-HSQC based NMR detection of both 13C-acetyl and 13C-propionyl probes on the histone H4 tail using a mutant p300 lysine acetyltransferase (KAT) enzyme with enhanced activity. Additionally, we introduce a continuous evaluation method for acyltransferase reaction data, enabling the extraction of relative rate constants-a technique inspired by our laboratory's recent work on NMR methyltransferase kinetics. This study demonstrates that our NMR-based approach to assay enzymatic 13C-acylation is adaptable, providing a versatile platform for investigating a range of acylations, KAT enzymes, and protein substrates. Notably, in the process of developing these methods, we observed that p300 KAT may display distinct modification site preferences and regulatory mechanisms depending on the acyl cofactor utilized, underscoring the method's potential to advance the emerging field of lysine acylation biochemistry.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1837-1847"},"PeriodicalIF":2.8,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12354013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lysine Acetylation of Plant α-Tubulins: Scaling Up the Local Effect to Large System Transformations. 植物α-微管蛋白赖氨酸乙酰化：放大局部效应到大系统转化。

IF 2.8 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-01 Epub Date: 2025-06-04 DOI: 10.1002/prot.26846

Alexey Rayevsky, Elijah Bulgakov, Rostyslav Blume, Dmytro Novozhylov, Mariia Stykhylias, Serhii Ozheredov, Pavlo Karpov, Yaroslav Blume

{"title":"Lysine Acetylation of Plant α-Tubulins: Scaling Up the Local Effect to Large System Transformations.","authors":"Alexey Rayevsky, Elijah Bulgakov, Rostyslav Blume, Dmytro Novozhylov, Mariia Stykhylias, Serhii Ozheredov, Pavlo Karpov, Yaroslav Blume","doi":"10.1002/prot.26846","DOIUrl":"10.1002/prot.26846","url":null,"abstract":"Cell migration and motility, cell division, biogenesis and renewal of cell and tissue integrity, and the assembly and retention of cell or tissue architecture, to name but a few, represent increasingly vital processes at the cellular and whole-body levels. These biological processes are closely connected with the major structural transformations that cytoskeletal proteins undergo due to numerous post-translational modifications, including acetylation, tyrosynation, polyglutamylation, etc. We collected all the information on tubulin acetylation and data on related cellular manifestations. This work expands upon our previous investigations into PTM-associated microtubule remodeling by incorporating K60, K163, and K326 into our analysis. Subsequently, we applied the refined protocol to examine the impact of acetylation on the most prevalent tubulin isoforms: TBA1, TBA2, and TBA3. Our analysis identified three distinct patterns on the α-tubulin surface where interactions with neighboring subunits were altered upon acetylation. These findings suggest that acetylation significantly influences the inter-subunit interactions within the microtubule polymer. To assess the likelihood of rearrangement at each of the three acetylation sites (K60, K163, K326), we conducted a series of simulations involving nine tubulin molecules (representing a microtubule lattice). These simulations aimed to quantify the degree of dissociation susceptibility upon acetylation at each of these specific lysine residues while focusing on residues that serve as substrates for HDAC6 deacetylation in plants, K60, K163, and K326. In this study, we have gathered all relevant evidence for the impact of different acetylation points on the assembly and lifespan of microtubule organelles, using A. thaliana tubulins as a model object.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1848-1861"},"PeriodicalIF":2.8,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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