Proteins-Structure Function and Bioinformatics最新文献

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Exploring the Hemoglobin T to R2 Path Using Gaussian Elastic Network Correlation Map Distance. 利用高斯弹性网络相关图距离探索血红蛋白T到R2的路径。
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-05 DOI: 10.1002/prot.70014
Yuval Valenci, Dror Tobi
{"title":"Exploring the Hemoglobin T to R2 Path Using Gaussian Elastic Network Correlation Map Distance.","authors":"Yuval Valenci, Dror Tobi","doi":"10.1002/prot.70014","DOIUrl":"https://doi.org/10.1002/prot.70014","url":null,"abstract":"<p><p>Proteins are dynamic and undergo conformational changes. These changes may affect the motions executed by different regions of the proteins and are reflected in the motion correlation map. A method to accurately measure these changes is presented and exemplified on a set of tetrameric Hemoglobin structures. Using the Gaussian Network Model, the motion correlation map of each structure is calculated. The root of the square differences between the elements of the map of different structures is used to calculate their distance. Using this novel distance, the path between the T and R2 states is calculated. The intermediates along the path show gradual inter and intradimer correlation changes. The correlation of each subunit with the other in the same dimer becomes increasingly positive upon the T → R2 transition. Meanwhile, the interdomain correlation, as seen from the interface (α1β2 / β1α2), becomes increasingly negative. In addition, these distances are used to cluster the Hb structures. The newly suggested distance does not correlate with structure-based distances and offers a new way to explore the conformational space of proteins.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568142","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
Role of the DPP4 Receptor in SARS-CoV Entry: Insights From Docking and Molecular Dynamics Simulations. DPP4受体在SARS-CoV进入中的作用:来自对接和分子动力学模拟的见解
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-02 DOI: 10.1002/prot.70011
Patrícia Pereira Duzi Carvalho, Nelson Augusto Alves
{"title":"Role of the DPP4 Receptor in SARS-CoV Entry: Insights From Docking and Molecular Dynamics Simulations.","authors":"Patrícia Pereira Duzi Carvalho, Nelson Augusto Alves","doi":"10.1002/prot.70011","DOIUrl":"https://doi.org/10.1002/prot.70011","url":null,"abstract":"<p><p>Protein-receptor interactions play a critical role in viral entry and pathogenesis. While ACE2 is the primary receptor for SARS-CoV, the role of DPP4 as potential coreceptor remains underexplored. This study investigates the binding mechanisms and dissociation dynamics of the SARS-CoV/DPP4, SARS-CoV/ACE2 and MERS-CoV/DPP4 complexes using molecular docking and molecular dynamics simulations. The SARS-CoV/DPP4 complex exhibited the highest free-energy barrier ( <math> <semantics><mrow><mi>Δ</mi> <mi>F</mi> <mo>=</mo> <mn>6.77</mn> <mspace></mspace> <msub><mi>k</mi> <mi>B</mi></msub> <mi>T</mi></mrow> <annotation>$$ Delta F=6.77kern0.1em {k}_BT $$</annotation></semantics> </math> ), suggesting significant stability despite being energetically unfavorable. In contrast, the MERS-CoV/DPP4 complex, with the lowest free-energy barrier ( <math> <semantics><mrow><mi>Δ</mi> <mi>F</mi> <mo>=</mo> <mn>2.17</mn> <mspace></mspace> <msub><mi>k</mi> <mi>B</mi></msub> <mi>T</mi></mrow> <annotation>$$ Delta F=2.17kern0.1em {k}_BT $$</annotation></semantics> </math> ), was the most likely to form and the least resistant to dissociation. The SARS-CoV/ACE2 complex demonstrated the highest <math> <semantics> <mrow><msub><mi>Q</mi> <mtext>bound</mtext></msub> </mrow> <annotation>$$ {Q}_{mathrm{bound}} $$</annotation></semantics> </math> , reflecting well-organized interfacial side chains that facilitate hydrogen bonding, yet its relatively low free-energy barrier and dissociation temperature made it prone to dissociation. These findings highlight an inverse relationship between electrostatic complementarity and protein-protein complex stability, where increased electrostatic complementarity correlates with reduced stability due to frustration from competing interactions. While DPP4 may serve as a coreceptor for SARS-CoV, its interaction is constrained by significant energy barriers, suggesting it may only occur under specific biological conditions or alternative binding pathways.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546333","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
Simpler Protein Domain Identification Using Spectral Clustering. 利用光谱聚类技术简化蛋白质域识别。
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 Epub Date: 2025-02-13 DOI: 10.1002/prot.26808
Frédéric Cazals, Jules Herrmann, Edoardo Sarti
{"title":"Simpler Protein Domain Identification Using Spectral Clustering.","authors":"Frédéric Cazals, Jules Herrmann, Edoardo Sarti","doi":"10.1002/prot.26808","DOIUrl":"10.1002/prot.26808","url":null,"abstract":"<p><p>The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spectral clustering applied to a graph coding inter-atomic fluctuations derived from an elastic network model. We present SPECTRALDOM, which makes three straightforward and useful additions to SPECTRUS. For single structures, we show that high quality partitionings can be obtained from a graph Laplacian derived from pairwise interactions-without normal modes. For sets of homologous structures, we introduce a Multiple Sequence Alignment mode, exploiting both the sequence based information (MSA) and the geometric information embodied in experimental structures. Finally, we propose to analyze the clusters/domains delivered using the so-called <math> <semantics><mrow><mi>D</mi></mrow> </semantics> </math> -family-matching algorithm, which establishes a correspondence between domains yielded by two decompositions, and can be used to handle fragmentation issues. Our domains compare favorably to those of the original SPECTRUS, and those of the deep learning based method Chainsaw. Using two complex cases, we show in particular that SPECTRALDOM is the only method handling complex conformational changes involving several sub-domains. Finally, a comparison of SPECTRALDOM and Chainsaw on the manually curated domain classification ECOD as a reference shows that high quality domains are obtained without using any evolutionary related piece of information. SPECTRALDOM is provided in the Structural Bioinformatics Library, see http://sbl.inria.fr and https://sbl.inria.fr/doc/Spectral_domain_explorer-user-manual.html.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1212-1225"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411913","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
Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis. 密歇根克雷伯菌DUF152家族耐热漆酶的克隆、鉴定和计算机辅助进化。
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 Epub Date: 2025-02-14 DOI: 10.1002/prot.26784
Ting Cui, Kathrin Brückner, Stephan Schilling, Hans-Jürgen Mägert
{"title":"Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.","authors":"Ting Cui, Kathrin Brückner, Stephan Schilling, Hans-Jürgen Mägert","doi":"10.1002/prot.26784","DOIUrl":"10.1002/prot.26784","url":null,"abstract":"<p><p>Bacterial laccases exhibit relatively high optimal reaction temperatures and possess a broad substrate spectrum, thereby expanding the range of potential applications for laccase enzymes. This study aims to investigate the molecular evolution of bacterial laccases using computational 3D-structure prediction and molecular docking tools such as AlphaFold2, Metal3D, AutoDockVina, and Rosetta. We isolated a bacterium with laccase activities from fecal samples from a Hermann's tortoise (Testudo hermanni), identified it as Klebsiella michiganensis using 16S rRNA sequencing and nanopore genome sequencing, and then identified a sequence encoding a laccase with a predicted molecular weight of approximately 27.5 kDa. Expression of the corresponding, chemically synthesized DNA fragment resulted in the isolation of an active laccase. The enzyme showed considerable thermostability, retaining 21% of its activity after boiling for 30 min. Using state-of-the-art information technology and machine learning techniques, we conducted 3D-structure prediction on this sequence, predicted its copper-ion binding sites, and validated these predictions through site-directed mutagenesis and expression. Subsequently, we performed computer-aided evolution studies on this sequence and found that 90% of the results from the selected mutations exhibited improved performance. In summary, this study not only revealed a novel laccase but also demonstrated an efficient approach for advancing research on the molecular evolution of bacterial laccases using cutting-edge machine learning, next-generation sequencing, traditional bioinformatics approaches, and laboratory techniques, providing an effective strategy for discovering and design new bacterial laccases.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1226-1237"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12127718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416025","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
Correction to Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi. 修正刚性的柔性位点:一个有前途的策略,以提高溶血磷脂酶的热稳定性从深渊焦球菌。
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 Epub Date: 2025-01-31 DOI: 10.1002/prot.26804
{"title":"Correction to Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi.","authors":"","doi":"10.1002/prot.26804","DOIUrl":"10.1002/prot.26804","url":null,"abstract":"","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1295"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071260","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
pH-Dependent β-Strand Alignment of the Alzheimer's Amyloid-β (16-22) Peptide. 阿尔茨海默病淀粉样蛋白-β(16-22)肽的ph依赖性β-链排列。
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 DOI: 10.1002/prot.70012
Junfeng Wan, Yin Luo, Philippe Derreumaux, Guanghong Wei, Huiyu Li
{"title":"pH-Dependent β-Strand Alignment of the Alzheimer's Amyloid-β (16-22) Peptide.","authors":"Junfeng Wan, Yin Luo, Philippe Derreumaux, Guanghong Wei, Huiyu Li","doi":"10.1002/prot.70012","DOIUrl":"https://doi.org/10.1002/prot.70012","url":null,"abstract":"<p><p>The extracellular amyloid plaques of amyloid-β (Aβ) peptides formed in the human brain are an important pathological hallmark of Alzheimer's disease. There is evidence that pH affects the morphologies of fibrils and the kinetics of amyloid fibril formation. However, the underlying molecular mechanism is not well understood. In this study, as a first step to understand pH-modulated Aβ fibril formation, we investigated the conformations of Aβ (16-22) octamers by performing extensive all-atom replica exchange molecular dynamics simulations at both neutral and acidic pH. Our simulations showed that the residues Phe20 and Ala21 in the C terminal have higher β-sheet probability (78.8%, 55.8%) at acidic pH than (62.3%, 43.6%) at neutral pH. Out-of-register antiparallel β-strand alignments of the Aβ (16-22) peptide are predominantly in the 1-, 2-, and 3-residue shifts at both pH conditions, which agrees well with solid-state NMR results on Aβ peptides. We also found that there are multiple in-register and out-of-register parallel β-strand alignments under both pH conditions. However, the pH conditions affect the probability of β-strand alignments for the Aβ (16-22) peptide, and the residue-residue interaction of bilayer β-sheet and β-barrel are different at different pH conditions. Our analysis showed that the electrostatic interactions among peptides are much stronger at neutral pH than at acidic pH, while the vdW interactions are slightly stronger at acidic pH than at neutral pH. These results provide atomistic insight into the early stage of aggregation of amyloid-β (Aβ) peptides at acidic and neutral pH conditions.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546332","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
Skittles: GNN-Assisted Pseudo-Ligands Generation and Its Application for Binding Sites Classification and Affinity Prediction. 彩虹图:gnn辅助伪配体的生成及其在结合位点分类和亲和力预测中的应用。
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 Epub Date: 2025-02-28 DOI: 10.1002/prot.26816
Sergei Evteev, Alexey Ereshchenko, Denis Adjugim, Alexey Vyacheslavov, Anna Pastukhova, Alexander Malyshev, Victor Terentiev, Yan Ivanenkov
{"title":"Skittles: GNN-Assisted Pseudo-Ligands Generation and Its Application for Binding Sites Classification and Affinity Prediction.","authors":"Sergei Evteev, Alexey Ereshchenko, Denis Adjugim, Alexey Vyacheslavov, Anna Pastukhova, Alexander Malyshev, Victor Terentiev, Yan Ivanenkov","doi":"10.1002/prot.26816","DOIUrl":"10.1002/prot.26816","url":null,"abstract":"<p><p>Nowadays, multiple solutions are known for identifying ligand-protein binding sites. Another important task is labeling each point of a binding site with the appropriate atom type, a process known as pseudo-ligand generation. The number of solutions for pseudo-ligand generation is limited, and, to our knowledge, the influence of machine learning techniques has not been studied previously. Here, we describe Skittles, a new graph neural network-assisted pseudo-ligand generation approach, and compare it with known force-field-based methods. We also demonstrate the application of Skittles-based data for solving several important problems in structural biology, including ligand-protein binding site classification and ligand-protein affinity prediction.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1269-1280"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143525333","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
SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling. SARS-CoV-2 Mpro二面角揭示变构信号
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 Epub Date: 2025-03-03 DOI: 10.1002/prot.26814
Daniel Evans, Samreen Sheraz, Albert Y Lau
{"title":"SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.","authors":"Daniel Evans, Samreen Sheraz, Albert Y Lau","doi":"10.1002/prot.26814","DOIUrl":"10.1002/prot.26814","url":null,"abstract":"<p><p>In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated by the goals of understanding particular macromolecular systems of interest and creating general methods for their study. An especially important protein that is the subject of many investigations in allostery is the SARS-CoV-2 main protease (Mpro), which is necessary for coronaviral replication. It is both an attractive drug target and, due to intense interest in it for the development of pharmaceutical compounds, a gauge of the state of the art approaches in studying protein inhibition. Here we develop a computational method for characterizing protein allostery and use it to study Mpro. We propose a role of the protein's C-terminal tail in allosteric modulation and warn of unintuitive traps that can plague studies of the role of protein dihedral angles in transmitting allosteric signals.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1281-1289"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12129682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544684","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
Evaluation of the Ability of Wasp Venom Bioinspired Peptides (Fraternine-10 and Octovespin) in the Disaggregation and Anti-Aggregation of Amyloid-β Fibrils. 蜂毒生物诱导肽(frater9 -10和Octovespin)对淀粉样蛋白-β原纤维解聚和抗聚能力的评价。
IF 3.2 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 Epub Date: 2025-02-24 DOI: 10.1002/prot.26806
Yuri Alves de Oliveira Só, Caio Vinícius Sousa Costa, Luana Cristina Camargo, Letícia Germino Veras, Luiz Antônio Ribeiro Júnior, Márcia Renata Mortari, Ricardo Gargano
{"title":"Evaluation of the Ability of Wasp Venom Bioinspired Peptides (Fraternine-10 and Octovespin) in the Disaggregation and Anti-Aggregation of Amyloid-β Fibrils.","authors":"Yuri Alves de Oliveira Só, Caio Vinícius Sousa Costa, Luana Cristina Camargo, Letícia Germino Veras, Luiz Antônio Ribeiro Júnior, Márcia Renata Mortari, Ricardo Gargano","doi":"10.1002/prot.26806","DOIUrl":"10.1002/prot.26806","url":null,"abstract":"<p><p>Many neurodegenerative diseases are directly related to the formation of toxic protein aggregates, such as Alzheimer's disease, which is associated with the aggregation of amyloid-beta (Aβ). In this context, protein fibrils are the hallmark of these neurodegenerative diseases. In this sense, developing compounds capable of preventing or reducing the formation of protein aggregation in the brain can be of fundamental importance for the curative treatment of these diseases. Animals' venom compounds are known to be selected for nervous system targets, therefore, they are considered an interesting platform for developing pharmacological tools. This work presents a study of the ligands Octovespin (bioinspired by the wasp venom Polybia occidentalis) and Fraternine-10 (bioinspired by the wasp venom Parachartergus fraternus) concerning the disaggregation and anti-aggregation of fibrils of Aβ(17-42) sheets. First, we performed in silico calculations using molecular docking and molecular dynamics simulations with 200 ns. The results indicate that Octovespin and Fraternine-10 interact with the Aβ protein fibrils throughout all simulation time. The RMSD, RMSF, number of hydrogen and radius of gyration values and the interactions with amino acids responsible for fibril aggregation demonstrate that both Octovespin and Fraternine-10 have a significant disaggregation potential, which corroborates the in vitro and in vivo experimental observations. Furthermore, experimental data of Fraternine-10 demonstrated an anti-aggregation effect, indicating that it can promote fibril disaggregation and prevent them from aggregating again to form oligomers. However, in vivo data of Fraternine-10 did not show improvement. Even though in vivo results were not promising, the in vitro and in silico discoveries qualify these molecules as potential sources for developing new candidates to become medicines against Alzheimer's disease.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1257-1268"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484969","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
Structural Insight Into the SKP1-CUL1-FBXO3-RBX1 Complex. SKP1-CUL1-FBXO3-RBX1复合物的结构分析。
IF 2.8 4区 生物学
Proteins-Structure Function and Bioinformatics Pub Date : 2025-07-01 Epub Date: 2025-02-08 DOI: 10.1002/prot.26809
Jiajia Wei, Chao Xu
{"title":"Structural Insight Into the SKP1-CUL1-FBXO3-RBX1 Complex.","authors":"Jiajia Wei, Chao Xu","doi":"10.1002/prot.26809","DOIUrl":"10.1002/prot.26809","url":null,"abstract":"<p><p>The cryo-EM structure of human SCF<sup>FBXO3</sup>, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ApaG domain, how FBXO3 is incorporated into the SCF complex remains elusive. In the cryo-EM structure of SCF<sup>FBXO3</sup>, the F-box domain of FBXO3 primarily associates with SKP1 via extensive hydrophobic interactions and interacts with the N-terminal region of CUL1 via hydrophobic interactions. The weak cryo-EM map of the RBX1 globular region is close to the FBXO3 ApaG domain, suggesting that unmodified SCF<sup>FBXO3</sup> exhibits a closed conformation and that CUL1 neddylation is likely required to achieve high E3 activity. The structural study provides insight into the assembly of SCF<sup>FBXO3</sup> and its activation mediated by CUL1 neddylation.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1290-1294"},"PeriodicalIF":2.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375054","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
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