Protein Science最新文献

筛选
英文 中文
Native ion mobility-mass spectrometry reveals the binding mechanisms of anti-amyloid therapeutic antibodies. 原生离子迁移质谱法揭示了抗淀粉样蛋白治疗性抗体的结合机制。
IF 4.5 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5008
Yilin Han, Alec A Desai, Jennifer M Zupancic, Matthew D Smith, Peter M Tessier, Brandon T Ruotolo
{"title":"Native ion mobility-mass spectrometry reveals the binding mechanisms of anti-amyloid therapeutic antibodies.","authors":"Yilin Han, Alec A Desai, Jennifer M Zupancic, Matthew D Smith, Peter M Tessier, Brandon T Ruotolo","doi":"10.1002/pro.5008","DOIUrl":"10.1002/pro.5008","url":null,"abstract":"<p><p>One of the most important attributes of anti-amyloid antibodies is their selective binding to oligomeric and amyloid aggregates. However, current methods of examining the binding specificities of anti-amyloid β (Aβ) antibodies have limited ability to differentiate between complexes that form between antibodies and monomeric or oligomeric Aβ species during the dynamic Aβ aggregation process. Here, we present a high-resolution native ion-mobility mass spectrometry (nIM-MS) method to investigate complexes formed between a variety of Aβ oligomers and three Aβ-specific IgGs, namely two antibodies with relatively high conformational specificity (aducanumab and A34) and one antibody with low conformational specificity (crenezumab). We found that crenezumab primarily binds Aβ monomers, while aducanumab preferentially binds Aβ monomers and dimers and A34 preferentially binds Aβ dimers, trimers, and tetrameters. Through collision induced unfolding (CIU) analysis, our data indicate that antibody stability is increased upon Aβ binding and, surprisingly, this stabilization involves the Fc region. Together, we conclude that nIM-MS and CIU enable the identification of Aβ antibody binding stoichiometries and provide important details regarding antibody binding mechanisms.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5008"},"PeriodicalIF":4.5,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140899343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Reconstitution and characterization of BRAF in complex with 14-3-3 and KRAS4B on nanodiscs. BRAF 与 14-3-3 和 KRAS4B 复合物在纳米盘上的重构和特征描述。
IF 8 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5016
Ningdi F Liu, Masahiro Enomoto, Christopher B Marshall, Mitsuhiko Ikura
{"title":"Reconstitution and characterization of BRAF in complex with 14-3-3 and KRAS4B on nanodiscs.","authors":"Ningdi F Liu, Masahiro Enomoto, Christopher B Marshall, Mitsuhiko Ikura","doi":"10.1002/pro.5016","DOIUrl":"10.1002/pro.5016","url":null,"abstract":"<p><p>RAF kinases are key components of the RAS-MAPK signaling pathway, which drives cell growth and is frequently overactivated in cancer. Upstream signaling activates the small GTPase RAS, which recruits RAF to the cell membrane, driving a transition of the latter from an auto-inhibited monomeric conformation to an active dimer. Despite recent progress, mechanistic details underlying RAF activation remain unclear, particularly the role of RAS and the membrane in mediating this conformational rearrangement of RAF together with 14-3-3 to permit RAF kinase domain dimerization. Here, we reconstituted an active complex of dimeric BRAF, a 14-3-3 dimer and two KRAS4B on a nanodisc bilayer and verified that its assembly is GTP-dependent. Biolayer interferometry (BLI) was used to compare the binding affinities of monomeric versus dimeric full-length BRAF:14-3-3 complexes for KRAS4B-conjugated nanodiscs (RAS-ND) and to investigate the effects of membrane lipid composition and spatial density of KRAS4B on binding. 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and higher KRAS4B density enhanced the interaction of BRAF:14-3-3 with RAS-ND to different degrees depending on BRAF oligomeric state. We utilized our reconstituted system to dissect the effects of KRAS4B and the membrane on the kinase activity of monomeric and dimeric BRAF:14-3-3 complexes, finding that KRAS4B or nanodiscs alone were insufficient to stimulate activity, whereas RAS-ND increased activity of both states of BRAF. The reconstituted assembly of full-length BRAF with 14-3-3 and KRAS on a cell-free, defined lipid bilayer offers a more holistic biophysical perspective to probe regulation of this multimeric signaling complex at the membrane surface.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5016"},"PeriodicalIF":8.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins. ProkDBP:更精确地鉴定原核生物 DNA 结合蛋白。
IF 8 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5015
Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Ritwika Das, Ajit Gupta, Rajender Parsad
{"title":"ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.","authors":"Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Ritwika Das, Ajit Gupta, Rajender Parsad","doi":"10.1002/pro.5015","DOIUrl":"10.1002/pro.5015","url":null,"abstract":"<p><p>Prokaryotic DNA binding proteins (DBPs) play pivotal roles in governing gene regulation, DNA replication, and various cellular functions. Accurate computational models for predicting prokaryotic DBPs hold immense promise in accelerating the discovery of novel proteins, fostering a deeper understanding of prokaryotic biology, and facilitating the development of therapeutics targeting for potential disease interventions. However, existing generic prediction models often exhibit lower accuracy in predicting prokaryotic DBPs. To address this gap, we introduce ProkDBP, a novel machine learning-driven computational model for prediction of prokaryotic DBPs. For prediction, a total of nine shallow learning algorithms and five deep learning models were utilized, with the shallow learning models demonstrating higher performance metrics compared to their deep learning counterparts. The light gradient boosting machine (LGBM), coupled with evolutionarily significant features selected via random forest variable importance measure (RF-VIM) yielded the highest five-fold cross-validation accuracy. The model achieved the highest auROC (0.9534) and auPRC (0.9575) among the 14 machine learning models evaluated. Additionally, ProkDBP demonstrated substantial performance with an independent dataset, exhibiting higher values of auROC (0.9332) and auPRC (0.9371). Notably, when benchmarked against several cutting-edge existing models, ProkDBP showcased superior predictive accuracy. Furthermore, to promote accessibility and usability, ProkDBP (https://iasri-sg.icar.gov.in/prokdbp/) is available as an online prediction tool, enabling free access to interested users. This tool stands as a significant contribution, enhancing the repertoire of resources for accurate and efficient prediction of prokaryotic DBPs.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5015"},"PeriodicalIF":8.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
An ensemble machine learning model generates a focused screening library for the identification of CDK8 inhibitors. 一个集合机器学习模型生成了一个重点筛选库,用于鉴定 CDK8 抑制剂。
IF 8 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5007
Tony Eight Lin, Dyan Yen, Wei-Chun HuangFu, Yi-Wen Wu, Jui-Yi Hsu, Shih-Chung Yen, Tzu-Ying Sung, Jui-Hua Hsieh, Shiow-Lin Pan, Chia-Ron Yang, Wei-Jan Huang, Kai-Cheng Hsu
{"title":"An ensemble machine learning model generates a focused screening library for the identification of CDK8 inhibitors.","authors":"Tony Eight Lin, Dyan Yen, Wei-Chun HuangFu, Yi-Wen Wu, Jui-Yi Hsu, Shih-Chung Yen, Tzu-Ying Sung, Jui-Hua Hsieh, Shiow-Lin Pan, Chia-Ron Yang, Wei-Jan Huang, Kai-Cheng Hsu","doi":"10.1002/pro.5007","DOIUrl":"10.1002/pro.5007","url":null,"abstract":"<p><p>The identification of an effective inhibitor is an important starting step in drug development. Unfortunately, many issues such as the characterization of protein binding sites, the screening library, materials for assays, etc., make drug screening a difficult proposition. As the size of screening libraries increases, more resources will be inefficiently consumed. Thus, new strategies are needed to preprocess and focus a screening library towards a targeted protein. Herein, we report an ensemble machine learning (ML) model to generate a CDK8-focused screening library. The ensemble model consists of six different algorithms optimized for CDK8 inhibitor classification. The models were trained using a CDK8-specific fragment library along with molecules containing CDK8 activity. The optimized ensemble model processed a commercial library containing 1.6 million molecules. This resulted in a CDK8-focused screening library containing 1,672 molecules, a reduction of more than 99.90%. The CDK8-focused library was then subjected to molecular docking, and 25 candidate compounds were selected. Enzymatic assays confirmed six CDK8 inhibitors, with one compound producing an IC<sub>50</sub> value of ≤100 nM. Analysis of the ensemble ML model reveals the role of the CDK8 fragment library during training. Structural analysis of molecules reveals the hit compounds to be structurally novel CDK8 inhibitors. Together, the results highlight a pipeline for curating a focused library for a specific protein target, such as CDK8.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5007"},"PeriodicalIF":8.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140899312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Adaptive evolution: Eukaryotic enzyme's specificity shift to a bacterial substrate. 适应性进化:真核生物酶对细菌底物的特异性转变。
IF 4.5 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5028
Emi Latifah, Indira Rizqita Ivanesthi, Yi-Kuan Tseng, Hung-Chuan Pan, Chien-Chia Wang
{"title":"Adaptive evolution: Eukaryotic enzyme's specificity shift to a bacterial substrate.","authors":"Emi Latifah, Indira Rizqita Ivanesthi, Yi-Kuan Tseng, Hung-Chuan Pan, Chien-Chia Wang","doi":"10.1002/pro.5028","DOIUrl":"10.1002/pro.5028","url":null,"abstract":"<p><p>Prolyl-tRNA synthetase (ProRS), belonging to the family of aminoacyl-tRNA synthetases responsible for pairing specific amino acids with their respective tRNAs, is categorized into two distinct types: the eukaryote/archaeon-like type (E-type) and the prokaryote-like type (P-type). Notably, these types are specific to their corresponding cognate tRNAs. In an intriguing paradox, Thermus thermophilus ProRS (TtProRS) aligns with the E-type ProRS but selectively charges the P-type tRNA<sup>Pro</sup>, featuring the bacterium-specific acceptor-stem elements G72 and A73. This investigation reveals TtProRS's notable resilience to the inhibitor halofuginone, a synthetic derivative of febrifugine emulating Pro-A76, resembling the characteristics of the P-type ProRS. Furthermore, akin to the P-type ProRS, TtProRS identifies its cognate tRNA through recognition of the acceptor-stem elements G72/A73, along with the anticodon elements G35/G36. However, in contrast to the P-type ProRS, which relies on a strictly conserved R residue within the bacterium-like motif 2 loop for recognizing G72/A73, TtProRS achieves this through a non-conserved sequence, RTR, within the otherwise non-interacting eukaryote-like motif 2 loop. This investigation sheds light on the adaptive capacity of a typically conserved housekeeping enzyme to accommodate a novel substrate.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5028"},"PeriodicalIF":4.5,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11099734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140959204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
A fluorescence-based sensor for calibrated measurement of protein kinase stability in live cells. 用于校准测量活细胞中蛋白激酶稳定性的荧光传感器。
IF 8 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5023
Joseph W Paul, Serena Muratcioğlu, John Kuriyan
{"title":"A fluorescence-based sensor for calibrated measurement of protein kinase stability in live cells.","authors":"Joseph W Paul, Serena Muratcioğlu, John Kuriyan","doi":"10.1002/pro.5023","DOIUrl":"10.1002/pro.5023","url":null,"abstract":"<p><p>Oncogenic mutations can destabilize signaling proteins, resulting in increased or unregulated activity. Thus, there is considerable interest in mapping the relationship between mutations and the stability of signaling proteins, to better understand the consequences of oncogenic mutations and potentially inform the development of new therapeutics. Here, we develop a tool to study protein-kinase stability in live mammalian cells and the effects of the HSP90 chaperone system on the stability of these kinases. We determine the expression levels of protein kinases by monitoring the fluorescence of fluorescent proteins fused to those kinases, normalized to that of co-expressed reference fluorescent proteins. We used this tool to study the dependence of Src- and Raf-family kinases on the HSP90 system. We demonstrate that this sensor reports on destabilization induced by oncogenic mutations in these kinases. We also show that Src-homology 2 and Src-homology 3 domains, which are required for autoinhibition of Src-family kinases, stabilize these kinase domains in the cell. Our expression-calibrated sensor enables the facile characterization of the effects of mutations and small-molecule drugs on protein-kinase stability.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5023"},"PeriodicalIF":8.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11129626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141154271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Site-directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus. 定点突变揭示了 Capra hircus RidA 的稳定性、结构和酶活性之间的相互作用。
IF 8 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5036
Giulia Rizzi, Stefania Digiovanni, Genny Degani, Alberto Barbiroli, Flavio Di Pisa, Laura Popolo, Cristina Visentin, Maria Antonietta Vanoni, Stefano Ricagno
{"title":"Site-directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus.","authors":"Giulia Rizzi, Stefania Digiovanni, Genny Degani, Alberto Barbiroli, Flavio Di Pisa, Laura Popolo, Cristina Visentin, Maria Antonietta Vanoni, Stefano Ricagno","doi":"10.1002/pro.5036","DOIUrl":"10.1002/pro.5036","url":null,"abstract":"<p><p>Reactive intermediate deaminase A (RidA) is a highly conserved enzyme that catalyzes the hydrolysis of 2-imino acids to the corresponding 2-keto acids and ammonia. RidA thus prevents the accumulation of such potentially harmful compounds in the cell, as exemplified by its role in the degradation of 2-aminoacrylate, formed during the metabolism of cysteine and serine, catalyzing the conversion of its stable 2-iminopyruvate tautomer into pyruvate. Capra hircus (goat) RidA (<sub>Ch</sub>RidA) was the first mammalian RidA to be isolated and described. It has the typical homotrimeric fold of the Rid superfamily, characterized by remarkably high thermal stability, with three active sites located at the interface between adjacent subunits. <sub>Ch</sub>RidA exhibits a broad substrate specificity with a preference for 2-iminopyruvate and other 2-imino acids derived from amino acids with non-polar non-bulky side chains. Here we report a biophysical and biochemical characterization of eight <sub>Ch</sub>RidA variants obtained by site-directed mutagenesis to gain insight into the role of specific residues in protein stability and catalytic activity. Each mutant was produced in Escherichia coli cells, purified and characterized in terms of quaternary structure, thermal stability and substrate specificity. The results are rationalized in the context of the high-resolution structures obtained by x-ray crystallography.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5036"},"PeriodicalIF":8.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11129622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141154526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Characterization of the interaction between the Sec61 translocon complex and ppαF using optical tweezers. 利用光学镊子鉴定 Sec61 转座子复合物与 ppαF 之间的相互作用。
IF 8 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.4996
Luka Robeson, Nathalie Casanova-Morales, Francesca Burgos-Bravo, Hilda M Alfaro-Valdés, Robert Lesch, Carolina Ramírez-Álvarez, Mauricio Valdivia-Delgado, Marcela Vega, Ricardo A Matute, Randy Schekman, Christian A M Wilson
{"title":"Characterization of the interaction between the Sec61 translocon complex and ppαF using optical tweezers.","authors":"Luka Robeson, Nathalie Casanova-Morales, Francesca Burgos-Bravo, Hilda M Alfaro-Valdés, Robert Lesch, Carolina Ramírez-Álvarez, Mauricio Valdivia-Delgado, Marcela Vega, Ricardo A Matute, Randy Schekman, Christian A M Wilson","doi":"10.1002/pro.4996","DOIUrl":"10.1002/pro.4996","url":null,"abstract":"<p><p>The Sec61 translocon allows the translocation of secretory preproteins from the cytosol to the endoplasmic reticulum lumen during polypeptide biosynthesis. These proteins possess an N-terminal signal peptide (SP) which docks at the translocon. SP mutations can abolish translocation and cause diseases, suggesting an essential role for this SP/Sec61 interaction. However, a detailed biophysical characterization of this binding is still missing. Here, optical tweezers force spectroscopy was used to characterize the kinetic parameters of the dissociation process between Sec61 and the SP of prepro-alpha-factor. The unbinding parameters including off-rate constant and distance to the transition state were obtained by fitting rupture force data to Dudko-Hummer-Szabo models. Interestingly, the translocation inhibitor mycolactone increases the off-rate and accelerates the SP/Sec61 dissociation, while also weakening the interaction. Whereas the translocation deficient mutant containing a single point mutation in the SP abolished the specificity of the SP/Sec61 binding, resulting in an unstable interaction. In conclusion, we characterize quantitatively the dissociation process between the signal peptide and the translocon, and how the unbinding parameters are modified by a translocation inhibitor.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e4996"},"PeriodicalIF":8.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors. 内在紊乱的 MLL 融合蛋白 AF9 与拟肽抑制剂复合物的结构研究。
IF 8 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5019
Yuting Yang, Ejaz Ahmad, Vidhya Premkumar, Alicen Liu, S M Ashikur Rahman, Zaneta Nikolovska-Coleska
{"title":"Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors.","authors":"Yuting Yang, Ejaz Ahmad, Vidhya Premkumar, Alicen Liu, S M Ashikur Rahman, Zaneta Nikolovska-Coleska","doi":"10.1002/pro.5019","DOIUrl":"10.1002/pro.5019","url":null,"abstract":"<p><p>AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL-rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP-AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1-2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein-inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5019"},"PeriodicalIF":8.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria. 耐万古霉素细菌中 D-Ala-D-Ala 金属肽酶 VanX 的同源二聚体结构分析。
IF 4.5 3区 生物学
Protein Science Pub Date : 2024-06-01 DOI: 10.1002/pro.5002
Tsuyoshi Konuma, Tomoyo Takai, Chieko Tsuchiya, Masayuki Nishida, Miyu Hashiba, Yudai Yamada, Haruka Shirai, Yoko Motoda, Aritaka Nagadoi, Eriko Chikaishi, Ken-Ichi Akagi, Satoko Akashi, Toshio Yamazaki, Hideo Akutsu, Takahisa Ikegami
{"title":"Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria.","authors":"Tsuyoshi Konuma, Tomoyo Takai, Chieko Tsuchiya, Masayuki Nishida, Miyu Hashiba, Yudai Yamada, Haruka Shirai, Yoko Motoda, Aritaka Nagadoi, Eriko Chikaishi, Ken-Ichi Akagi, Satoko Akashi, Toshio Yamazaki, Hideo Akutsu, Takahisa Ikegami","doi":"10.1002/pro.5002","DOIUrl":"10.1002/pro.5002","url":null,"abstract":"<p><p>Bacteria that have acquired resistance to most antibiotics, particularly those causing nosocomial infections, create serious problems. Among these, the emergence of vancomycin-resistant enterococci was a tremendous shock, considering that vancomycin is the last resort for controlling methicillin-resistant Staphylococcus aureus. Therefore, there is an urgent need to develop an inhibitor of VanX, a protein involved in vancomycin resistance. Although the crystal structure of VanX has been resolved, its asymmetric unit contains six molecules aligned in a row. We have developed a structural model of VanX as a stable dimer in solution, primarily utilizing nuclear magnetic resonance (NMR) residual dipolar coupling. Despite the 46 kDa molecular mass of the dimer, the analyses, which are typically not as straightforward as those of small proteins around 10 kDa, were successfully conducted. We assigned the main chain using an amino acid-selective unlabeling method. Because we found that the zinc ion-coordinating active sites in the dimer structure were situated in the opposite direction to the dimer interface, we generated an active monomer by replacing an amino acid at the dimer interface. The monomer consists of only 202 amino acids and is expected to be used in future studies to screen and improve inhibitors using NMR.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5002"},"PeriodicalIF":4.5,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140899314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信