Protein Science最新文献_第10页

Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity 配体诱导的 CaMKIIα 中枢 Trp403 翻转、枢纽结构域堆叠和激酶活性调节

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5152

Dilip Narayanan, Anne Sofie G. Larsen, Stine Juul Gauger, Ruth Adafia, Rikke Bartschick Hammershøi, Louise Hamborg, Jesper Bruus‐Jensen, Nane Griem‐Krey, Christine L. Gee, Bente Frølund, Margaret M. Stratton, John Kuriyan, Jette Sandholm Kastrup, Annette E. Langkilde, Petrine Wellendorph, Sara M. Ø. Solbak

{"title":"Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity","authors":"Dilip Narayanan, Anne Sofie G. Larsen, Stine Juul Gauger, Ruth Adafia, Rikke Bartschick Hammershøi, Louise Hamborg, Jesper Bruus‐Jensen, Nane Griem‐Krey, Christine L. Gee, Bente Frølund, Margaret M. Stratton, John Kuriyan, Jette Sandholm Kastrup, Annette E. Langkilde, Petrine Wellendorph, Sara M. Ø. Solbak","doi":"10.1002/pro.5152","DOIUrl":"https://doi.org/10.1002/pro.5152","url":null,"abstract":"γ‐Hydroxybutyric acid (GHB) analogs are small molecules that bind competitively to a specific cavity in the oligomeric CaMKIIα hub domain. Binding affects conformation and stability of the hub domain, which may explain the neuroprotective action of some of these compounds. Here, we describe molecular details of interaction of the larger‐type GHB analog 2‐(6‐(4‐chlorophenyl)imidazo[1,2‐b]pyridazine‐2‐yl)acetic acid (PIPA). Like smaller‐type analogs, PIPA binding to the CaMKIIα hub domain promoted thermal stability. PIPA additionally modulated CaMKIIα activity under sub‐maximal CaM concentrations and ultimately led to reduced substrate phosphorylation. A high‐resolution X‐ray crystal structure of a stabilized CaMKIIα (6x mutant) hub construct revealed details of the binding mode of PIPA, which involved outward placement of tryptophan 403 (Trp403), a central residue in a flexible loop close to the upper hub cavity. Small‐angle X‐ray scattering (SAXS) solution structures and mass photometry of the CaMKIIα wild‐type hub domain in the presence of PIPA revealed a high degree of ordered self‐association (stacks of CaMKIIα hub domains). This stacking neither occurred with the smaller compound 3‐hydroxycyclopent‐1‐enecarboxylic acid (HOCPCA), nor when Trp403 was replaced with leucine (W403L). Additionally, CaMKIIα W403L hub was stabilized to a larger extent by PIPA compared to CaMKIIα hub wild type, indicating that loop flexibility is important for holoenzyme stability. Thus, we propose that ligand‐induced outward placement of Trp403 by PIPA, which promotes an unforeseen mechanism of hub domain stacking, may be involved in the observed reduction in CaMKIIα kinase activity. Altogether, this sheds new light on allosteric regulation of CaMKIIα activity via the hub domain.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"39 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Integration of proteomic data with genome‐scale metabolic models: A methodological overview 蛋白质组数据与基因组尺度代谢模型的整合：方法概述

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5150

Farid Zare, Ronan M. T. Fleming

{"title":"Integration of proteomic data with genome‐scale metabolic models: A methodological overview","authors":"Farid Zare, Ronan M. T. Fleming","doi":"10.1002/pro.5150","DOIUrl":"https://doi.org/10.1002/pro.5150","url":null,"abstract":"The integration of proteomics data with constraint‐based reconstruction and analysis (COBRA) models plays a pivotal role in understanding the relationship between genotype and phenotype and bridges the gap between genome‐level phenomena and functional adaptations. Integrating a generic genome‐scale model with information on proteins enables generation of a context‐specific metabolic model which improves the accuracy of model prediction. This review explores methodologies for incorporating proteomics data into genome‐scale models. Available methods are grouped into four distinct categories based on their approach to integrate proteomics data and their depth of modeling. Within each category section various methods are introduced in chronological order of publication demonstrating the progress of this field. Furthermore, challenges and potential solutions to further progress are outlined, including the limited availability of appropriate in vitro data, experimental enzyme turnover rates, and the trade‐off between model accuracy, computational tractability, and data scarcity. In conclusion, methods employing simpler approaches demand fewer kinetic and omics data, consequently leading to a less complex mathematical problem and reduced computational expenses. On the other hand, approaches that delve deeper into cellular mechanisms and aim to create detailed mathematical models necessitate more extensive kinetic and omics data, resulting in a more complex and computationally demanding problem. However, in some cases, this increased cost can be justified by the potential for more precise predictions.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"22 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Engineering and physicochemical characterization of a novel, stable, symmetric bispecific antibody with dual target‐binding using a common light chain 一种新型、稳定、对称的双特异性抗体的工程设计和理化表征--利用共同的轻链实现双目标结合

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5121

Seiji Saito, Makoto Nakayama, Kaori Yamazaki, Yuya Miyamoto, Keiko Hiraishi, Daisuke Tomioka, Sayaka Takagi‐Maeda, Katsuaki Usami, Nobuaki Takahashi, Shinji Nara, Eiichiro Imai

{"title":"Engineering and physicochemical characterization of a novel, stable, symmetric bispecific antibody with dual target‐binding using a common light chain","authors":"Seiji Saito, Makoto Nakayama, Kaori Yamazaki, Yuya Miyamoto, Keiko Hiraishi, Daisuke Tomioka, Sayaka Takagi‐Maeda, Katsuaki Usami, Nobuaki Takahashi, Shinji Nara, Eiichiro Imai","doi":"10.1002/pro.5121","DOIUrl":"https://doi.org/10.1002/pro.5121","url":null,"abstract":"Bispecific antibodies (BsAbs) have emerged as a major class of antibody therapeutics owing to their substantial potential in disease treatment. While several BsAbs have been successfully approved in recent years, ongoing development efforts continue to focus on optimizing various BsAbs tailored to particular antigens and action mechanisms, aiming to achieve favorable physicochemical properties. BsAbs generally encounter challenges due to their unfavorable physicochemical characteristics and poor manufacturing efficiencies, highlighting the need for optimization to achieve reliable productivity and developability. Herein, we describe the development of a novel symmetric BsAb, REGULGENT™ (N‐term/C‐term), comprising two Fab domains, using a common light chain. The heavy chain fragment encoded two antigen‐binding determinants in one chain. The design and production of REGULGENT™ (N‐term/C‐term) are simple owing to the use of the same light chain, which does not induce heavy and light chain mispairing, frequently observed with the asymmetric BsAb format. REGULGENT™ (N‐term/C‐term) exhibited high expression and low aggregation characteristics during cell culture and stress treatment under low pH conditions. Differential scanning calorimetric data indicated that REGULGENT™ molecules had high conformational stability, similar to that of stabilized monoclonal antibodies. Surface plasmon resonance data showed that REGULGENT™ (N‐term/C‐term) could bind to two antigens simultaneously and exhibited a high affinity for two antigens. In summary, the symmetric BsAb format of REGULGENT™ confers its desirable IgG‐like physicochemical properties, thus making it an excellent candidate for commercial development. The findings demonstrate a novel BsAb with substantial development potential for clinical applications.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"14 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Mining unique cysteine synthetases and computational study on thoroughly eliminating feedback inhibition through tunnel engineering 挖掘独特的半胱氨酸合成酶，并对通过隧道工程彻底消除反馈抑制进行计算研究

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5160

Shuai Xu, Zong‐Lin Li, Zhi‐Min Li, Hong‐Lai Liu

{"title":"Mining unique cysteine synthetases and computational study on thoroughly eliminating feedback inhibition through tunnel engineering","authors":"Shuai Xu, Zong‐Lin Li, Zhi‐Min Li, Hong‐Lai Liu","doi":"10.1002/pro.5160","DOIUrl":"https://doi.org/10.1002/pro.5160","url":null,"abstract":"L‐cysteine is an essential component in pharmaceutical and agricultural industries, and synthetic biology has made strides in developing new metabolic pathways for its production, particularly in archaea with unique O‐phosphoserine sulfhydrylases (OPSS) as key enzymes. In this study, we employed database mining to identify a highly catalytic activity OPSS from Acetobacterium sp. (AsOPSS). However, it was observed that the enzymatic activity of AsOPSS suffered significant feedback inhibition from the product L‐cysteine, exhibiting an IC50 value of merely 1.2 mM. A semi‐rational design combined with tunnel analysis strategy was conducted to engineer AsOPSS. The best variant, AsOPSSA218R was achieved, totally eliminating product inhibition without sacrificing catalytic efficiency. Molecular docking and molecular dynamic simulations indicated that the binding conformation of AsOPSSA218R with L‐cys was altered, leading to a reduced affinity between L‐cysteine and the active pocket. Tunnel analysis revealed that the AsOPSSA218R variant reshaped the landscape of the tunnel, resulting in the construction of a new tunnel. Furthermore, random acceleration molecular dynamics simulation and umbrella sampling simulation demonstrated that the novel tunnel improved the suitability for product release and effectively separated the interference between the product release and substrate binding processes. Finally, more than 45 mM of L‐cysteine was produced in vitro within 2 h using the AsOPSSA218R variant. Our findings emphasize the potential for relieving feedback inhibition by artificially generating new product release channels, while also laying an enzymatic foundation for efficient L‐cysteine production.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"82 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Benchmarking reverse docking through AlphaFold2 human proteome 通过 AlphaFold2 人类蛋白质组进行反向对接基准测试

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5167

Qing Luo, Sheng Wang, Hoi Yeung Li, Liangzhen Zheng, Yuguang Mu, Jingjing Guo

{"title":"Benchmarking reverse docking through AlphaFold2 human proteome","authors":"Qing Luo, Sheng Wang, Hoi Yeung Li, Liangzhen Zheng, Yuguang Mu, Jingjing Guo","doi":"10.1002/pro.5167","DOIUrl":"https://doi.org/10.1002/pro.5167","url":null,"abstract":"Predicting the binding of ligands to the human proteome via reverse‐docking methods enables the understanding of ligand's interactions with potential protein targets in the human body, thereby facilitating drug repositioning and the evaluation of potential off‐target effects or toxic side effects of drugs. In this study, we constructed 11 reverse docking pipelines by integrating site prediction tools (PointSite and SiteMap), docking programs (Glide and AutoDock Vina), and scoring functions (Glide, Autodock Vina, RTMScore, DeepRMSD, and OnionNet‐SFCT), and then thoroughly benchmarked their predictive capabilities. The results show that the Glide_SFCT (PS) pipeline exhibited the best target prediction performance based on the atomic structure models in AlphaFold2 human proteome. It achieved a success rate of 27.8% when considering the top 100 ranked prediction. This pipeline effectively narrows the range of potential targets within the human proteome, laying a foundation for drug target prediction, off‐target assessment, and toxicity prediction, ultimately boosting drug development. By facilitating these critical aspects of drug discovery and development, our work has the potential to ultimately accelerate the identification of new therapeutic agents and improve drug safety.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"5 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

AlzDiscovery: A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure information AlzDiscovery：利用蛋白质结构信息识别阿尔茨海默病致病错义突变的计算工具

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5147

Qisheng Pan, Georgina Becerra Parra, Yoochan Myung, Stephanie Portelli, Thanh Binh Nguyen, David B. Ascher

{"title":"AlzDiscovery: A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure information","authors":"Qisheng Pan, Georgina Becerra Parra, Yoochan Myung, Stephanie Portelli, Thanh Binh Nguyen, David B. Ascher","doi":"10.1002/pro.5147","DOIUrl":"https://doi.org/10.1002/pro.5147","url":null,"abstract":"Alzheimer's disease (AD) is one of the most common forms of dementia and neurodegenerative diseases, characterized by the formation of neuritic plaques and neurofibrillary tangles. Many different proteins participate in this complicated pathogenic mechanism, and missense mutations can alter the folding and functions of these proteins, significantly increasing the risk of AD. However, many methods to identify AD‐causing variants did not consider the effect of mutations from the perspective of a protein three‐dimensional environment. Here, we present a machine learning‐based analysis to classify the AD‐causing mutations from their benign counterparts in 21 AD‐related proteins leveraging both sequence‐ and structure‐based features. Using computational tools to estimate the effect of mutations on protein stability, we first observed a bias of the pathogenic mutations with significant destabilizing effects on family AD‐related proteins. Combining this insight, we built a generic predictive model, and improved the performance by tuning the sample weights in the training process. Our final model achieved the performance on area under the receiver operating characteristic curve up to 0.95 in the blind test and 0.70 in an independent clinical validation, outperforming all the state‐of‐the‐art methods. Feature interpretation indicated that the hydrophobic environment and polar interaction contacts were crucial to the decision on pathogenic phenotypes of missense mutations. Finally, we presented a user‐friendly web server, AlzDiscovery, for researchers to browse the predicted phenotypes of all possible missense mutations on these 21 AD‐related proteins. Our study will be a valuable resource for AD screening and the development of personalized treatment.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"22 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis 开发基于设计蛋白质的人工光合系统，深入了解光合作用的机理

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5164

Gonzalo Pérez Serrano, Claudia F. Echavarría, Sara H. Mejias

{"title":"Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis","authors":"Gonzalo Pérez Serrano, Claudia F. Echavarría, Sara H. Mejias","doi":"10.1002/pro.5164","DOIUrl":"https://doi.org/10.1002/pro.5164","url":null,"abstract":"This review aims to provide an overview of the progress in protein‐based artificial photosystem design and their potential to uncover the underlying principles governing light‐harvesting in photosynthesis. While significant advances have been made in this area, a gap persists in reviewing these advances. This review provides a perspective of the field, pinpointing knowledge gaps and unresolved challenges that warrant further inquiry. In particular, it delves into the key considerations when designing photosystems based on the chromophore and protein scaffold characteristics, presents the established strategies for artificial photosystems engineering with their advantages and disadvantages, and underscores the recent breakthroughs in understanding the molecular mechanisms governing light‐harvesting, charge separation, and the role of the protein motions in the chromophore's excited state relaxation. By disseminating this knowledge, this article provides a foundational resource for defining the field of bio‐hybrid photosystems and aims to inspire the continued exploration of artificial photosystems using protein design.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"2 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Cryo‐EM and solid state NMR together provide a more comprehensive structural investigation of protein fibrils 低温电子显微镜和固态核磁共振共同提供了更全面的蛋白质纤维结构研究

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5168

Blake D. Fonda, Masato Kato, Yang Li, Dylan T. Murray

引用次数: 0

Peptides inhibiting the assembly of monomeric human l‐lactate dehydrogenase into catalytically active homotetramer decrease the synthesis of lactate in cultured cells 抑制单体人乳酸脱氢酶组装成具有催化活性的同源四聚体的多肽可减少培养细胞中乳酸的合成

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5161

Alessandra Stefan, Luca Gentilucci, Francesca Ruffolo, Valentina Rossi, Sofia Sordi, Tingting He, Giuseppina di Stefano, Federica Santino, Maurizio Brigotti, Claudia Scotti, Luisa Iamele, Hugo de Jonge, Fabrizio Dal Piaz, Danilo Rocco Santarcangelo, Alejandro Hochkoeppler

{"title":"Peptides inhibiting the assembly of monomeric human l‐lactate dehydrogenase into catalytically active homotetramer decrease the synthesis of lactate in cultured cells","authors":"Alessandra Stefan, Luca Gentilucci, Francesca Ruffolo, Valentina Rossi, Sofia Sordi, Tingting He, Giuseppina di Stefano, Federica Santino, Maurizio Brigotti, Claudia Scotti, Luisa Iamele, Hugo de Jonge, Fabrizio Dal Piaz, Danilo Rocco Santarcangelo, Alejandro Hochkoeppler","doi":"10.1002/pro.5161","DOIUrl":"https://doi.org/10.1002/pro.5161","url":null,"abstract":"The energetic metabolism of cancer cells relies on a substantial commitment of pyruvate to the catalytic action of lactate‐generating dehydrogenases. This coupling mainly depends on lactate dehydrogenase A (LDH‐A), which is overexpressed in different types of cancers, and therefore represents an appealing therapeutic target. Taking into account that the activity of LDHs is exclusively exerted by their tetrameric forms, it was recently shown that peptides perturbing the monomers‐to‐tetramer assembly inhibit human LDH‐A (hLDH‐A). However, to identify these peptides, tetrameric hLDH‐A was transiently exposed to strongly acidic conditions inducing its dissociation into monomers, which were tested as a target for peptides at low pH. Nevertheless, the availability of native monomeric hLDH‐A would allow performing similar screenings under physiological conditions. Here we report on the unprecedented isolation of recombinant monomeric hLDH‐A at neutral pH, and on its use to identify peptides inhibiting the assembly of the tetrameric enzyme. Remarkably, the GQNGISDL octapeptide, mimicking the 296–303 portion of hLDH‐A C‐terminal region, was observed to effectively inhibit the target enzyme. Moreover, by dissecting the action of this octapeptide, the cGQND cyclic tetrapeptide was found to act as the parental compound. Furthermore, we performed assays using MCF7 and BxPC3 cultured cells, exclusively expressing hLDH‐A and hLDH‐B, respectively. By means of these assays we detected a selective action of linear and cyclic GQND tetrapeptides, inhibiting lactate secretion in MCF7 cells only. Overall, our observations suggest that peptides mimicking the C‐terminal region of hLDH‐A effectively interfere with protein–protein interactions responsible for the assembly of the tetrameric enzyme.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"8 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Substrate selectivity and inhibition of the human lysyl hydroxylase JMJD7 人类赖氨酰羟化酶 JMJD7 的底物选择性和抑制作用

IF 8 3区生物学

Protein Science Pub Date : 2024-09-14 DOI: 10.1002/pro.5162

Nurgül Bilgin, Anthony Tumber, Siddhant Dhingra, Eidarus Salah, Aziza Al‐Salmy, Sandra Pinzón Martín, Yicheng Wang, Christopher J. Schofield, Jasmin Mecinović

{"title":"Substrate selectivity and inhibition of the human lysyl hydroxylase JMJD7","authors":"Nurgül Bilgin, Anthony Tumber, Siddhant Dhingra, Eidarus Salah, Aziza Al‐Salmy, Sandra Pinzón Martín, Yicheng Wang, Christopher J. Schofield, Jasmin Mecinović","doi":"10.1002/pro.5162","DOIUrl":"https://doi.org/10.1002/pro.5162","url":null,"abstract":"Jumonji‐C (JmjC) domain‐containing protein 7 (JMJD7) is a human Fe(II) and 2‐oxoglutarate dependent oxygenase that catalyzes stereospecific C3‐hydroxylation of lysyl‐residues in developmentally regulated GTP binding proteins 1 and 2 (DRG1/2). We report studies exploring a diverse set of lysine derivatives incorporated into the DRG1 peptides as potential human JMJD7 substrates and inhibitors. The results indicate that human JMJD7 has a relatively narrow substrate scope beyond lysine compared to some other JmjC hydroxylases and lysine‐modifying enzymes. The geometrically constrained (E)‐dehydrolysine is an efficient alternative to lysine for JMJD7‐catalyzed C3‐hydroxylation. γ‐Thialysine and γ‐azalysine undergo C3‐hydroxylation, followed by degradation to formylglycine. JMJD7 also catalyzes the S‐oxidation of DRG1‐derived peptides possessing methionine and homomethionine residues in place of lysine. Inhibition assays show that DRG1 variants possessing cysteine/selenocysteine instead of the lysine residue efficiently inhibit JMJD7 via cross‐linking. The overall results inform on the substrate selectivity and inhibition of human JMJD7, which will help enable the rational design of selective small‐molecule and peptidomimetic inhibitors of JMJD7.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"15 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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