Protein Engineering Design & Selection最新文献_第5页

Rational design of selective bispecific EPO-R/CD131 agonists. 选择性双特异性EPO-R/CD131激动剂的合理设计。

IF 3.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2025-01-10 DOI: 10.1093/protein/gzaf013

Kailyn E Doiron, Jeffrey C Way, Pamela A Silver

引用次数: 0

Design of a ligand-dependent fluorescent biosensor, based on an engineered lipocalin (anticalin), for the sensitive detection of the Alzheimer β-amyloid peptide. 基于工程脂钙蛋白（antialin）的配体依赖性荧光生物传感器的设计，用于阿尔茨海默病β-淀粉样肽的敏感检测。

IF 3.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2025-01-10 DOI: 10.1093/protein/gzaf012

Anna Feuerbach, Arne Skerra

引用次数: 0

Optimized single-cell gates for yeast display screening. 优化单细胞门酵母显示筛选。

IF 3.5 4区生物学

Protein Engineering Design & Selection Pub Date : 2025-01-10 DOI: 10.1093/protein/gzae018

Xiaoli Pan, Matheus O de Souza, Francisco M Figueiras, Aric Huang, Bailey B Banach, Jacy R Wolfe, Azady Pirhanov, Bharat Madan, Brandon J DeKosky

引用次数: 0

Enhancing the Thermostability and solubility of a single-domain catalytic antibody. 提高单结构域催化抗体的热稳定性和溶解度。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2025-01-10 DOI: 10.1093/protein/gzaf002

Yunhang Cui, Xuchen Zhou, Sainan Li, Jingfei Chen, Mingming Qin, Liaoyuan An, Yefei Wang, Lishan Yao

{"title":"Enhancing the Thermostability and solubility of a single-domain catalytic antibody.","authors":"Yunhang Cui, Xuchen Zhou, Sainan Li, Jingfei Chen, Mingming Qin, Liaoyuan An, Yefei Wang, Lishan Yao","doi":"10.1093/protein/gzaf002","DOIUrl":"10.1093/protein/gzaf002","url":null,"abstract":"Catalytic antibodies have the ability to bind to and degrade antigens, offering a significant potential for therapeutic use. The light chain of an antibody, UA15-L, can cleave the peptide bond of Helicobacter pylori urease, thus inhibiting the spread of the bacteria. However, the variable domain of UA15-L has a poor thermostability and solubility. In this study, we employed a combined computational and experimental approach to enhance the protein's stability and solubility properties. The protein unfolding hotspots were initially identified using molecular dynamics simulations. Following this, a disulfide bond was designed in an unfolding hotspot to stabilize the protein. Subsequently, protein solubility was enhanced with the assistance of computational methods by introducing polar or charged residues on the protein surface. The combination of multiple mutations resulted in UA15-L variable domain variants with improved thermostability, solubility, expression, and enhanced activity at elevated temperatures. These variants represent promising candidates for further engineering of catalytic activity and specificity.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442797","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

Linker minimization and characterization of Fc-fused interleukin-17A for increased in vivo half-life. fc融合白细胞介素- 17a体内半衰期增加的连接子最小化和表征。

IF 3.5 4区生物学

Protein Engineering Design & Selection Pub Date : 2025-01-10 DOI: 10.1093/protein/gzaf009

Qiu C Wu, Jungmin Lee, Aishwarya Swaminathan, Ashley Winward, Yung Hwang, Merav Socolovsky, Jeffrey C Way, Allon M Klein

{"title":"Linker minimization and characterization of Fc-fused interleukin-17A for increased in vivo half-life.","authors":"Qiu C Wu, Jungmin Lee, Aishwarya Swaminathan, Ashley Winward, Yung Hwang, Merav Socolovsky, Jeffrey C Way, Allon M Klein","doi":"10.1093/protein/gzaf009","DOIUrl":"10.1093/protein/gzaf009","url":null,"abstract":"Interleukin-17A (IL-17A) is a cytokine involved in pro-inflammatory responses and tissue regeneration, with potential therapeutic and research applications. However, its short serum half-life limits in vivo use. Here, we report the systematic design of fc-IL-17A fusion proteins for extended half-life. Through computational analysis of 25 design variants using AlphaFold, we found that IL-17A's native N-terminal unstructured region functions as a crucial natural linker that cannot be effectively replaced by artificial sequences. We therefore generated mouse and human fc-IL-17A variants using direct N-terminal fusion without additional linkers. The resulting proteins retain IL-17A's ability to stimulate IL-6 production and erythroid cell growth. Pharmacokinetic analysis confirms that the Fc fusion increases the serum half-life in mice from 1.5 to 13 hours post-subcutaneous injection. This enables tractable experimental use of IL-17A in vivo for studying its role in inflammation and tissue repair. We further perform pharmacokinetics and pharmacodynamics modeling and propose a dosing regimen with reduced frequency of injection for delivering comparable IL-17A activity. This work provides a valuable pharmacological tool for injectable delivery, enabling investigation of IL-17A's biological functions in homeostasis and disease and exploration of its therapeutic potential in tissue regeneration.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13396947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585630","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

Improving the production and stability of nanobodies. 提高纳米体的制备和稳定性。

IF 3.5 4区生物学

Protein Engineering Design & Selection Pub Date : 2025-01-10 DOI: 10.1093/protein/gzaf010

Alba Pejenaute, Laura Gálvez-Larrosa, Cristina M Segovia, Pablo Herrero-Alfonso, David Fernández-Ramos, Fernando Lopitz-Otsoa, Óscar Millet, Francesca Peccati, Gonzalo Jiménez-Osés, Gabriel Ortega-Quintanilla

{"title":"Improving the production and stability of nanobodies.","authors":"Alba Pejenaute, Laura Gálvez-Larrosa, Cristina M Segovia, Pablo Herrero-Alfonso, David Fernández-Ramos, Fernando Lopitz-Otsoa, Óscar Millet, Francesca Peccati, Gonzalo Jiménez-Osés, Gabriel Ortega-Quintanilla","doi":"10.1093/protein/gzaf010","DOIUrl":"10.1093/protein/gzaf010","url":null,"abstract":"Nanobodies offer unique advantages in biomedical and biotechnological applications due to their smaller size, ability to bind challenging epitopes, and affordable production using recombinant technology. However, challenges in large-scale production, stability, and solubility limit their widespread use. To address this, we use artificial intelligence tools to optimize the scaffold region of nanobodies. We apply our approach to four nanobodies against clinically relevant targets: the cytokine tumor necrosis factor alpha, the chemotherapeutic drug methotrexate, the pancreatic biomarker amylase, and the placental hormone chorionic gonadotropin. For all the nanobodies tested, we improve stability, production, and intracellular stability while maintaining antigen-binding affinity. Our results thus demonstrate the potential for using AI-driven protein engineering to enhance the properties of nanobodies, offering insights into the interplay between stability, solubility, and antigen binding. Given the high conservation of the scaffold, we propose some mutations that could directly transfer to other nanobodies, providing an easy-to-implement, generalizable engineering strategy.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12510460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126207","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

A his-to-Gln mutation in catechol 2,3-dioxygenase catalyzes 2,3-dihydroxybenzoic acid cleavage by an intradiol pathway. 邻苯二酚2,3-双加氧酶His-to-Gln突变通过醇内途径催化2,3-二羟基苯甲酸裂解。

IF 3.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2025-01-10 DOI: 10.1093/protein/gzaf015

Deepti Singh, Gurunath Ramanathan

{"title":"A his-to-Gln mutation in catechol 2,3-dioxygenase catalyzes 2,3-dihydroxybenzoic acid cleavage by an intradiol pathway.","authors":"Deepti Singh, Gurunath Ramanathan","doi":"10.1093/protein/gzaf015","DOIUrl":"10.1093/protein/gzaf015","url":null,"abstract":"Catechol 2,3-dioxygenases (C23DO) catalyze extradiol cleavage of catechol in aromatic hydrocarbon degradation pathways. Here, we report mutagenesis studies on two C23DO isoenzymes from Diaphorobacter sp. strain DS2, aimed at elucidating the mechanism. Docking studies with various substrates on the two isozymes identified critical active-site residues and second-sphere interactions contributing to substrate binding and catalysis. These modeling studies identified eight site-directed mutants, which were designed, produced, and kinetically characterized. Substitution of histidine-to-glutamine (His-to-Gln) (H206Q64/H200Q68) activates the previously inert substrate 2,3-dihydroxybenzoic acid (2,3-DHBA), allowing its intradiol cleavage under strong acidic conditions. The mutants retained ~20-30% of their native activity toward catechol but exhibited a mechanistic switch from Fe2+-assisted extradiol to Fe3+-mediated intradiol cleavage with 2,3-DHBA. These results highlight the catalytic adaptability of acid-base residues and demonstrate how subtle second-sphere mutation can alter dioxygenase regiospecificity, providing new insights for biocatalyst engineering and environmental bioremediation.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145716710","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

Correction to: Variable heavy-variable light domain and Fab-arm CrossMabs with charged residue exchanges to enforce correct light chain assembly. 更正为可变重型-可变轻型结构域和带电荷残基交换的 Fab 臂 CrossMabs，以执行正确的轻链组装。

IF 3.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae017

引用次数: 0

Correction to: Growing ecosystem of deep learning methods for modeling protein-protein interactions. 更正：用于蛋白质-蛋白质相互作用建模的深度学习方法生态系统日益壮大。

IF 3.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae016

引用次数: 0

Computational methods for protein design. 蛋白质设计计算方法

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae011