Protein Engineering, Design and Selection最新文献

Supercharged Phosphotriesterase for improved Paraoxon activity 增压磷酸酯酶可提高副氧自由基的活性

Protein Engineering, Design and Selection Pub Date : 2024-09-18 DOI: 10.1093/protein/gzae015

Jacob Kronenberg, Dustin Britton, Leif Halvorsen, Stanley Chu, Maria Jinu Kulapurathazhe, Jason Chen, Ashwitha Lakshmi, P Douglas Renfrew, Richard Bonneau, Jin Kim Montclare

{"title":"Supercharged Phosphotriesterase for improved Paraoxon activity","authors":"Jacob Kronenberg, Dustin Britton, Leif Halvorsen, Stanley Chu, Maria Jinu Kulapurathazhe, Jason Chen, Ashwitha Lakshmi, P Douglas Renfrew, Richard Bonneau, Jin Kim Montclare","doi":"10.1093/protein/gzae015","DOIUrl":"https://doi.org/10.1093/protein/gzae015","url":null,"abstract":"Phosphotriesterases (PTEs) represent a class of enzymes capable of efficient neutralization of organophosphates (OPs), a dangerous class of neurotoxic chemicals. PTEs suffer from low catalytic activity, particularly at higher temperatures, due to low thermostability and low solubility. Supercharging, a protein engineering approach via selective mutation of surface residues to charged residues, has been successfully employed to generate proteins with increased solubility and thermostability by promoting charge–charge repulsion between proteins. We set out to overcome the challenges in improving PTE activity against OPs by employing a computational protein supercharging algorithm in Rosetta. Here, we discover two supercharged PTE variants, one negatively supercharged (with −14 net charge) and one positively supercharged (with +12 net charge) and characterize them for their thermostability and catalytic activity. We find that positively supercharged PTE possesses slight but significant losses in thermostability, which correlates to losses in catalytic efficiency at all temperatures, whereas negatively supercharged PTE possesses increased catalytic activity across 25°C – 55°C while offering similar thermostability characteristic to the parent PTE. The impact of supercharging on catalytic efficiency will inform the design of shelf-stable PTE and criteria for enzyme engineering.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineered FHA domains can bind to a variety of Phosphothreonine-containing peptides 设计的 FHA 结构域可与多种含磷苏氨酸的肽结合

Protein Engineering, Design and Selection Pub Date : 2024-09-13 DOI: 10.1093/protein/gzae014

Srinivas S Thota, Grace L Allen, Ashley K Grahn, Brian K Kay

引用次数: 0

Modular and integrative activity reporters enhance biochemical studies in the yeast ER 模块化和综合活动报告器加强了酵母ER的生化研究

Protein Engineering, Design and Selection Pub Date : 2024-05-02 DOI: 10.1093/protein/gzae008

Samantha G Martinusen, Ethan W Slaton, Sage E Nelson, Marian A Pulgar, Julia T Besu, Cassidy F Simas, Carl A Denard

{"title":"Modular and integrative activity reporters enhance biochemical studies in the yeast ER","authors":"Samantha G Martinusen, Ethan W Slaton, Sage E Nelson, Marian A Pulgar, Julia T Besu, Cassidy F Simas, Carl A Denard","doi":"10.1093/protein/gzae008","DOIUrl":"https://doi.org/10.1093/protein/gzae008","url":null,"abstract":"The yeast endoplasmic reticulum sequestration and screening (YESS) system is a generalizable platform that has become highly useful to investigate post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CLpro), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140833194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protein sequence design on given backbones with deep learning 利用深度学习在给定骨架上设计蛋白质序列

Protein Engineering, Design and Selection Pub Date : 2023-12-29 DOI: 10.1093/protein/gzad024

Yufeng Liu, Haiyan Liu

引用次数: 0

Growing ecosystem of deep learning methods for modeling protein–protein interactions 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

Protein Engineering, Design and Selection Pub Date : 2023-12-15 DOI: 10.1093/protein/gzad023

Julia R Rogers, Gergö Nikolényi, Mohammed AlQuraishi

{"title":"Growing ecosystem of deep learning methods for modeling protein–protein interactions","authors":"Julia R Rogers, Gergö Nikolényi, Mohammed AlQuraishi","doi":"10.1093/protein/gzad023","DOIUrl":"https://doi.org/10.1093/protein/gzad023","url":null,"abstract":"Numerous cellular functions rely on protein–protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep learning has emerged as a promising approach for tackling this problem by exploiting both experimental data and basic biophysical knowledge about protein interactions. Here, we review the growing ecosystem of deep learning methods for modeling protein interactions, highlighting the diversity of these biophysically-informed models and their respective trade-offs. We discuss recent successes in using representation learning to capture complex features pertinent to predicting protein interactions and interaction sites, geometric deep learning to reason over protein structures and predict complex structures, and generative modeling to design de novo protein assemblies. We also outline some of the outstanding challenges and promising new directions. Opportunities abound to discover novel interactions, elucidate their physical mechanisms, and engineer binders to modulate their functions using deep learning and, ultimately, unravel how protein interactions orchestrate complex cellular behaviors.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138690954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cyan fluorescent proteins derived from mNeonGreen. 源自 mNeonGreen 的青色荧光蛋白。

Protein Engineering, Design and Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac004

Landon Zarowny, Damien Clavel, Ryan Johannson, Kévin Duarte, Hadrien Depernet, Jérôme Dupuy, Heather Baker, Alex Brown, Antoine Royant, Robert E Campbell

{"title":"Cyan fluorescent proteins derived from mNeonGreen.","authors":"Landon Zarowny, Damien Clavel, Ryan Johannson, Kévin Duarte, Hadrien Depernet, Jérôme Dupuy, Heather Baker, Alex Brown, Antoine Royant, Robert E Campbell","doi":"10.1093/protein/gzac004","DOIUrl":"10.1093/protein/gzac004","url":null,"abstract":"mNeonGreen, an engineered green fluorescent protein (GFP) derived from lancelet, is one of the most brightly fluorescent homologs of Aequorea victoria jellyfish GFP (avGFP) yet reported. In this work, we investigated whether this bright fluorescence might be retained in homologs of mNeonGreen with modified chromophore structures and altered fluorescent hues. We found mNeonGreen to be generally less tolerant than avGFP to chromophore modification by substitution of the key chromophore-forming tyrosine residue with other aromatic amino acids. However, we were ultimately successful in creating a variant, designated as NeonCyan1, with a tryptophan-derived cyan fluorescent protein (CFP)-type chromophore, and two additional mutants with distinct spectral hues. Structural, computational, and photophysical characterization of NeonCyan1 and its variants provided insight into the factors that control the fluorescence emission color. Though not recommended as replacements for contemporary CFP variants, we demonstrate that NeonCyan1 variants are potentially suitable for live cell imaging applications.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9083105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77444746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism. 内皮素1与人内皮素B型受体分子相互作用的自由能格局:飞投机制。

Protein Engineering, Design and Selection Pub Date : 2019-12-31 DOI: 10.1093/protein/gzz029

Junichi Higo, Kota Kasahara, Mitsuhito Wada, Bhaskar Dasgupta, Narutoshi Kamiya, Tomonori Hayami, Ikuo Fukuda, Yoshifumi Fukunishi, Haruki Nakamura

{"title":"Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.","authors":"Junichi Higo, Kota Kasahara, Mitsuhito Wada, Bhaskar Dasgupta, Narutoshi Kamiya, Tomonori Hayami, Ikuo Fukuda, Yoshifumi Fukunishi, Haruki Nakamura","doi":"10.1093/protein/gzz029","DOIUrl":"10.1093/protein/gzz029","url":null,"abstract":"The free-energy landscape of interaction between a medium-sized peptide, endothelin 1 (ET1), and its receptor, human endothelin type B receptor (hETB), was computed using multidimensional virtual-system coupled molecular dynamics, which controls the system's motions by introducing multiple reaction coordinates. The hETB embedded in lipid bilayer was immersed in explicit solvent. All molecules were expressed as all-atom models. The resultant free-energy landscape had five ranges with decreasing ET1-hETB distance: completely dissociative, outside-gate, gate, binding pocket, and genuine-bound ranges. In the completely dissociative range, no ET1-hETB interaction appeared. In the outside-gate range, an ET1-hETB attractive interaction was the fly-casting mechanism. In the gate range, the ET1 orientational variety decreased rapidly. In the binding pocket range, ET1 was in a narrow pathway with a steep free-energy slope. In the genuine-bound range, ET1 was in a stable free-energy basin. A G-protein-coupled receptor (GPCR) might capture its ligand from a distant place.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzz029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83595146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Synaptic vesicle mimics affect the aggregation of wild-type and A53T α-synuclein variants differently albeit similar membrane affinity. 突触小泡模拟物对野生型和 A53T α-突触核蛋白变体的聚集有不同的影响，尽管它们的膜亲和力相似。

Protein Engineering, Design and Selection Pub Date : 2019-12-13 DOI: 10.1093/protein/gzz021

Sandra Rocha, Ranjeet Kumar, Istvan Horvath, Pernilla Wittung-Stafshede

{"title":"Synaptic vesicle mimics affect the aggregation of wild-type and A53T α-synuclein variants differently albeit similar membrane affinity.","authors":"Sandra Rocha, Ranjeet Kumar, Istvan Horvath, Pernilla Wittung-Stafshede","doi":"10.1093/protein/gzz021","DOIUrl":"10.1093/protein/gzz021","url":null,"abstract":"α-Synuclein misfolding results in the accumulation of amyloid fibrils in Parkinson's disease. Missense protein mutations (e.g. A53T) have been linked to early onset disease. Although α-synuclein interacts with synaptic vesicles in the brain, it is not clear what role they play in the protein aggregation process. Here, we compare the effect of small unilamellar vesicles (lipid composition similar to synaptic vesicles) on wild-type (WT) and A53T α-synuclein aggregation. Using biophysical techniques, we reveal that binding affinity to the vesicles is similar for the two proteins, and both interact with the helix long axis parallel to the membrane surface. Still, the vesicles affect the aggregation of the variants differently: effects on secondary processes such as fragmentation dominate for WT, whereas for A53T, fibril elongation is mostly affected. We speculate that vesicle interactions with aggregate intermediate species, in addition to monomer binding, vary between WT and A53T, resulting in different consequences for amyloid formation.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91516466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantifying the nativeness of antibody sequences using long short-term memory networks 利用长短期记忆网络定量抗体序列的原生性

Protein Engineering, Design and Selection Pub Date : 2019-07-01 DOI: 10.1093/protein/gzz031

A. Wollacott, Chonghua Xue, Qiuyuan Qin, June Hua, T. Bohnuud, Karthik Viswanathan, V. Kolachalama

引用次数: 15

Information theoretic measures for quantifying sequence–ensemble relationships of intrinsically disordered proteins 定量内在无序蛋白质序列集合关系的信息论方法

Protein Engineering, Design and Selection Pub Date : 2019-04-01 DOI: 10.1093/protein/gzz014

Megan C. Cohan, Kiersten M. Ruff, R. Pappu

引用次数: 18