Protein Engineering Design & Selection最新文献_第2页

Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. 交互式计算和实验方法提高了基于外质结合蛋白的尼古丁生物传感器在生物流体中测量的灵敏度。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae003

Nandan Haloi, Shan Huang, Aaron L Nichols, Eve J Fine, Nicholas J Friesenhahn, Christopher B Marotta, Dennis A Dougherty, Erik Lindahl, Rebecca J Howard, Stephen L Mayo, Henry A Lester

{"title":"Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids.","authors":"Nandan Haloi, Shan Huang, Aaron L Nichols, Eve J Fine, Nicholas J Friesenhahn, Christopher B Marotta, Dennis A Dougherty, Erik Lindahl, Rebecca J Howard, Stephen L Mayo, Henry A Lester","doi":"10.1093/protein/gzae003","DOIUrl":"10.1093/protein/gzae003","url":null,"abstract":"We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for ∆F/F0vs [nicotine] (δ-slope, 2.7 μM-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the 'candle snuffer' mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10896302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139673699","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

TIMED-Design: flexible and accessible protein sequence design with convolutional neural networks. TIMED-Design：利用卷积神经网络设计灵活易用的蛋白质序列。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae002

Leonardo V Castorina, Suleyman Mert Ünal, Kartic Subr, Christopher W Wood

{"title":"TIMED-Design: flexible and accessible protein sequence design with convolutional neural networks.","authors":"Leonardo V Castorina, Suleyman Mert Ünal, Kartic Subr, Christopher W Wood","doi":"10.1093/protein/gzae002","DOIUrl":"10.1093/protein/gzae002","url":null,"abstract":"Sequence design is a crucial step in the process of designing or engineering proteins. Traditionally, physics-based methods have been used to solve for optimal sequences, with the main disadvantages being that they are computationally intensive for the end user. Deep learning-based methods offer an attractive alternative, outperforming physics-based methods at a significantly lower computational cost. In this paper, we explore the application of Convolutional Neural Networks (CNNs) for sequence design. We describe the development and benchmarking of a range of networks, as well as reimplementations of previously described CNNs. We demonstrate the flexibility of representing proteins in a three-dimensional voxel grid by encoding additional design constraints into the input data. Finally, we describe TIMED-Design, a web application and command line tool for exploring and applying the models described in this paper. The user interface will be available at the URL: https://pragmaticproteindesign.bio.ed.ac.uk/timed. The source code for TIMED-Design is available at https://github.com/wells-wood-research/timed-design.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139577130","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: De novo design of a polycarbonate hydrolase. 更正：聚碳酸酯水解酶的全新设计。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae001

引用次数: 0

Improving plastic degrading enzymes via directed evolution. 通过定向进化改进塑料降解酶。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae009

Yvonne Joho, Vanessa Vongsouthi, Chloe Gomez, Joachim S Larsen, Albert Ardevol, Colin J Jackson

引用次数: 0

The shortest path method (SPM) webserver for computational enzyme design. 用于计算酶设计的最短路径法（SPM）网络服务器。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2024-01-29 DOI: 10.1093/protein/gzae005

Guillem Casadevall, Jordi Casadevall, Cristina Duran, Sílvia Osuna

{"title":"The shortest path method (SPM) webserver for computational enzyme design.","authors":"Guillem Casadevall, Jordi Casadevall, Cristina Duran, Sílvia Osuna","doi":"10.1093/protein/gzae005","DOIUrl":"10.1093/protein/gzae005","url":null,"abstract":"SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally-relevant positions of a given enzyme structure and dynamics. The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. We provide in this publication information on how to generate the files for SPM construction even for non-expert users and discuss the most relevant parameters that can be modified. The tool is extremely fast (it takes less than one minute per job), thus allowing the rapid identification of distal positions connected to the active site pocket of the enzyme. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community. SPMweb is freely available for academia at http://spmosuna.com/.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140023291","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: Engineering the enzyme toolbox to tailor glycosylation in small molecule natural products and protein biologics. 修正:设计酶工具箱来定制小分子天然产物和蛋白质生物制剂中的糖基化。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad010

引用次数: 0

Enzyme design pioneer Steve Mayo: I was trying to capture the fundamental physics of the problem as a way to elucidate mechanisms. 酶设计先驱史蒂夫·梅奥:我试图抓住这个问题的基本物理原理，作为一种阐明机制的方法。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad004

Roberto A Chica, Brett M Garabedian

引用次数: 0

Benchmarking TriadAb using targets from the second antibody modeling assessment. 使用来自第二抗体建模评估的靶标对TriadAb进行基准测试。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad013

Frederick S Lee, Amos G Anderson, Barry D Olafson

引用次数: 0

Enhancing the activity of a monomeric alcohol dehydrogenase for site-specific applications by site-directed mutagenesis. 通过位点定向诱变提高单体醇脱氢酶的活性，用于位点特异性应用。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad006

Arabella Essert, Kathrin Castiglione

{"title":"Enhancing the activity of a monomeric alcohol dehydrogenase for site-specific applications by site-directed mutagenesis.","authors":"Arabella Essert, Kathrin Castiglione","doi":"10.1093/protein/gzad006","DOIUrl":"https://doi.org/10.1093/protein/gzad006","url":null,"abstract":"Gene fusion or co-immobilization are key tools to optimize enzymatic reaction cascades by modulating catalytic features, stability and applicability. Achieving a defined spatial organization between biocatalysts by site-specific applications is complicated by the involvement of oligomeric enzymes. It can lead to activity losses due to disturbances of the quaternary structures and difficulties in stoichiometric control. Thus, a toolkit of active and robust monomeric enzymes is desirable for such applications. In this study, we engineered one of the rare examples of monomeric alcohol dehydrogenases for improved catalytic characteristics by site-directed mutagenesis. The enzyme from the hyperthermophilic archaeon Thermococcus kodakarensis naturally exhibits high thermostability and a broad substrate spectrum, but only low activity at moderate temperatures. The best enzyme variants showed an approximately 5-fold (2-heptanol) and 9-fold (3-heptanol) higher activity while preserving enantioselectivity and good thermodynamic stability. These variants also exhibited modified kinetic characteristics regarding regioselectivity, pH dependence and activation by NaCl.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":"36 ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2023-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10126899","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

Yeast biopanning against site-specific phosphorylations in tau. 针对 tau 中特异位点磷酸化的酵母生物扫描。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad005

Monika Arbaciauskaite, Azady Pirhanov, Erik Ammermann, Yu Lei, Yong Ku Cho

{"title":"Yeast biopanning against site-specific phosphorylations in tau.","authors":"Monika Arbaciauskaite, Azady Pirhanov, Erik Ammermann, Yu Lei, Yong Ku Cho","doi":"10.1093/protein/gzad005","DOIUrl":"10.1093/protein/gzad005","url":null,"abstract":"The detection of site-specific phosphorylation in the microtubule-associated protein tau is emerging as a means to diagnose and monitor the progression of Alzheimer's Disease and other neurodegenerative diseases. However, there is a lack of phospho-specific monoclonal antibodies and limited validation of their binding specificity. Here, we report a novel approach using yeast biopanning against synthetic peptides containing site-specific phosphorylations. Using yeast cells displaying a previously validated phospho-tau (p-tau) single-chain variable region fragment (scFv), we show selective yeast cell binding based on single amino acid phosphorylation on the antigen. We identify conditions that allow phospho-specific biopanning using scFvs with a wide range of affinities (KD = 0.2 to 60 nM). Finally, we demonstrate the capability of screening large libraries by performing biopanning in 6-well plates. These results show that biopanning can effectively select yeast cells based on phospho-site specific antibody binding, opening doors for the facile identification of high-quality monoclonal antibodies.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":"36 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10281017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9707844","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