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

Contributions from ClpS surface residues in modulating N-terminal peptide binding and their implications for NAAB development. ClpS表面残基在调节N-末端肽结合中的贡献及其对NAAB发育的影响。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad007

Nicholas Callahan, William B Siegall, Christina Bergonzo, John P Marino, Zvi Kelman

{"title":"Contributions from ClpS surface residues in modulating N-terminal peptide binding and their implications for NAAB development.","authors":"Nicholas Callahan, William B Siegall, Christina Bergonzo, John P Marino, Zvi Kelman","doi":"10.1093/protein/gzad007","DOIUrl":"10.1093/protein/gzad007","url":null,"abstract":"Numerous technologies are currently in development for use in next-generation protein sequencing platforms. A notable published approach employs fluorescently-tagged binding proteins to identity the N-terminus of immobilized peptides, in-between rounds of digestion. This approach makes use of N-terminal amino acid binder (NAAB) proteins, which would identify amino acids by chemical and shape complementarity. One source of NAABs is the ClpS protein family, which serve to recruit proteins to bacterial proteosomes based on the identity of the N-terminal amino acid. In this study, a Thermosynechococcus vestitus (also known as Thermosynechococcus elongatus) ClpS2 protein was used as the starting point for direct evolution of an NAAB with affinity and specificity for N-terminal leucine. Enriched variants were analyzed and shown to improve the interaction between the ClpS surface and the peptide chain, without increasing promiscuity. Interestingly, interactions were found that were unanticipated which favor different charged residues located at position 5 from the N-terminus of a target peptide.","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":"10076735","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

Enzyme redesign and genetic code expansion. 酶的重新设计和遗传密码的扩展。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad017

Vaitea Opuu, Thomas Simonson

引用次数: 0

Analysis of conformational stability of interacting residues in protein binding interfaces. 蛋白质结合界面中相互作用残基构象稳定性的分析。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad016

Varun M Chauhan, Robert J Pantazes

引用次数: 0

Strategies for enriching and characterizing proteins with inhibitory properties on the yeast surface. 富集和鉴定酵母表面具有抑制特性的蛋白质的策略。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzac017

Arlinda Rezhdo, Catherine T Lessard, Mariha Islam, James A Van Deventer

{"title":"Strategies for enriching and characterizing proteins with inhibitory properties on the yeast surface.","authors":"Arlinda Rezhdo, Catherine T Lessard, Mariha Islam, James A Van Deventer","doi":"10.1093/protein/gzac017","DOIUrl":"10.1093/protein/gzac017","url":null,"abstract":"Display technologies are powerful tools for discovering binding proteins against a broad range of biological targets. However, it remains challenging to adapt display technologies for the discovery of proteins that inhibit the enzymatic activities of targets. Here, we investigate approaches for discovering and characterizing inhibitory antibodies in yeast display format using a well-defined series of constructs and the target matrix metalloproteinase-9. Three previously reported antibodies were used to create model libraries consisting of inhibitory, non-inhibitory, and non-binding constructs. Conditions that preferentially enrich for inhibitory clones were identified for both magnetic bead-based enrichments and fluorescence-activated cell sorting. Half maximal inhibitory concentration (IC50) was obtained through yeast titration assays. The IC50 of the inhibitory antibody obtained in yeast display format falls within the confidence interval of the IC50 value determined in soluble form. Overall, this study identifies strategies for the discovery and characterization of inhibitory clones directly in yeast display format.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10365883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10244236","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

Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs. 基于物理的方法，以合理设计的螺旋-环-螺旋图案扩展全新TIM桶。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad012

Sina Kordes, Julian Beck, Sooruban Shanmugaratnam, Merle Flecks, Birte Höcker

{"title":"Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs.","authors":"Sina Kordes, Julian Beck, Sooruban Shanmugaratnam, Merle Flecks, Birte Höcker","doi":"10.1093/protein/gzad012","DOIUrl":"10.1093/protein/gzad012","url":null,"abstract":"Computational protein design promises the ability to build tailor-made proteins de novo. While a range of de novo proteins have been constructed so far, the majority of these designs have idealized topologies that lack larger cavities which are necessary for the incorporation of small molecule binding sites or enzymatic functions. One attractive target for enzyme design is the TIM-barrel fold, due to its ubiquity in nature and capability to host versatile functions. With the successful de novo design of a 4-fold symmetric TIM barrel, sTIM11, an idealized, minimalistic scaffold was created. In this work, we attempted to extend this de novo TIM barrel by incorporating a helix-loop-helix motif into its βα-loops by applying a physics-based modular design approach using Rosetta. Further diversification was performed by exploiting the symmetry of the scaffold to integrate two helix-loop-helix motifs into the scaffold. Analysis with AlphaFold2 and biochemical characterization demonstrate the formation of additional α-helical secondary structure elements supporting the successful extension as intended.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2023-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10287313","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

Immortalization and functional screening of natively paired human T cell receptor repertoires. 天然配对人T细胞受体库的永生化和功能筛选。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzab034

Ahmed S Fahad, Cheng-Yu Chung, Sheila N Lopez Acevedo, Nicoleen Boyle, Bharat Madan, Matias F Gutiérrez-González, Rodrigo Matus-Nicodemos, Amy D Laflin, Rukmini R Ladi, John Zhou, Jacy Wolfe, Sian Llewellyn-Lacey, Richard A Koup, Daniel C Douek, Henry H Balfour, David A Price, Brandon J DeKosky

{"title":"Immortalization and functional screening of natively paired human T cell receptor repertoires.","authors":"Ahmed S Fahad, Cheng-Yu Chung, Sheila N Lopez Acevedo, Nicoleen Boyle, Bharat Madan, Matias F Gutiérrez-González, Rodrigo Matus-Nicodemos, Amy D Laflin, Rukmini R Ladi, John Zhou, Jacy Wolfe, Sian Llewellyn-Lacey, Richard A Koup, Daniel C Douek, Henry H Balfour, David A Price, Brandon J DeKosky","doi":"10.1093/protein/gzab034","DOIUrl":"10.1093/protein/gzab034","url":null,"abstract":"Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. We developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale, and to exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen-specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of disease-relevant antigen interactions with human TCRs.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":"35 ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2022-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9005053/pdf/gzab034.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9162629","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

Integrating dynamics into enzyme engineering. 将动力学整合到酶工程中。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac015

Claudèle Lemay-St-Denis, Nicolas Doucet, Joelle N Pelletier

引用次数: 1

Comprehensive mapping of SARS-CoV-2 peptide epitopes for development of a highly sensitive serological test for total and neutralizing antibodies. 全面绘制 SARS-CoV-2 多肽表位图，开发高灵敏度的总抗体和中和抗体血清学检验。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzab033

Garima Kumar, Sarah Sterrett, Lucinda Hall, Edlue Tabengwa, Kazuhito Honjo, Michael Larimer, Randall S Davis, Paul A Goepfert, Benjamin M Larimer

{"title":"Comprehensive mapping of SARS-CoV-2 peptide epitopes for development of a highly sensitive serological test for total and neutralizing antibodies.","authors":"Garima Kumar, Sarah Sterrett, Lucinda Hall, Edlue Tabengwa, Kazuhito Honjo, Michael Larimer, Randall S Davis, Paul A Goepfert, Benjamin M Larimer","doi":"10.1093/protein/gzab033","DOIUrl":"10.1093/protein/gzab033","url":null,"abstract":"Quantification of the anti-SARS-CoV-2 antibody response has proven to be a prominent diagnostic tool during the COVID-19 pandemic. Antibody measurements have aided in the determination of humoral protection following infection or vaccination and will likely be essential for predicting the prevalence of population level immunity over the next several years. Despite widespread use, current tests remain limited in part, because antibody capture is accomplished through the use of complete spike and nucleocapsid proteins that contain significant regions of overlap with common circulating coronaviruses. To address this limitation, a unique epitope display platform utilizing monovalent display and protease-driven capture of peptide epitopes was used to select high affinity peptides. A single round of selection using this strategy with COVID-19 positive patient plasma samples revealed surprising differences and specific patterns in the antigenicity of SARS-CoV-2 proteins, especially the spike protein. Putative epitopes were assayed for specificity with convalescent and control samples, and the individual binding kinetics of peptides were also determined. A subset of prioritized peptides was used to develop an antibody diagnostic assay that showed low cross reactivity while detecting 37% more positive antibody cases than a gold standard FDA EUA test. Finally, a subset of peptides were compared with serum neutralization activity to establish a 2 peptide assay that strongly correlates with neutralization. Together, these data demonstrate a novel phage display method that is capable of comprehensively and rapidly mapping patient viral antibody responses and selecting high affinity public epitopes for the diagnosis of humoral immunity.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":"35 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9005051/pdf/gzab033.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9571501","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

Engineering Pseudomonas aeruginosa arylsulfatase for hydrolysis of α-configured steroid sulfates. 工程铜绿假单胞菌芳基硫酸酯酶水解α-构型类固醇硫酸盐。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac007

Bradley J Stevenson, Andy Pranata, Malcolm D McLeod

{"title":"Engineering Pseudomonas aeruginosa arylsulfatase for hydrolysis of α-configured steroid sulfates.","authors":"Bradley J Stevenson, Andy Pranata, Malcolm D McLeod","doi":"10.1093/protein/gzac007","DOIUrl":"https://doi.org/10.1093/protein/gzac007","url":null,"abstract":"Steroid sulfate esters are important metabolites for anti-doping efforts in sports, pathology and research. Analysis of these metabolites is facilitated by hydrolysis using either acid or enzymatic catalysis. Although enzymatic hydrolysis is preferred for operating at neutral pH, no known enzyme is capable of hydrolyzing all steroid sulfate metabolites. Pseudomonas aeruginosa arylsulfatase (PaS) is ideal for the hydrolysis of β-configured steroid sulfates but like other known class I sulfatases it is inefficient at hydrolyzing α-configured steroid sulfates. We have used directed evolution with liquid chromatography mass spectrometry screening to find variants capable of hydrolyzing a α-configured steroid sulfate: etiocholanolone sulfate (ECS). After targeting two regions of PaS, four residues were identified and optimized to yield a final variant with a total of seven mutations (DRN-PaS) capable of hydrolyzing ECS ~80 times faster than the best PaS variant previously available. This DRN-PaS also shows improved activity for other α-configured steroid sulfates. Simultaneous mutagenesis was essential to obtain DRN-PaS due to complementarity between targeted residues.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":"35 ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2022-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10373470","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

Antibody-mediated delivery of CRISPR-Cas9 ribonucleoproteins in human cells. 抗体介导的 CRISPR-Cas9 核糖核蛋白在人体细胞中的传递。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac011

Stephanie Ubiparipovic, Daniel Christ, Romain Rouet

引用次数: 1