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

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

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":null,"pages":null},"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

Modifying pH-sensitive PCSK9/LDLR interactions as a strategy to enhance hepatic cell uptake of low-density lipoprotein cholesterol (LDL-C). 改变ph敏感的PCSK9/LDLR相互作用作为增强肝细胞对低密度脂蛋白胆固醇(LDL-C)摄取的策略

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzab032

Lital Ben-Naim, Isam Khalaila, Niv Papo

引用次数: 1

Affinity maturation of TCR-like antibodies using phage display guided by structural modeling. 在结构建模指导下利用噬菌体展示技术实现 TCR 类抗体的亲和成熟。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac005

Rahel Frick, Lene S Høydahl, Ina Hodnebrug, Erik S Vik, Bjørn Dalhus, Ludvig M Sollid, Jeffrey J Gray, Inger Sandlie, Geir Åge Løset

引用次数: 0

Reducing substrate inhibition of malate dehydrogenase from Geobacillus stearothermophilus by C-terminal truncation. c端截断法降低嗜热硬脂地杆菌苹果酸脱氢酶的底物抑制作用。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac008

Yuya Shimozawa, Hinano Matsuhisa, Tsutomu Nakamura, Tomoki Himiyama, Yoshiaki Nishiya

{"title":"Reducing substrate inhibition of malate dehydrogenase from Geobacillus stearothermophilus by C-terminal truncation.","authors":"Yuya Shimozawa, Hinano Matsuhisa, Tsutomu Nakamura, Tomoki Himiyama, Yoshiaki Nishiya","doi":"10.1093/protein/gzac008","DOIUrl":"https://doi.org/10.1093/protein/gzac008","url":null,"abstract":"Malate dehydrogenase (MDH) catalyzes the reduction of oxaloacetate to L-malate. Geobacillus stearothermophilus MDH (gs-MDH) is used as a diagnostic reagent; however, gs-MDH is robustly inhibited at high substrate concentrations, which limits its reaction rate. Here, we reduced substrate inhibition of gs-MDH by deleting its C-terminal residues. Computational analysis showed that C-terminal residues regulate the position of the active site loop. C-terminal deletions of gs-MDH successfully increased Ki values by 5- to 8-fold with maintained thermal stability (>90% of the wild-type enzyme), although kcat/Km values were decreased by <2-fold. The structure of the mutant showed a shift in the location of the active site loop and a decrease in its volume, suggesting that substrate inhibition was reduced by eliminating the putative substrate binding site causing inhibition. Our results provide an effective method to reduce substrate inhibition of the enzyme without loss of other parameters, including binding and stability constants.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2022-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10384924","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

Protein engineering approach to enhance activity assays of mono-ADP-ribosyltransferases through proximity. 通过蛋白质工程学方法增强单-ADP-核糖转移酶的活性检测。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac006

Albert Galera-Prat, Juho Alaviuhkola, Heli I Alanen, Lari Lehtiö

引用次数: 0

Correction to: Protease-stable DARPins as promising oral therapeutics. 更正:蛋白酶稳定的DARPins作为有前途的口服治疗药物。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac003

Rudo A Simeon, Yu Zeng, Vikas Chonira, Andrea Martinez Aguirre, Mauricio Lasagna, Marko Baloh, Joseph A Sorg, Cecilia Tommos, Zhilei Chen

引用次数: 0

Bispecific antibodies-effects of point mutations on CH3-CH3 interface stability. 点突变对 CH3-CH3 界面稳定性的影响。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac012

Nancy D Pomarici, Monica L Fernández-Quintero, Patrick K Quoika, Franz Waibl, Alexander Bujotzek, Guy Georges, Klaus R Liedl

{"title":"Bispecific antibodies-effects of point mutations on CH3-CH3 interface stability.","authors":"Nancy D Pomarici, Monica L Fernández-Quintero, Patrick K Quoika, Franz Waibl, Alexander Bujotzek, Guy Georges, Klaus R Liedl","doi":"10.1093/protein/gzac012","DOIUrl":"10.1093/protein/gzac012","url":null,"abstract":"A new format of therapeutic proteins is bispecific antibodies, in which two different heavy chains heterodimerize to obtain two different binding sites. Therefore, it is crucial to understand and optimize the third constant domain (CH3-CH3) interface to favor heterodimerization over homodimerization, and to preserve the physicochemical properties, as thermal stability. Here, we use molecular dynamics simulations to investigate the dissociation process of 19 CH3-CH3 crystal structures that differ from each other in few point mutations. We describe the dissociation of the dimeric interface as a two-steps mechanism. As confirmed by a Markov state model, apart from the bound and the dissociated state, we observe an additional intermediate state, which corresponds to an encounter complex. The analysis of the interdomain contacts reveals key residues that stabilize the interface. We expect that our results will improve the understanding of the CH3-CH3 interface interactions and thus advance the developability and design of new antibodies formats.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9741699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10353046","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

Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning. 通过蛋白质核心重新设计和深度突变扫描稳定 SARS-CoV-2 受体结合域。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac002

Alison C Leonard, Jonathan J Weinstein, Paul J Steiner, Annette H Erbse, Sarel J Fleishman, Timothy A Whitehead

{"title":"Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning.","authors":"Alison C Leonard, Jonathan J Weinstein, Paul J Steiner, Annette H Erbse, Sarel J Fleishman, Timothy A Whitehead","doi":"10.1093/protein/gzac002","DOIUrl":"10.1093/protein/gzac002","url":null,"abstract":"Stabilizing antigenic proteins as vaccine immunogens or diagnostic reagents is a stringent case of protein engineering and design as the exterior surface must maintain recognition by receptor(s) and antigen-specific antibodies at multiple distinct epitopes. This is a challenge, as stability enhancing mutations must be focused on the protein core, whereas successful computational stabilization algorithms typically select mutations at solvent-facing positions. In this study, we report the stabilization of SARS-CoV-2 Wuhan Hu-1 Spike receptor binding domain using a combination of deep mutational scanning and computational design, including the FuncLib algorithm. Our most successful design encodes I358F, Y365W, T430I, and I513L receptor binding domain mutations, maintains recognition by the receptor ACE2 and a panel of different anti-receptor binding domain monoclonal antibodies, is between 1 and 2°C more thermally stable than the original receptor binding domain using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original receptor binding domain. Our approach could be applied to the computational stabilization of a wide range of proteins without requiring detailed knowledge of active sites or binding epitopes. We envision that this strategy may be particularly powerful for cases when there are multiple or unknown binding sites.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9077414/pdf/gzac002.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9166459","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