Protein Engineering Design & Selection最新文献_第7页

Protein-based lateral flow assays for COVID-19 detection. 用于新冠肺炎检测的基于蛋白质的横向流动测定。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab010

Farbod Mahmoudinobar, Dustin Britton, Jin Kim Montclare

引用次数: 0

Breakthroughs in computational design methods open up new frontiers for de novo protein engineering. 计算设计方法的突破为从头开始的蛋白质工程开辟了新的领域。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab007

Ben A Meinen, Christopher D Bahl

引用次数: 9

Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase. 来源于海洋热托加二氨基二聚物脱羧酶的耐热D-氨基酸脱羧酶。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab016

Antonija Marjanovic, Carlos J Ramírez-Palacios, Marcelo F Masman, Jeroen Drenth, Marleen Otzen, Siewert-Jan Marrink, Dick B Janssen

{"title":"Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase.","authors":"Antonija Marjanovic, Carlos J Ramírez-Palacios, Marcelo F Masman, Jeroen Drenth, Marleen Otzen, Siewert-Jan Marrink, Dick B Janssen","doi":"10.1093/protein/gzab016","DOIUrl":"10.1093/protein/gzab016","url":null,"abstract":"Diaminopimelate decarboxylases (DAPDCs) are highly selective enzymes that catalyze the common final step in different lysine biosynthetic pathways, i.e. the conversion of meso-diaminopimelate (DAP) to L-lysine. We examined the modification of the substrate specificity of the thermostable decarboxylase from Thermotoga maritima with the aim to introduce activity with 2-aminopimelic acid (2-APA) since its decarboxylation leads to 6-aminocaproic acid (6-ACA), a building block for the synthesis of nylon-6. Structure-based mutagenesis of the distal carboxylate binding site resulted in a set of enzyme variants with new activities toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily acted as a 2-APA decarboxylase. We next used computational modeling to explain the observed shift in catalytic activities of the mutants. The results suggest that predictive computational protocols can support the redesign of the catalytic properties of this class of decarboxylating PLP-dependent enzymes.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8277567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39181574","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: 3

Optimization of multi-site nicking mutagenesis for generation of large, user-defined combinatorial libraries. 优化多位点缺口诱变以生成大型用户定义的组合文库。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab017

Monica B Kirby, Angélica V Medina-Cucurella, Zachary T Baumer, Timothy A Whitehead

{"title":"Optimization of multi-site nicking mutagenesis for generation of large, user-defined combinatorial libraries.","authors":"Monica B Kirby, Angélica V Medina-Cucurella, Zachary T Baumer, Timothy A Whitehead","doi":"10.1093/protein/gzab017","DOIUrl":"10.1093/protein/gzab017","url":null,"abstract":"Generating combinatorial libraries of specific sets of mutations are essential for addressing protein engineering questions involving contingency in molecular evolution, epistatic relationships between mutations, as well as functional antibody and enzyme engineering. Here we present optimization of a combinatorial mutagenesis method involving template-based nicking mutagenesis, which allows for the generation of libraries with >99% coverage for tens of thousands of user-defined variants. The non-optimized method resulted in low library coverage, which could be rationalized by a model of oligonucleotide annealing bias resulting from the nucleotide mismatch free-energy difference between mutagenic oligo and template. The optimized method mitigated this thermodynamic bias using longer primer sets and faster annealing conditions. Our updated method, applied to two antibody fragments, delivered between 99.0% (32451/32768 library members) to >99.9% coverage (32757/32768) for our desired libraries in 2 days and at an approximate 140-fold sequencing depth of coverage.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8502461/pdf/gzab017.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39272019","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: 3

Linking thermodynamics and measurements of protein stability. 把热力学和蛋白质稳定性的测量联系起来。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab002

Kresten Lindorff-Larsen, Kaare Teilum

引用次数: 9

Rational engineering of an erythropoietin fusion protein to treat hypoxia. 合理设计促红细胞生成素融合蛋白治疗缺氧。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab025

Jungmin Lee, Andyna Vernet, Nathalie G Gruber, Kasia M Kready, Devin R Burrill, Jeffrey C Way, Pamela A Silver

{"title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia.","authors":"Jungmin Lee, Andyna Vernet, Nathalie G Gruber, Kasia M Kready, Devin R Burrill, Jeffrey C Way, Pamela A Silver","doi":"10.1093/protein/gzab025","DOIUrl":"https://doi.org/10.1093/protein/gzab025","url":null,"abstract":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10-14 M, allowing an estimate of the number of receptor-ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39835737","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: 1

High-efficacy, high-manufacturability human VH domain antibody therapeutics from transgenic sources. 来自转基因来源的高效、高可制造性人VH结构域抗体疗法。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab012

Kasandra Bélanger, Jamshid Tanha

{"title":"High-efficacy, high-manufacturability human VH domain antibody therapeutics from transgenic sources.","authors":"Kasandra Bélanger, Jamshid Tanha","doi":"10.1093/protein/gzab012","DOIUrl":"https://doi.org/10.1093/protein/gzab012","url":null,"abstract":"Interest in single-domain antibodies (sdAbs) stems from their unique structural/pronounced, hence therapeutically desirable, features. From the outset-as therapeutic modalities-human antibody heavy chain variable domains (VHs) attracted a particular attention compared with 'naturally-occurring' camelid and shark heavy-chain-only antibody variable domains (VHHs and VNARs, respectively) due to their perceived lack of immunogenicity. However, they have not quite lived up to their initial promise as the VH hits, primarily mined from synthetic VH phage display libraries, have too often been plagued with aggregation tendencies, low solubility and low affinity. Largely unexplored, synthetic camelized human VH display libraries appeared to have remediated the aggregation problem, but the low affinity of the VH hits still persisted, requiring undertaking additional, laborious affinity maturation steps to render VHs therapeutically feasible. A wholesome resolution has recently emerged with the development of non-canonical transgenic rodent antibody discovery platforms that appear to facilely and profusely generate high affinity, high solubility and aggregation-resistant human VHs.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzab012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38914156","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: 2

Engineering stable carbonic anhydrases for CO2 capture: a critical review. 工程稳定的碳酸酐酶用于二氧化碳捕获:一个重要的回顾。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab021

Mirfath Sultana Mesbahuddin, Aravindhan Ganesan, Subha Kalyaanamoorthy

引用次数: 7

A versatile assay platform for enzymatic poly(ethylene-terephthalate) degradation. 一个通用的酶促聚对苯二甲酸乙酯降解测定平台。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab022

Sebastian Weigert, Andreas Gagsteiger, Teresa Menzel, Birte Höcker

引用次数: 3

Computational design and experimental optimization of protein binders with prospects for biomedical applications. 具有生物医学应用前景的蛋白质结合物的计算设计和实验优化。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab020

Alessandro Bonadio, Julia M Shifman

引用次数: 7