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

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

Engineering the enzyme toolbox to tailor glycosylation in small molecule natural products and protein biologics. 设计酶工具箱，以定制小分子天然产物和蛋白质生物制品的糖基化。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzac010

Sara Ouadhi, Dulce María Valdez López, F Ifthiha Mohideen, David H Kwan

{"title":"Engineering the enzyme toolbox to tailor glycosylation in small molecule natural products and protein biologics.","authors":"Sara Ouadhi, Dulce María Valdez López, F Ifthiha Mohideen, David H Kwan","doi":"10.1093/protein/gzac010","DOIUrl":"https://doi.org/10.1093/protein/gzac010","url":null,"abstract":"Many glycosylated small molecule natural products and glycoprotein biologics are important in a broad range of therapeutic and industrial applications. The sugar moieties that decorate these compounds often show a profound impact on their biological functions, thus biocatalytic methods for controlling their glycosylation are valuable. Enzymes from nature are useful tools to tailor bioproduct glycosylation but these sometimes have limitations in their catalytic efficiency, substrate specificity, regiospecificity, stereospecificity, or stability. Enzyme engineering strategies such as directed evolution or semi-rational and rational design have addressed some of the challenges presented by these limitations. In this review, we highlight some of the recent research on engineering enzymes to tailor the glycosylation of small molecule natural products (including alkaloids, terpenoids, polyketides, and peptides), as well as the glycosylation of protein biologics (including hormones, enzyme-replacement therapies, enzyme inhibitors, vaccines, and antibodies).","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10592744","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

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

Effect of alanine versus serine at position 88 of human transthyretin mutants on the protein stability. 人转甲状腺素突变体88位丙氨酸和丝氨酸对蛋白质稳定性的影响。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzad001

Kyung-Hoon Lee, Krzysztof Kuczera

{"title":"Effect of alanine versus serine at position 88 of human transthyretin mutants on the protein stability.","authors":"Kyung-Hoon Lee, Krzysztof Kuczera","doi":"10.1093/protein/gzad001","DOIUrl":"https://doi.org/10.1093/protein/gzad001","url":null,"abstract":"Human transthyretin (TTR) is a homo-tetrameric plasma protein associated with a high percentage of β-sheet forming amyloid fibrils. It accumulates in tissues or extracellular matrices to cause amyloid diseases. Free energy simulations with thermodynamic integration based on all-atom molecular dynamics simulations have been carried out to analyze the effects of the His88 → Ala and Ser mutations on the stability of human TTR. The calculated free energy change differences (ΔΔG) caused by the His88 → Ala and His88 → Ser mutations are -1.84 ± 0.86 and 7.56 ± 0.55 kcal/mol, respectively, which are in excellent agreement with prior reported experimental values. The simulation results show that the H88A mutant is more stable than the wild type, whereas the H88S mutant is less stable than the wild type. The free energy component analysis shows that the contribution to the free energy change difference (ΔΔG) for the His88 → Ala and His88 → Ser mutations mainly arise from electrostatic and van der Waals interactions, respectively. The electrostatic term stabilizes the H88A mutant more than the wild type, but the van der Waals interaction destabilizes the H88S mutant relative to the wild type. Individual residue contributions to the free energy change show neighboring residues exert stabilizing and destabilizing influence on the mutants. The implications of the simulation results for understanding the stabilizing and destabilizing effect and its contribution to protein stability are discussed.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9125553","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

Engineering enzyme activity using an expanded amino acid alphabet. 利用扩展的氨基酸字母表工程酶活性。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2023-01-21 DOI: 10.1093/protein/gzac013

Zachary Birch-Price, Christopher J Taylor, Mary Ortmayer, Anthony P Green

引用次数: 3