Protein Engineering Design & Selection最新文献_第6页

A multivalent antibody assembled from different building blocks using tag/catcher systems: a case study. 使用标签/捕集器系统从不同构建块组装的多价抗体:一个案例研究。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac014

Christof Schindler, Christine Faust, Hanno Sjuts, Christian Lange, Jennifer Kühn, Werner Dittrich, Wulf Dirk Leuschner, Werner Schiebler, Joachim Hofmann, Ercole Rao, Thomas Langer

{"title":"A multivalent antibody assembled from different building blocks using tag/catcher systems: a case study.","authors":"Christof Schindler, Christine Faust, Hanno Sjuts, Christian Lange, Jennifer Kühn, Werner Dittrich, Wulf Dirk Leuschner, Werner Schiebler, Joachim Hofmann, Ercole Rao, Thomas Langer","doi":"10.1093/protein/gzac014","DOIUrl":"https://doi.org/10.1093/protein/gzac014","url":null,"abstract":"The field of therapeutic antibodies and, especially bi- or multispecific antibodies, is growing rapidly. Especially for treating cancers, multispecific antibodies are very promising, as there are multiple pathways involved and multispecific antibodies offer the possibility to interfere at two or more sites. Besides being used as therapeutic, multispecific antibodies can be helpful tools in basic research. However, the design and choice of the most appropriate multispecific antibody format are far from trivial. The generation of multispecific antibodies starts with the generation of antibodies directed against the desired targets and then combining the different antigen-binding sites in one molecule. This is a time-consuming and laborious approach since the most suitable geometry cannot be predicted. The SpyTag technology is based on a split-protein system, where a small peptide of said protein, the SpyTag, can bind to the remaining protein, the SpyCatcher. An irreversible isopeptide bond between the SpyTag and the SpyCatcher is formed. A related Tag-Catcher system is the SnoopTag-SnoopCatcher. These systems offer the opportunity to separately produce proteins fused to the tag-peptides and to the catcher-domains and assemble them in vitro. Our goal was to design and produce different antibody fragments, Fab domains and Fc-containing domains, with different tags and/or catchers as building blocks for the assembly of different multivalent antibodies. We have shown that large multivalent antibodies consisting of up to seven building blocks can be prepared. Binding experiments demonstrated that all binding sites in such a large molecule retained their accessibility to their corresponding antigens.","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":"9226656","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

Structure-based engineering of minimal proline dehydrogenase domains for inhibitor discovery. 基于结构工程的最小脯氨酸脱氢酶结构域抑制剂发现。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac016

Alexandra N Bogner, Juan Ji, John J Tanner

{"title":"Structure-based engineering of minimal proline dehydrogenase domains for inhibitor discovery.","authors":"Alexandra N Bogner, Juan Ji, John J Tanner","doi":"10.1093/protein/gzac016","DOIUrl":"10.1093/protein/gzac016","url":null,"abstract":"Proline dehydrogenase (PRODH) catalyzes the FAD-dependent oxidation of l-proline to Δ1-pyrroline-5-carboxylate and is a target for inhibitor discovery because of its importance in cancer cell metabolism. Because human PRODH is challenging to purify, the PRODH domains of the bacterial bifunctional enzyme proline utilization A (PutA) have been used for inhibitor development. These systems have limitations due to large polypeptide chain length, conformational flexibility and the presence of domains unrelated to PRODH activity. Herein, we report the engineering of minimal PRODH domains for inhibitor discovery. The best designs contain one-third of the 1233-residue PutA from Sinorhizobium meliloti and include a linker that replaces the PutA α-domain. The minimal PRODHs exhibit near wild-type enzymatic activity and are susceptible to known inhibitors and inactivators. Crystal structures of minimal PRODHs inhibited by S-(-)-tetrahydro-2-furoic acid and 2-(furan-2-yl)acetic acid were determined at 1.23 and 1.72 Å resolution. Minimal PRODHs should be useful in chemical probe discovery.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9801229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10670094","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

Yeast surface display-based identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species. 基于酵母表面展示的 ACE2 突变鉴定可调节多种哺乳动物的 SARS-CoV-2 穗状结合。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzab035

Pete Heinzelman, Jonathan C Greenhalgh, Philip A Romero

引用次数: 0

The stability and dynamics of computationally designed proteins. 计算设计蛋白质的稳定性和动力学。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2022-02-17 DOI: 10.1093/protein/gzac001

Natali A Gonzalez, Brigitte A Li, Michelle E McCully

{"title":"The stability and dynamics of computationally designed proteins.","authors":"Natali A Gonzalez, Brigitte A Li, Michelle E McCully","doi":"10.1093/protein/gzac001","DOIUrl":"10.1093/protein/gzac001","url":null,"abstract":"Protein stability, dynamics and function are intricately linked. Accordingly, protein designers leverage dynamics in their designs and gain insight to their successes and failures by analyzing their proteins' dynamics. Molecular dynamics (MD) simulations are a powerful computational tool for quantifying both local and global protein dynamics. This review highlights studies where MD simulations were applied to characterize the stability and dynamics of designed proteins and where dynamics were incorporated into computational protein design. First, we discuss the structural basis underlying the extreme stability and thermostability frequently observed in computationally designed proteins. Next, we discuss examples of designed proteins, where dynamics were not explicitly accounted for in the design process, whose coordinated motions or active site dynamics, as observed by MD simulation, enhanced or detracted from their function. Many protein functions depend on sizeable or subtle conformational changes, so we finally discuss the computational design of proteins to perform a specific function that requires consideration of motion by multi-state design.","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/PMC9214642/pdf/gzac001.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39638976","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

Structure-guided protein engineering of human cathepsin L for efficient collagenolytic activity. 结构导向的人组织蛋白酶L高效胶原溶解活性蛋白工程。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab005

Debi Choudhury, Sampa Biswas

{"title":"Structure-guided protein engineering of human cathepsin L for efficient collagenolytic activity.","authors":"Debi Choudhury, Sampa Biswas","doi":"10.1093/protein/gzab005","DOIUrl":"https://doi.org/10.1093/protein/gzab005","url":null,"abstract":"Engineering precise substrate specificity of proteases advances the potential to use them in biotechnological and therapeutic applications. Collagen degradation, a physiological process mediated by collagenases, is an integral part of extracellular matrix remodeling and when uncontrolled, implicated in different pathological conditions. Lysosomal cathepsin-K cleaves triple helical collagen fiber, whereas cathepsin-L cannot do so. In this study, we have imparted collagenolytic property to cathepsin-L, by systematically engineering proline-specificity and glycosaminoglycans (GAG)-binding surface in the protease. The proline-specific mutant shows high specificity for prolyl-peptidic substrate but is incapable of cleaving collagen. Engineering a GAG-binding surface on the proline-specific mutant enabled it to degrade type-I collagen in the presence of chondroitin-4-sulfate (C4-S). We also present the crystal structures of proline-specific (1.4 Å) and collagen-specific (1.8 Å) mutants. Finally docking studies with prolyl-peptidic substrate (Ala-Gly-Pro-Arg-Ala) at the active site and a C4-S molecule at the GAG-binding site enable us to identify key structural features responsible for collagenolytic activity of cysteine cathepsins.","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/gzab005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25566737","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: 5

Hypomorphic mutations in human DNA ligase IV lead to compromised DNA binding efficiency, hydrophobicity and thermal stability. 人类DNA连接酶IV的半胚突变导致DNA结合效率、疏水性和热稳定性受损。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab001

Eswar Reddy Maddi, Sathees C Raghavan, Ramanathan Natesh

{"title":"Hypomorphic mutations in human DNA ligase IV lead to compromised DNA binding efficiency, hydrophobicity and thermal stability.","authors":"Eswar Reddy Maddi, Sathees C Raghavan, Ramanathan Natesh","doi":"10.1093/protein/gzab001","DOIUrl":"https://doi.org/10.1093/protein/gzab001","url":null,"abstract":"Studies have shown that Lig4 syndrome mutations in DNA ligase IV (LigIV) are compromised in its function with residual level of double strand break ligation activity in vivo. It was speculated that Lig4 syndrome mutations adversely affect protein folding and stability. Though there are crystal structures of LigIV, there are no reports of crystal structures of Lig4 syndrome mutants and their biophysical characterization to date. Here, we have examined the conformational states, thermal stability, hydrophobicity and DNA binding efficiency of human DNA LigIV wild type and its hypomorphic mutants by far-UV circular dichroism, tyrosine and tryptophan fluorescence, and 1-anilino-8-naphthalene-sulfonate binding, dynamic light scattering, size exclusion chromatography, multi-angle light scattering and electrophoretic mobility shift assay. We show here that LigIV hypomorphic mutants have reduced DNA-binding efficiency, a shift in secondary structure content from the helical to random coil, marginal reduction in their thermal stability and increased hydrophobicity as compared to the wild-type LigIV.","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/gzab001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25373436","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

A fragment-based protein interface design algorithm for symmetric assemblies. 基于片段的对称组装蛋白质界面设计算法。

IF 2.6 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab008

Joshua Laniado, Kyle Meador, Todd O Yeates

{"title":"A fragment-based protein interface design algorithm for symmetric assemblies.","authors":"Joshua Laniado, Kyle Meador, Todd O Yeates","doi":"10.1093/protein/gzab008","DOIUrl":"10.1093/protein/gzab008","url":null,"abstract":"Theoretical and experimental advances in protein engineering have led to the creation of precisely defined, novel protein assemblies of great size and complexity, with diverse applications. One powerful approach involves designing a new attachment or binding interface between two simpler symmetric oligomeric protein components. The required methods of design, which present both similarities and key differences compared to problems in protein docking, remain challenging and are not yet routine. With the aim of more fully enabling this emerging area of protein material engineering, we developed a computer program, nanohedra, to introduce two key advances. First, we encoded in the program the construction rules (i.e. the search space parameters) that underlie all possible symmetric material constructions. Second, we developed algorithms for rapidly identifying favorable docking/interface arrangements based on tabulations of empirical patterns of known protein fragment-pair associations. As a result, the candidate poses that nanohedra generates for subsequent amino acid interface design appear highly native-like (at the protein backbone level), while simultaneously conforming to the exacting requirements for symmetry-based assembly. A retrospective computational analysis of successful vs failed experimental studies supports the expectation that this should improve the success rate for this challenging area of protein engineering.","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8101011/pdf/gzab008.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38965020","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

Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis. 人造金属蛋白的设计与工程:从从头金属配位到催化。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab003

Andreas S Klein, Cathleen Zeymer

引用次数: 9

Machine learning for enzyme engineering, selection and design. 酶工程，选择和设计的机器学习。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab019

Ryan Feehan, Daniel Montezano, Joanna S G Slusky

引用次数: 12

Improved thermostability of proteinase K and recognizing the synergistic effect of Rosetta and FoldX approaches. 改善蛋白酶K的热稳定性，并认识到Rosetta和FoldX方法的协同效应。

IF 2.4 4区生物学

Protein Engineering Design & Selection Pub Date : 2021-02-15 DOI: 10.1093/protein/gzab024

Yang Zhao, Daixi Li, Xue Bai, Manjie Luo, Yan Feng, Yilei Zhao, Fuqiang Ma, Guang-Yu Yang

{"title":"Improved thermostability of proteinase K and recognizing the synergistic effect of Rosetta and FoldX approaches.","authors":"Yang Zhao, Daixi Li, Xue Bai, Manjie Luo, Yan Feng, Yilei Zhao, Fuqiang Ma, Guang-Yu Yang","doi":"10.1093/protein/gzab024","DOIUrl":"https://doi.org/10.1093/protein/gzab024","url":null,"abstract":"Proteinase K (PRK) is a proteolytic enzyme that has been widely used in industrial applications. However, poor stability has severely limited the uses of PRK. In this work, we used two structure-guided rational design methods, Rosetta and FoldX, to modify PRK thermostability. Fifty-two single amino acid conversion mutants were constructed based on software predictions of residues that could affect protein stability. Experimental characterization revealed that 46% (21 mutants) exhibited enhanced thermostability. The top four variants, D260V, T4Y, S216Q, and S219Q, showed improved half-lives at 69°C by 12.4-, 2.6-, 2.3-, and 2.2-fold that of the parent enzyme, respectively. We also found that selecting mutations predicted by both methods could increase the predictive accuracy over that of either method alone, with 73% of the shared predicted mutations resulting in higher thermostability. In addition to providing promising new variants of PRK in industrial applications, our findings also show that combining these programs may synergistically improve their predictive accuracy.","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":"39535240","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: 4