Protein Engineering, Design and Selection最新文献_第3页

Overcoming an optimization plateau in the directed evolution of highly efficient nerve agent bioscavengers 克服高效神经毒剂生物清除剂定向进化中的优化平台期

Protein Engineering, Design and Selection Pub Date : 2017-02-04 DOI: 10.1093/protein/gzx003

M. Goldsmith, N. Aggarwal, Y. Ashani, H. Jubran, Per Greisen, S. Ovchinnikov, H. Leader, D. Baker, J. Sussman, A. Goldenzweig, S. Fleishman, Dan S. Tawfik

{"title":"Overcoming an optimization plateau in the directed evolution of highly efficient nerve agent bioscavengers","authors":"M. Goldsmith, N. Aggarwal, Y. Ashani, H. Jubran, Per Greisen, S. Ovchinnikov, H. Leader, D. Baker, J. Sussman, A. Goldenzweig, S. Fleishman, Dan S. Tawfik","doi":"10.1093/protein/gzx003","DOIUrl":"https://doi.org/10.1093/protein/gzx003","url":null,"abstract":"Improving an enzyme's initially low catalytic efficiency with a new target substrate by an order of magnitude or two may require only a few rounds of mutagenesis and screening or selection. However, subsequent rounds of optimization tend to yield decreasing degrees of improvement (diminishing returns) eventually leading to an optimization plateau. We aimed to optimize the catalytic efficiency of bacterial phosphotriesterase (PTE) toward V-type nerve agents. Previously, we improved the catalytic efficiency of wild-type PTE toward the nerve agent VX by 500-fold, to a catalytic efficiency (kcat/KM) of 5 × 106 M-1 min-1. However, effective in vivo detoxification demands an enzyme with a catalytic efficiency of >107 M-1 min-1. Here, following eight additional rounds of directed evolution and the computational design of a stabilized variant, we evolved PTE variants that detoxify VX with a kcat/KM ≥ 5 × 107 M-1 min-1 and Russian VX (RVX) with a kcat/KM ≥ 107 M-1 min-1. These final 10-fold improvements were the most time consuming and laborious, as most libraries yielded either minor or no improvements. Stabilizing the evolving enzyme, and avoiding tradeoffs in activity with different substrates, enabled us to obtain further improvements beyond the optimization plateau and evolve PTE variants that were overall improved by >5000-fold with VX and by >17 000-fold with RVX. The resulting variants also hydrolyze G-type nerve agents with high efficiency (GA, GB at kcat/KM > 5 × 107 M-1 min-1) and can thus serve as candidates for broad-spectrum nerve-agent prophylaxis and post-exposure therapy using low enzyme doses.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"29 1","pages":"333–345"},"PeriodicalIF":0.0,"publicationDate":"2017-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85375983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 49

Annexin-directed &bgr;-glucuronidase for the targeted treatment of solid tumors 膜联蛋白导向的葡糖苷酶用于实体瘤的靶向治疗

Protein Engineering, Design and Selection Pub Date : 2017-02-01 DOI: 10.1093/protein/gzw063

Katrin P. Guillen, E. Ruben, N. Virani, R. Harrison

{"title":"Annexin-directed &bgr;-glucuronidase for the targeted treatment of solid tumors","authors":"Katrin P. Guillen, E. Ruben, N. Virani, R. Harrison","doi":"10.1093/protein/gzw063","DOIUrl":"https://doi.org/10.1093/protein/gzw063","url":null,"abstract":"Enzyme prodrug therapy has the potential to remedy the lack of selectivity associated with the systemic administration of chemotherapy. However, most current systems are immunogenic and constrained to a monotherapeutic approach. We developed a new class of fusion proteins centered about the human enzyme &bgr;-glucuronidase (&bgr;G), capable of converting several innocuous prodrugs into chemotherapeutics. We targeted &bgr;G to phosphatidylserine on tumor cells, tumor vasculature and metastases via annexin A1/A5. Phosphatidylserine shows promise as a universal marker for solid tumors and allows for tumor type-independent targeting. To create fusion proteins, human annexin A1/A5 was genetically fused to the activity-enhancing 16a3 mutant of human &bgr;G, expressed in chemically defined, fed-batch suspension culture, and chromatographically purified. All fusion constructs achieved >95% purity with yields up to 740 &mgr;g/l. Fusion proteins displayed cancer selective cell-surface binding with cell line-dependent binding stability. One fusion protein in combination with the prodrug SN-38 glucuronide was as effective as the drug SN-38 on Panc-1 pancreatic cancer cells and HAAE-1 endothelial cells, and demonstrated efficacy against MCF-7 breast cancer cells. &bgr;G fusion proteins effectively enable localized combination therapy that can be tailored to each patient via prodrug selection, with promising clinical potential based on their near fully human design.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"23 1","pages":"85–94"},"PeriodicalIF":0.0,"publicationDate":"2017-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85052688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Directed evolution of P450cin for mediated electron transfer P450cin介导电子转移的定向进化

Protein Engineering, Design and Selection Pub Date : 2017-02-01 DOI: 10.1093/protein/gzw072

Ketaki D. Belsare, Thomas Horn, A. J. Ruff, Ronny Martínez, Anders O. Magnusson, D. Holtmann, J. Schrader, U. Schwaneberg

{"title":"Directed evolution of P450cin for mediated electron transfer","authors":"Ketaki D. Belsare, Thomas Horn, A. J. Ruff, Ronny Martínez, Anders O. Magnusson, D. Holtmann, J. Schrader, U. Schwaneberg","doi":"10.1093/protein/gzw072","DOIUrl":"https://doi.org/10.1093/protein/gzw072","url":null,"abstract":"Directed evolution is a powerful method to optimize enzyme properties for application demands. Interesting targets are P450 monooxygenases which catalyze the stereo- and regiospecific hydroxylation of chemically inert C–H bonds. Synthesis employing P450s under cell-free reaction conditions is limited by low total turnover numbers, enzyme instability, low product yields and the requirement of the expensive co-factor NADPH. Bioelectrocatalysis is an alternative to replace NADPH in cell-free P450-catalyzed reactions. However, natural enzymes are often not suitable for using non-natural electron delivery systems. Here we report the directed evolution of a previously engineered P450 CinA-10aa-CinC fusion protein (named P450cin-ADD-CinC) to use zinc/cobalt(III)sepulchrate as electron delivery system for an increased hydroxylation activity of 1,8-cineole. Two rounds of Sequence Saturation Mutagenesis (SeSaM) each followed by one round of multiple site-saturation mutagenesis of the P450 CinA-10aa-CinC fusion protein generated a variant (Gln385His, Val386Ser, Thr77Asn, Leu88Arg; named KB8) with a 3.8-fold increase in catalytic efficiency (28 µM−1 min−1) compared to P450cin-ADD-CinC (7 µM−1 min−1). Furthermore, variant KB8 exhibited a 1.5-fold higher product formation (500 µM µM−1 P450) compared to the equimolar mixture of CinA, CinC and Fpr using NADPH as co-factor (315 µM µM−1 P450). In addition, electrochemical experiments with the electron delivery system platinum/cobalt(III)sepulchrate showed that the KB8 variant had a 4-fold higher product formation rate (0.16 nmol (nmol) P450−1 min−1 cm−2) than the P450cin-ADD-CinC (0.04 nmol (nmol) P450−1 min−1 cm−2). In summary, the current work shows prospects of using directed evolution to generate P450 enzymes suitable for use with alternative electron delivery systems.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"3 1","pages":"119–127"},"PeriodicalIF":0.0,"publicationDate":"2017-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87335022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 16

Production and characterization of functional recombinant hybrid heteropolymers of camel hepcidin and human ferritin H and L chains 骆驼铁蛋白与人铁蛋白H链、L链功能性杂交物的制备与表征

Protein Engineering, Design and Selection Pub Date : 2017-02-01 DOI: 10.1093/protein/gzw066

Mohamed Boumaiza, Fernando Carmona, M. Poli, M. Asperti, A. Gianoncelli, Michela Bertuzzi, Paola Ruzzenenti, P. Arosio, M. Marzouki

{"title":"Production and characterization of functional recombinant hybrid heteropolymers of camel hepcidin and human ferritin H and L chains","authors":"Mohamed Boumaiza, Fernando Carmona, M. Poli, M. Asperti, A. Gianoncelli, Michela Bertuzzi, Paola Ruzzenenti, P. Arosio, M. Marzouki","doi":"10.1093/protein/gzw066","DOIUrl":"https://doi.org/10.1093/protein/gzw066","url":null,"abstract":"Hepcidin is a liver-synthesized hormone that plays a central role in the regulation of systemic iron homeostasis. To produce a new tool for its functional properties the cDNA coding for camel hepcidin-25 was cloned at the 5’end of human FTH sequence into the pASK-IBA43plus vector for expression in Escherichia coli. The recombinant fusion hepcidin–ferritin-H subunit was isolated as an insoluble iron-containing protein. When alone it did not refold in a 24-mer ferritin molecule, but it did when renatured together with H- or L-ferritin chains. We obtained stable ferritin shells exposing about 4 hepcidin peptides per 24-mer shell. The molecules were then reduced and re-oxidized in a controlled manner to allow the formation of the proper hepcidin disulfide bridges. The functionality of the exposed hepcidin was confirmed by its ability to specifically bind the mouse macrophage cell line J774 that express ferroportin and to promote ferroportin degradation. This chimeric protein may be useful for studying the hepcidin–ferroportin interaction in cells and also as drug-delivery agent.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"1 1","pages":"77–84"},"PeriodicalIF":0.0,"publicationDate":"2017-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79942638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Chimeric approach for narrowing a membrane-inserting region within human perforin 缩小人穿孔膜插入区域的嵌合方法

Protein Engineering, Design and Selection Pub Date : 2017-02-01 DOI: 10.1093/protein/gzw069

Amy E. Neely, Kimberly A Mandigo, R. Robinson, T. Ness, M. H. Weiland

{"title":"Chimeric approach for narrowing a membrane-inserting region within human perforin","authors":"Amy E. Neely, Kimberly A Mandigo, R. Robinson, T. Ness, M. H. Weiland","doi":"10.1093/protein/gzw069","DOIUrl":"https://doi.org/10.1093/protein/gzw069","url":null,"abstract":"Perforin is a pore-forming, immune protein that functions to deliver an apoptotic cocktail of proteins into a target pathogen. Recent studies of the bacterial cholesterol-dependent cytolysins (CDCs) have provided a model for perforin's pore-forming mechanism. Both perforin and CDC family members share a conserved &bgr;-sheet flanked by two clusters of &agr;-helices. Within the CDCs, these helices refold into two transmembrane &bgr;-hairpins, TMH1 and TMH2. Based upon structural conservation and electron microscopy imaging, the analogous helices within perforin are predicted to also be membrane inserting; however, these regions are approximately twice the length of the CDC TMHs. To test the membrane-insertion potential of one of these regions, chimeras were created using a well-characterized CDC, perfringolysin-O (PFO), as the backbone of these constructs. PFO's TMH2 region was replaced with perforin's corresponding helical region. Although hemolytic activity was observed, the chimera was poorly soluble. A second chimera contained the same region truncated to match the length of the PFO TMH2 region. The truncated chimera demonstrated improved solubility, significant hemolytic activity and the ability to form pores characteristic of those created by PFO. These results provide the first evidence that perforin's helices function as TMHs and more importantly narrows the residues responsible for membrane insertion.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"1 1","pages":"105–111"},"PeriodicalIF":0.0,"publicationDate":"2017-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79949987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dual chemistry catalyzed by human acireductone dioxygenase 人酸还原酮双加氧酶催化的双化学反应

Protein Engineering, Design and Selection Pub Date : 2017-01-05 DOI: 10.1093/protein/gzw078

A. Deshpande, T. Pochapsky, G. Petsko, D. Ringe

{"title":"Dual chemistry catalyzed by human acireductone dioxygenase","authors":"A. Deshpande, T. Pochapsky, G. Petsko, D. Ringe","doi":"10.1093/protein/gzw078","DOIUrl":"https://doi.org/10.1093/protein/gzw078","url":null,"abstract":"Acireductone dioxygenase (ARD) from the methionine salvage pathway of Klebsiella oxytoca is the only known naturally occurring metalloenzyme that catalyzes different reactions in vivo based solely on the identity of the divalent transition metal ion (Fe2+ or Ni2+) bound in the active site. The iron-containing isozyme catalyzes the cleavage of substrate 1,2-dihydroxy-3-keto-5-(thiomethyl)pent-1-ene (acireductone) by O2 to formate and the ketoacid precursor of methionine, whereas the nickel-containing isozyme uses the same substrates to catalyze an off-pathway shunt to form methylthiopropionate, carbon monoxide and formate. This dual chemistry was recently demonstrated in vitro by ARD from Mus musculus (MmARD), providing the first example of a mammalian ARD exhibiting metal-dependent catalysis. We now show that human ARD (HsARD) is also capable of metal-dependent dual chemistry. Recombinant HsARD was expressed and purified to obtain a homogeneous enzyme with a single transition metal ion bound. As with MmARD, the Fe2+-bound HsARD shows the highest activity and catalyzes on-pathway chemistry, whereas Ni2+, Co2+ or Mn2+ forms catalyze off-pathway chemistry. The thermal stability of the HsARD isozymes is a function of the metal ion identity, with Ni2+-bound HsARD being the most stable followed by Co2+ and Fe2+, and Mn2+-bound HsARD being the least stable. As with the bacterial ARD, solution NMR data suggest that HsARD isozymes can have significant structural differences depending upon the metal ion bound.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"186 1","pages":"197–204"},"PeriodicalIF":0.0,"publicationDate":"2017-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77928171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

On the effect of alkaline pH and cofactor availability in the conformational and oligomeric state of Escherichia coli glutamate decarboxylase 碱性pH和辅助因子可用性对大肠杆菌谷氨酸脱羧酶构象和寡聚状态的影响

Protein Engineering, Design and Selection Pub Date : 2017-01-05 DOI: 10.1093/protein/gzw076

Fabio Giovannercole, C. Mérigoux, C. Zamparelli, D. Verzili, G. Grassini, Malcolm Buckle, P. Vachette, D. Biase

{"title":"On the effect of alkaline pH and cofactor availability in the conformational and oligomeric state of Escherichia coli glutamate decarboxylase","authors":"Fabio Giovannercole, C. Mérigoux, C. Zamparelli, D. Verzili, G. Grassini, Malcolm Buckle, P. Vachette, D. Biase","doi":"10.1093/protein/gzw076","DOIUrl":"https://doi.org/10.1093/protein/gzw076","url":null,"abstract":"Escherichia coli glutamate decarboxylase (EcGad) is a homohexameric pyridoxal 5'-phosphate (PLP)-dependent enzyme. It is the structural component of the major acid resistance system that protects E. coli from strong acid stress (pH < 3), typically encountered in the mammalian gastrointestinal tract. In fact EcGad consumes one proton/catalytic cycle while yielding γ-aminobutyrate and carbon dioxide from the decarboxylation of l-glutamate. Two isoforms of Gad occur in E. coli (GadA and GadB) that are 99% identical in sequence. GadB is the most intensively investigated. Prompted by the observation that some transcriptomic and proteomic studies show EcGad to be expressed in conditions far from acidic, we investigated the structural organization of EcGadB in solution in the pH range 7.5-8.6. Small angle X-ray scattering, combined with size exclusion chromatography, and analytical ultracentrifugation analysis show that the compact and entangled EcGadB hexameric structure undergoes dissociation into dimers as pH alkalinizes. When PLP is not present, the dimeric species is the most abundant in solution, though evidence for the occurrence of a likely tetrameric species was also obtained. Trp fluorescence emission spectra as well as limited proteolysis studies suggest that PLP plays a key role in the acquisition of a folding necessary for the canonical catalytic activity.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"62 1","pages":"235–244"},"PeriodicalIF":0.0,"publicationDate":"2017-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90401219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Generation of camelid VHH bispecific constructs via in-cell intein-mediated protein trans-splicing 通过细胞内蛋白介导的反式剪接产生骆驼类VHH双特异性构建体

Protein Engineering, Design and Selection Pub Date : 2017-01-01 DOI: 10.1093/protein/gzw057

Yukihiko Shibuya, N. Haga, R. Asano, H. Nakazawa, T. Hattori, D. Takeda, Aruto Sugiyama, R. Kurotani, I. Kumagai, M. Umetsu, K. Makabe

引用次数: 8

Chaetomium thermophilum formate dehydrogenase has high activity in the reduction of hydrogen carbonate (HCO3 −) to formate 热毛毛菌甲酸脱氢酶在还原碳酸氢(HCO3−)生成甲酸中具有高活性

Protein Engineering, Design and Selection Pub Date : 2017-01-01 DOI: 10.1093/protein/gzw062

Aşkın Sevinç Aslan, J. Valjakka, Jouni Ruupunen, D. Yıldırım, N. Turner, O. Turunen, Barış Binay

{"title":"Chaetomium thermophilum formate dehydrogenase has high activity in the reduction of hydrogen carbonate (HCO3 −) to formate","authors":"Aşkın Sevinç Aslan, J. Valjakka, Jouni Ruupunen, D. Yıldırım, N. Turner, O. Turunen, Barış Binay","doi":"10.1093/protein/gzw062","DOIUrl":"https://doi.org/10.1093/protein/gzw062","url":null,"abstract":"While formate dehydrogenases (FDHs) have been used for cofactor recycling in chemoenzymatic synthesis, the ability of FDH to reduce CO2 could also be utilized in the conversion of CO2 to useful products via formate (HCOO−). In this study, we investigated the reduction of CO2 in the form of hydrogen carbonate (HCO3 −) to formate by FDHs from Candida methylica (CmFDH) and Chaetomium thermophilum (CtFDH) in a NADH-dependent reaction. The catalytic performance with HCO3 − as a substrate was evaluated by measuring the kinetic rates and conducting productivity assays. CtFDH showed a higher efficiency in converting HCO3 − to formate than CmFDH, whereas CmFDH was better in the oxidation of formate. The pH optimum of the reduction was at pH 7–8. However, the high concentrations of HCO3 − reduced the reaction rate. CtFDH was modeled in the presence of HCO3 − showing that it fits to the active site. The active site setting for hydride transfer in CO2 reduction was modeled. The hydride donated by NADH would form a favorable contact to the carbon atom of HCO3 −, resulting in a surplus of electrons within the molecule. This would cause the complex formed by hydrogen carbonate and the hydride to break into formate and hydroxide ions.","PeriodicalId":20681,"journal":{"name":"Protein Engineering, Design and Selection","volume":"62 1","pages":"47–55"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88253575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 29

Stabilization of luciferase from Renilla reniformis using random mutations 随机突变稳定Renilla reniformis荧光素酶

Protein Engineering, Design and Selection Pub Date : 2017-01-01 DOI: 10.1093/protein/gzw056

M. Shigehisa, Norie Amaba, S. Arai, Chisato Higashi, Ryo Kawanabe, Ayano Matsunaga, F. A. Laksmi, M. Tokunaga, M. Ishibashi

引用次数: 12