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Your search keyword '"Boersma, Ykelien L."' showing total 33 results
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33 results on '"Boersma, Ykelien L."'

7. Phage display of an intracellular carboxylesterase of Bacillus subtilis: Comparison of Sec and Tat pathway export capabilities

Author

Droge, Melloney J., Boersma, Ykelien L., Braun, Peter G., Buining, Robbert Jan, Julsing, Mattijs K., Selles, Karin G.A., Van Dijl, Jan Maarten, and Quax, Wim J.

Subjects
Bacillus subtilis -- Genetic aspects, Esterases -- Chemical properties, Biological sciences
Abstract

The development of the phage display technology method is described for fusion of an intracellular carboxylesterase of Bacillus subtilis to the phage minor coat protein g3p. The effects of Sec dependent and Tat dependent signal peptides were assessed, on the translocation of carboxylesterase for optimizing the phage display of this enzyme normally restricted to the cytoplasm.

Published
2006

15. Precision-cut liver slices as a promising ex vivo model for nanosafety studies

Author

Bartucci, Roberta, Åberg, Christoffer, Boersma, Ykelien L., Olinga, Peter, Salvati, Anna, Nanomedicine & Drug Targeting, Pharmaceutical Analysis, Medicinal Chemistry and Bioanalysis (MCB), Chemical and Pharmaceutical Biology, Pharmaceutical Technology and Biopharmacy, Nanotechnology and Biophysics in Medicine (NANOBIOMED), and Biopharmaceuticals, Discovery, Design and Delivery (BDDD)

Published
2019

17. Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics

Author

Boersma, Ykelien L, Udit, A., and Chemical and Pharmaceutical Biology

Subjects
0301 basic medicine, Scaffold, Protein therapeutics, medicine.drug_class, Computational biology, Protein engineering, Biology, Monoclonal antibody, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, DARPin, 030220 oncology & carcinogenesis, medicine, Ankyrin repeat
Abstract

Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.

Published
2018

21. A novel genetic selection system for improved enantioselectivity of Bacillus subtilis lipase A

Author

Boersma, Ykelien L., Droge, Melloney J., van der Sloot, Almer M., Pijning, Tjaard, Cool, Robbert H., Dijkstra, Bauke W., Quax, Wim J., Dröge, Melloney J., Groningen Biomolecular Sciences and Biotechnology, X-ray Crystallography, Molecular Microbiology, Biopharmaceuticals, Discovery, Design and Delivery (BDDD), and Nanotechnology and Biophysics in Medicine (NANOBIOMED)

Subjects
Glycerol, Mutant, Bacillus subtilis, TOPOFIT METHOD, 01 natural sciences, Biochemistry, Substrate Specificity, chemistry.chemical_compound, Aspartic acid, PHAGE DISPLAY, INDUSTRIAL BIOCATALYSIS, 0303 health sciences, Hydrolysis, ALPHA/BETA-HYDROLASE FOLD, Stereoisomerism, Directed evolution, Phosphonate, SUBSTRATE-SPECIFICITY, ACYLASE, ESCHERICHIA-COLI, Periplasm, Molecular Medicine, dual selection, ENZYMES, Stereochemistry, DIRECTED EVOLUTION, Biology, Alkenes, 03 medical and health sciences, Catalytic triad, enantioselectivity, Escherichia coli, Lipase, Molecular Biology, 030304 developmental biology, Gene Library, Aspartic Acid, 010405 organic chemistry, Organic Chemistry, Gene Expression Regulation, Bacterial, biology.organism_classification, LIBRARIES, 0104 chemical sciences, chemistry, genetic selection, Mutation, biology.protein, Enantiomer, Directed Molecular Evolution, Bacillus subtilis lipase A
Abstract

In directed evolution experiments, success often depends on the efficacy of screening or selection methods. Genetic selections have proven to be extremely valuable for evolving enzymes with improved catalytic activity, improved stability, or with altered substrate specificity. In contrast, enantioselectivity is a difficult parameter to select for. In this study, we present a successful strategy that not only selects for catalytic activity, but for the first time also for enantioselectivity, as demonstrated by the selection of Bacillus subtilis lipase A variants with inverted and improved enantioselectivity, A lipase mutant library in an aspartate auxotroph Escherichia coli was plated on minimal medium that was supplemented with the aspartate ester of the desired enantiomer (S)-(+)-1,2-O-isopropylidene-sn-glycerol. To inhibit growth of less enantioselective variants, a covalently binding phosphonate ester of the opposite (R)- (-)- 1,2-O-isopropylidene-sn-glycerol enontiomer was added as well. After three selection rounds in which the selection pressure was increased by raising the phosphonate ester concentration, a mutant was selected with an improved enantioselectivity increased from an ee of -29.6% (conversion 23.4 %) to an ee of + 73. 1 % (conversion 28.9 916) towards the (S)(+)-enantiomer. Interestingly, its amino acid sequence showed that the acid of the catalytic triad hod migrated to a position further along the loop that connects beta 7 and alpha E; this shows that the position of the catalytic acid is not necessarily conserved in this lipase.

Published
2008

22. Biocatalyst produces enantiopure drugs: In vitro evolution

Author

Boersma, Ykelien L., Dröge, Melloney J., Quax, Wim J., Molecular Pharmacology, Nanotechnology and Biophysics in Medicine (NANOBIOMED), and Biopharmaceuticals, Discovery, Design and Delivery (BDDD)

Subjects
medical literature, biocatalyst, hydrolysis, enantiomer, enantioselectivity, article, drug industry, propranolol, carvedilol, sotalol
Published
2007

23. The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility

Author

Kiuchi, Tai, primary, Ortiz-Zapater, Elena, additional, Monypenny, James, additional, Matthews, Daniel R., additional, Nguyen, Lan K., additional, Barbeau, Jody, additional, Coban, Oana, additional, Lawler, Katherine, additional, Burford, Brian, additional, Rolfe, Daniel J., additional, de Rinaldis, Emanuele, additional, Dafou, Dimitra, additional, Simpson, Michael A., additional, Woodman, Natalie, additional, Pinder, Sarah, additional, Gillett, Cheryl E., additional, Devauges, Viviane, additional, Poland, Simon P., additional, Fruhwirth, Gilbert, additional, Marra, Pierfrancesco, additional, Boersma, Ykelien L., additional, Plückthun, Andreas, additional, Gullick, William J., additional, Yarden, Yosef, additional, Santis, George, additional, Winn, Martyn, additional, Kholodenko, Boris N., additional, Martin-Fernandez, Marisa L., additional, Parker, Peter, additional, Tutt, Andrew, additional, Ameer-Beg, Simon M., additional, and Ng, Tony, additional

Published
2014
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24. High-Throughput Screening in Protein Engineering: Recent Advances and Future Perspectives.

Author

Wójcik, Magdalena, Telzerow, Aline, Quax, Wim J., and Boersma, Ykelien L.

Subjects
PROTEIN engineering research, ENZYMES, THERAPEUTIC complications, MEDICAL screening, BIOCHEMICAL engineering
Abstract

Over the last three decades, protein engineering has established itself as an important tool for the development of enzymes and (therapeutic) proteins with improved characteristics. New mutagenesis techniques and computational design tools have greatly aided in the advancement of protein engineering. Yet, one of the pivotal components tofurther advance protein engineering strategies is the high-throughput screening of variants. Compartmentalization is one of the key features allowing miniaturization and acceleration of screening. This review focuses on novel screening technologies applied in protein engineering, highlighting flow cytometry- and microfluidics-based platforms. [ABSTRACT FROM AUTHOR]

Published
2015
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31. HPLC-photodiode array detection analysis of curcuminoids in Curcuma species indigenous to Indonesia.

Author

Bos, Rein, Windono, Tri, Woerdenbag, Herman J., Boersma, Ykelien L., Koulman, Albert, and Kayser, Oliver

Abstract

An optimized HPLC method with photodiode array detection was developed and applied to analyse the curcuminoids curcumin, demethoxycurcumin, and bis-demethoxycurcumin in rhizomes of Curcuma mangga Val &. v. Zijp, C. heyneana Val. & v. Zijp, C. aeruginosa Roxb. and C. soloensis Val. (Zingiberaceae), indigenous to Indonesia. The method was validated with an isocratic system, a short run time of 10 min and a baseline separation. The curcuminoid content was 0.18-0.47% for C. mangga, 0.98-3.21% for C. heyneana, 0.02-0.03% for C. aeruginosa and 0.40% for C. soloensis. Copyright © 2006 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Published
2007
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32. Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics.

Author

Boersma YL

Subjects
Animals, Biosensing Techniques, Chemical Phenomena, Clinical Trials as Topic, Humans, Models, Molecular, Protein Conformation, Ankyrin Repeat, Protein Engineering, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins therapeutic use, Research, Theranostic Nanomedicine
Abstract

Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.

Published
2018
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33. Directed evolution of Bacillus subtilis lipase A by use of enantiomeric phosphonate inhibitors: crystal structures and phage display selection.

Author

Dröge MJ, Boersma YL, van Pouderoyen G, Vrenken TE, Rüggeberg CJ, Reetz MT, Dijkstra BW, and Quax WJ

Subjects
Bacillus subtilis drug effects, Bacterial Proteins drug effects, Bacterial Proteins genetics, Cloning, Molecular, Crystallization, Crystallography, X-Ray, Enzyme Inhibitors chemistry, Hydrolysis, Models, Molecular, Molecular Structure, Mutation, Phosphates chemistry, Protein Conformation, Protein Structure, Tertiary, Stereoisomerism, Structure-Activity Relationship, Bacillus subtilis enzymology, Bacterial Proteins chemistry, Directed Molecular Evolution methods, Enzyme Inhibitors pharmacology, Peptide Library, Phosphates pharmacology
Abstract

Phage display can be used as a protein-engineering tool for the selection of proteins with desirable binding properties from a library of mutants. Here we describe the application of this method for the directed evolution of Bacillus subtilis lipase A, an enzyme that has important properties for the preparation of the pharmaceutically relevant chiral compound 1,2-O-isopropylidene-sn-glycerol (IPG). PCR mutagenesis with spiked oligonucleotides was employed for saturation mutagenesis of a stretch of amino acids near the active site. After expression of these mutants on bacteriophages, dual selection with (S)-(+)- and (R)-(-)-IPG stereoisomers covalently coupled to enantiomeric phosphonate suicide inhibitors (SIRAN Sc and Rc inhibitors, respectively) was used for the isolation of variants with inverted enantioselectivity. The mutants were further characterised by determination of their Michaelis-Menten parameters. The 3D structures of the Sc and Rc inhibitor-lipase complexes were determined and provided structural insight into the mechanism of enantioselectivity of the enzyme. In conclusion, we have used phage display as a fast and reproducible method for the selection of Bacillus lipase A mutant enzymes with inverted enantioselectivity.

Published
2006
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