Dr. L.J. (Leo) de Koning
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Swammerdam Institute for Life Sciences
Bezoekadres
- Science Park 904
Postadres
- Postbus 1212
1000 BE Amsterdam
Contactgegevens
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Publicaties
2021
Ursem, R., Swarge, B., Abhyankar, W. R., Buncherd, H., de Koning, L. J., Setlow, P., Brul, S., & Kramer, G. (2021). Identification of Native Cross-Links in Bacillus subtilis Spore Coat Proteins. Journal of Proteome Research, 20(3), 1809–1816. https://doi.org/10.1021/acs.jproteome.1c00025 [details]
2020
- Swarge, B., Abhyankar, W., Jonker, M., Hoefsloot, H., Kramer, G., Setlow, P., Brul, S., & de Koning, L. J. (2020). Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival. mSphere, 5(4), [e00463-20]. https://doi.org/10.1128/mSphere.00463-20 [details]
- Tu, Z., Abhyankar, W. R., Swarge, B. N., van der Wel, N., Kramer, G., Brul, S., & de Koning, L. J. (2020). Artificial Sporulation Induction (ASI) by kinA Overexpression Affects the Proteomes and Properties of Bacillus subtilis Spores. International Journal of Molecular Sciences, 21(12), [4315]. https://doi.org/10.3390/ijms21124315 [details]
2019
- Abhyankar, W. R., Wen, J., Swarge, B. N., Tu, Z., de Boer, R., Smelt, J. P. P. M., ... Brul, S. (2019). Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores. Food Microbiology, 81, 89-96. https://doi.org/10.1016/j.fm.2018.03.006 [details]
- Abhyankar, W. R., Zheng, L., Brul, S., de Koster, C. G., & de Koning, L. J. (2019). Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers. Journal of Proteome Research, 18(11), 3967-3976. https://doi.org/10.1021/acs.jproteome.9b00413 [details]
2018
- Roseboom, W., Nazir, M. G., Meiresonne, N. Y., Mohammadi, T., Verheul, J., Buncherd, H., Bonvin, A. M. J. J., de Koning, L. J., de Koster, C. G., De Jong, L., & Den Blaauwen, T. (2018). Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis. International Journal of Molecular Sciences, 19(10), [2928]. https://doi.org/10.3390/ijms19102928 [details]
- Stelder, S. K., Benito de Moya, C., Hoefsloot, H. C. J., de Koning, L. J., Brul, S., & de Koster, C. G. (2018). Correction to "Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach". Journal of Proteome Research, 17(7), 2562. https://doi.org/10.1021/acs.jproteome.8b00313
- Stelder, S. K., Benito de Moya, C., Hoefsloot, H. C. J., de Koning, L. J., Brul, S., & de Koster, C. G. (2018). Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach. Journal of Proteome Research, 17(2), 903-917. https://doi.org/10.1021/acs.jproteome.7b00732 [details]
- Swarge, B. N., Roseboom, W., Zheng, L., Abhyankar, W. R., Brul, S., de Koster, C. G., & de Koning, L. J. (2018). "One‐Pot" Sample Processing Method for Proteome‐Wide Analysis of Microbial Cells and Spores. Proteomics Clinical Applications, 12(5), [1700169 ]. https://doi.org/10.1002/prca.201700169 [details]
2017
- Abhyankar, W., Stelder, S., de Koning, L., de Koster, C., & Brul, S. (2017). 'Omics' for microbial food stability: Proteomics for the development of predictive models for bacterial spore stress survival and outgrowth. International Journal of Food Microbiology, 240, 11-18. https://doi.org/10.1016/j.ijfoodmicro.2016.05.008 [details]
2016
- Abhyankar, W. R., Kamphorst, K., Swarge, B. N., van Veen, H., van der Wel, N. N., Brul, S., ... de Koning, L. J. (2016). The Influence of Sporulation Conditions on the Spore Coat Protein Composition of Bacillus subtilis Spores. Frontiers in Microbiology, 7, [1636]. https://doi.org/10.3389/fmicb.2016.01636 [details]
- Zheng, L., Abhyankar, W., Ouwerling, N., Dekker, H. L., van Veen, H., van der Wel, N. N., Roseboom, W., de Koning, L. J., Brul, S., & de Koster, C. G. (2016). Bacillus subtilis Spore Inner Membrane Proteome. Journal of Proteome Research, 15(2), 585-594. https://doi.org/10.1021/acs.jproteome.5b00976 [details]
2015
- Abhyankar, W., Pandey, R., ter Beek, A., Brul, S., de Koning, L. J., & de Koster, C. G. (2015). Reinforcement of Bacillus subtilis spores by cross-linking of outer coat proteins during maturation. Food Microbiology, 45(Part A), 54-62. https://doi.org/10.1016/j.fm.2014.03.007 [details]
- Borirak, O., Rolfe, M. D., de Koning, L. J., Hoefsloot, H. C. J., Bekker, M., Dekker, H. L., Roseboom, W., Green, J., de Koster, C. G., & Hellingwerf, K. J. (2015). Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression. Biochimica et Biophysica Acta. Proteins and Proteomics, 1854(10, Part A), 1269-1279. https://doi.org/10.1016/j.bbapap.2015.05.017 [details]
- Borirak, O., de Koning, L. J., van der Woude, A. D., Hoefsloot, H. C. J., Dekker, H. L., Roseboom, W., de Koster, C. G., & Hellingwerf, K. J. (2015). Quantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803. Biotechnology for Biofuels, 8, [111]. https://doi.org/10.1186/s13068-015-0294-z [details]
- Stelder, S. K., Mahmud, S. A., Dekker, H. L., de Koning, L. J., Brul, S., & de Koster, C. G. (2015). Temperature Dependence of the Proteome Profile of the Psychrotolerant Pathogenic Food Spoiler Bacillus weihenstephanensis Type Strain WSBC 10204. Journal of Proteome Research, 14(5), 2169-2176. https://doi.org/10.1021/pr501307t [details]
- Vonk, R. J., Gargano, A. F. G., Davydova, E., Dekker, H. L., Eeltink, S., de Koning, L. J., & Schoenmakers, P. J. (2015). Comprehensive Two-Dimensional Liquid Chromatography with Stationary-Phase-Assisted Modulation Coupled to High-Resolution Mass Spectrometry Applied to Proteome Analysis of Saccharomyces cerevisiae. Analytical Chemistry, 87(10), 5387-5394. https://doi.org/10.1021/acs.analchem.5b00708 [details]
- Vonk, R. J., Wouters, S., Barcaru, A., Vivó-Truyols, G., Eeltink, S., de Koning, L. J., & Schoenmakers, P. J. (2015). Post-polymerization photografting on methacrylate-based monoliths for separation of intact proteins and protein digests with comprehensive two-dimensional liquid chromatography hyphenated with high-resolution mass spectrometry. Analytical and Bioanalytical Chemistry, 407(13), 3817-3829. https://doi.org/10.1007/s00216-015-8615-4 [details]
2014
- Abhyankar, W., de Koning, L. J., Brul, S., & de Koster, C. G. (2014). Spore Proteomics: The Past, Present and the Future. FEMS Microbiology Letters, 358(2), 137-144. https://doi.org/10.1111/1574-6968.12568 [details]
2013
- Abhyankar, W., Hossain, A. H., Djajasaputra, A., Permpoonpattana, P., ter Beek, A., Dekker, H. L., ... de Koster, C. G. (2013). In pursuit of protein targets: proteomic characterization of bacterial spore outer layers. Journal of Proteome Research, 12(10), 4507-4521. https://doi.org/10.1021/pr4005629 [details]
- Heilmann, C. J., Sorgo, A. G., Mohammadi, S., Sosinska, G. J., de Koster, C. G., Brul, S., ... Klis, F. M. (2013). Surface stress induces a conserved cell wall stress response in the pathogenic fungus Candida albicans. Eukaryotic Cell, 12(2), 254-264. https://doi.org/10.1128/EC.00278-12 [details]
- Sorgo, A. G., Brul, S., de Koster, C. G., de Koning, L. J., & Klis, F. M. (2013). Iron restriction-induced adaptations in the wall proteome of Candida albicans. Microbiology - SGM, 159(8), 1673-1682. https://doi.org/10.1099/mic.0.065599-0 [details]
2012
- Buncherd, H., Nessen, M. A., Nouse, N., Stelder, S. K., Roseboom, W., Dekker, H. L., Arents, J. C., Smeenk, L. E., Wanner, M. J., van Maarseveen, J. H., Yang, X., Lewis, P. J., de Koning, L. J., de Koster, C. G., & de Jong, L. (2012). Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry. Journal of Proteomics, 75(7), 2205-2215. https://doi.org/10.1016/j.jprot.2012.01.025 [details]
- Postmus, J., Aardema, R., de Koning, L. J., de Koster, C. G., Brul, S., & Smits, G. J. (2012). Isoenzyme expression changes in response to high temperature determine the metabolic regulation of increased glycolytic flux in yeast. FEMS Yeast Research, 12, 571-581. https://doi.org/10.1111/j.1567-1364.2012.00807.x [details]
2011
- Heijnis, W. H., Dekker, H. L., de Koning, L. J., Wierenga, P. A., Westphal, A. H., de Koster, C. G., ... van Berkel, W. J. H. (2011). Identification of the peroxidase-generated intermolecular dityrosine cross-link in bovine alfa-lactalbumin. Journal of Agricultural and Food Chemistry, 59(1), 444-449. https://doi.org/10.1021/jf104298y [details]
- Heilmann, C. J., Sorgo, A. G., Siliakus, A. R., Dekker, H. L., Brul, S., de Koster, C. G., ... Klis, F. M. (2011). Hyphal induction in the human fungal pathogen Candida albicans reveals a characteristic wall protein profile. Microbiology - SGM, 157(8), 2297-2307. https://doi.org/10.1099/mic.0.049395-0 [details]
- Sorgo, A. G., Heilmann, C. J., Dekker, H. L., Bekker, M., Brul, S., de Koster, C. G., ... Klis, F. M. (2011). Effects of fluconazole on the secretome, the wall proteome, and wall integrity of the clinical fungus Candida albicans. Eukaryotic Cell, 10(8), 1071-1081. https://doi.org/10.1128/EC.05011-11 [details]
- Sosinska, G. J., de Koning, L. J., de Groot, P. W. J., Manders, E. M. M., Dekker, H. L., Hellingwerf, K. J., ... Klis, F. M. (2011). Mass spectrometric quantification of the adaptations in the wall proteome of Candida albicans in response to ambient pH. Microbiology - SGM, 157(1), 136-146. https://doi.org/10.1099/mic.0.044206-0 [details]
2009
- Kramer, G., Sprenger, R. R., Back, J. W., Dekker, H. L., Nessen, M. A., van Maarseveen, J. H., ... de Koster, C. G. (2009). Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography. Molecular & Cellular Proteomics, 8(7), 1599-1611. https://doi.org/10.1074/mcp.M800392-MCP200 [details]
- Müller, M. Q., de Koning, L. J., Schmidt, A., Ihling, A., Syha, Y., Rau, O., ... Sinz, A. (2009). An innovative method to study target protein-drug interactions by mass spectrometry. Journal of Medicinal Chemistry, 52(9), 2875-2879. https://doi.org/10.1021/jm9000665 [details]
- Nessen, M. A., Kramer, G., Back, J. W., Baskin, J. M., Smeenk, L. E. J., de Koning, L. J., ... de Koster, C. G. (2009). Selective enrichment of azide-containing peptides from complex mixtures. Journal of Proteome Research, 8(7), 3702-3711. https://doi.org/10.1021/pr900257z [details]
2008
- Popolo, L., Ragni, E., Carotti, C., Palomares, O., Aardema, R., Back, J. W., ... de Koster, C. G. (2008). Disulfide bond structure and domain organization of yeast beta(1,3)-glucanosyltransferases involved in cell wall biogenesis. The Journal of Biological Chemistry, 283(27), 18553-18565. https://doi.org/10.1074/jbc.M801562200 [details]
2014
- Buncherd, H., Roseboom, W., Ghavim, B., Du, W., de Koning, L. J., de Koster, C. G., & de Jong, L. (2014). Isolation of cross-linked peptides by diagonal strong cation exchange chromatography for protein complex topology studies by peptide fragment fingerprinting from large sequence databases. Journal of Chromatography A, 1348, 34-46. https://doi.org/10.1016/j.chroma.2014.04.083 [details]
- Buncherd, H., Roseboom, W., de Koning, L. J., de Koster, C. G., & de Jong, L. (2014). A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database. Journal of Proteomics, 108, 65-77. https://doi.org/10.1016/j.jprot.2014.05.003 [details]
2013
- Borirak, O., Bekker, M., Rolfe, M. D., Dekker, H. L., de Jong, L., de Koster, C. G., ... Hellingwerf, K. J. (2013). Dynamic changes of the Escherichia coli transcriptome and proteome exerted by glucose repression. The FASEB Journal, 27(1 Supplement), [lb136]. [details]
This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list. -
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Geen nevenwerkzaamheden
Ursem, R., Swarge, B., Abhyankar, W. R., Buncherd, H., de Koning, L. J., Setlow, P., Brul, S., & Kramer, G. (2021). Identification of Native Cross-Links in Bacillus subtilis Spore Coat Proteins. Journal of Proteome Research, 20(3), 1809–1816.