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Randriantsilefisoa R, Cuellar-Camacho JL, Chowdhury MS, Dey P, Schedler U, Haag R. Highly sensitive detection of antibodies in a soft bioactive three-dimensional bioorthogonal hydrogel. J Mater Chem B 2019. [DOI: 10.1039/c9tb00234k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This three-dimensional detection method of antibodies offers a high sensitivity and good biomolecule stability for new biosensing devices.
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Affiliation(s)
| | | | | | - Pradip Dey
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- Takustr. 3
- Berlin
- Germany
| | - Uwe Schedler
- PolyAn GmbH
- Rudolf-Baschant-Strasse 2
- 13086 Berlin
- Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- Takustr. 3
- Berlin
- Germany
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2
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Sinzinger MD, Chung YD, Adjobo-Hermans MJW, Brock R. A microarray-based approach to evaluate the functional significance of protein-binding motifs. Anal Bioanal Chem 2016; 408:3177-84. [PMID: 26892640 PMCID: PMC4830892 DOI: 10.1007/s00216-016-9382-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 01/14/2016] [Accepted: 02/01/2016] [Indexed: 11/25/2022]
Abstract
Intracellular proteins comprise numerous peptide motifs that interact with protein-binding domains. However, using sequence information alone, the identification of functionally relevant interaction motifs remains a challenge. Here, we present a microarray-based approach for the evaluation of peptides as protein-binding motifs. To this end, peptides corresponding to protein interaction motifs were spotted as a microarray. First, peptides were titrated with a pan-specific binder and the apparent Kd value of this binder for each peptide was determined. For phosphotyrosine-containing peptides, an anti-phosphotyrosine antibody was employed. Then, in the presence of the pan-specific binder, arrays were competitively titrated with cell lysate and competition constants were determined. Using the Cheng-Prusoff equation, binding constants for the pan-specific binder and inhibition constants for the lysates were converted into affinity constants for the lysate. We experimentally validate this method using a phosphotyrosine-binding SH2 domain as a further reference. Furthermore, strong binders correlated with binding motifs engaging in numerous interactions as predicted by Scansite. This method provides a highly parallel and robust approach to identify peptides corresponding to interaction motifs with strong binding capacity for proteins in the cell lysate. Using an antibody as a pan-specific binder the capacity of interaction motifs to bind to proteins from cell lysates can be probed. Competition of the antibody is observed for only those peptides to which a lysate protein binds ![]()
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Affiliation(s)
- Michael D Sinzinger
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Yi-Da Chung
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.
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3
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Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL. Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm. Environ Microbiol 2015; 18:273-87. [PMID: 26279094 DOI: 10.1111/1462-2920.13019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 11/30/2022]
Abstract
Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal. Reactors formed two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods, we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high-stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.
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Affiliation(s)
- Jeremy J Barr
- Department of Biology, San Diego State University, San Diego, CA, USA.,Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomedical Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Connor T Skennerton
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Toshikazu Fukushima
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Division of Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Marcus L Hastie
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Jeffrey J Gorman
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Gene W Tyson
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Philip L Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
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