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Czerczak-Kwiatkowska K, Kaminska M, Fraczyk J, Majsterek I, Kolesinska B. Searching for EGF Fragments Recreating the Outer Sphere of the Growth Factor Involved in Receptor Interactions. Int J Mol Sci 2024; 25:1470. [PMID: 38338748 PMCID: PMC10855902 DOI: 10.3390/ijms25031470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
The aims of this study were to determine whether it is possible to use peptide microarrays obtained using the SPOT technique (immobilized on cellulose) and specific polyclonal antibodies to select fragments that reconstruct the outer sphere of proteins and to ascertain whether the selected peptide fragments can be useful in the study of their protein-protein and/or peptide-protein interactions. Using this approach, epidermal growth factor (EGF) fragments responsible for the interaction with the EGF receptor were searched. A library of EGF fragments immobilized on cellulose was obtained using triazine condensing reagents. Experiments on the interactions with EGFR confirmed the high affinity of the selected peptide fragments. Biological tests on cells showed the lack of cytotoxicity of the EGF fragments. Selected EGF fragments can be used in various areas of medicine.
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Affiliation(s)
- Katarzyna Czerczak-Kwiatkowska
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
| | - Marta Kaminska
- Division of Biophysics, Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-924 Lodz, Poland;
| | - Justyna Fraczyk
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland;
| | - Beata Kolesinska
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
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2
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Hilpert K, Munshi T, López-Pérez PM, Sequeira-Garcia J, Bull TJ. Redefining Peptide 14D: Substitutional Analysis for Accelerated TB Diagnosis and Enhanced Activity against Mycobacterium tuberculosis. Microorganisms 2024; 12:177. [PMID: 38258003 PMCID: PMC10819809 DOI: 10.3390/microorganisms12010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis remains a predominant cause of mortality, especially in low- and middle-income nations. Recently, antimicrobial peptides have been discovered that at low concentrations could stimulate the growth of M. tuberculosis (hormetic response). In this study, such a peptide was used to investigate the effects on the time to positivity (TTP). A systematic substitution analysis of peptide 14D was synthesized using Spot synthesis technology, resulting in 171 novel peptides. Our findings revealed a spectrum of interactions, with some peptides accelerating M. tuberculosis growth, potentially aiding in faster diagnostics, while others exhibited inhibitory effects. Notably, peptide NH2-wkivfiwrr-CONH2 significantly reduced the TTP by 25 h compared to the wild-type peptide 14D, highlighting its potential in improving TB diagnostics by culture. Several peptides demonstrated potent antimycobacterial activity, with a minimum inhibitory concentration (MIC) of 20 µg/mL against H37Rv and a multidrug-resistant M. tuberculosis strain. Additionally, for two peptides, a strongly diminished formation of cord-like structures was observed, which is indicative of reduced virulence and transmission potential. This study underscores the multifaceted roles of antimicrobial peptides in TB management, from enhancing diagnostic efficiency to offering therapeutic avenues against M. tuberculosis.
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Affiliation(s)
- Kai Hilpert
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Tulika Munshi
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | | | - Tim J. Bull
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
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3
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Schnatbaum K, Holenya P, Pfeil S, Drosch M, Eckey M, Reimer U, Wenschuh H, Kern F. An Overview of Peptides and Peptide Pools for Antigen-Specific Stimulation in T-Cell Assays. Methods Mol Biol 2024; 2768:29-50. [PMID: 38502386 DOI: 10.1007/978-1-0716-3690-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The analysis of antigen-specific T-cell responses has become routine in many laboratories. Functional T-cell assays like enzyme-linked-immuno-spot (ELISPOT), which depend on antigen-specific stimulation, increasingly use peptides to represent the antigen of interest. Besides single peptides, mixtures of peptides (peptide pools) are very frequently applied. Such peptide pools may, for example, represent entire proteins (with overlapping peptides covering a protein sequence) or include noncontiguous peptides such as a collection of T-cell-stimulating peptides. The optimum specification of single peptides or peptide pools for T-cell stimulation assays will depend on the purpose of the test, the target T-cell population, the availability of sample, requirements regarding reproducibility, and, last but not least, the available budget, to mention only the most important factors. Because of the way peptides are produced, they will always contain certain amounts of impurities such as peptides with deletions or truncated peptides, and there may be additional by-products of peptide synthesis. Optimized synthesis protocols as well as purification help reduce impurities that might otherwise cause false-positive assay results. However, specific requirements with respect to purity will vary depending on the purpose of an assay. Finally, storage conditions significantly affect the shelf life of peptides, which is relevant especially for longitudinal studies. The present book chapter addresses all of these aspects in detail. It should provide the researcher with all necessary background knowledge for making the right decisions when it comes to choosing, using, and storing peptides for ELISPOT and other T-cell stimulation assays.
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Affiliation(s)
| | | | | | | | | | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | | | - Florian Kern
- JPT Peptide Technologies, Berlin, Germany.
- Brighton and Sussex Medical School, Brighton, UK.
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4
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Khattab A, Rezola M, Barroso M, Kyrklund M, Pihlajamaa T, Freitag TL, van Gemert GJ, Bousema T, Permi P, Turunen O, Sauerwein R, Luty AJF, Meri S. Hijacking the human complement inhibitor C4b-binding protein by the sporozoite stage of the Plasmodium falciparum parasite. Front Immunol 2022; 13:1051161. [PMID: 36479121 PMCID: PMC9720182 DOI: 10.3389/fimmu.2022.1051161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/02/2022] [Indexed: 11/22/2022] Open
Abstract
The complement system is considered the first line of defense against pathogens. Hijacking complement regulators from blood is a common evasion tactic of pathogens to inhibit complement activation on their surfaces. Here, we report hijacking of the complement C4b-binding protein (C4bp), the regulator of the classical and lectin pathways of complement activation, by the sporozoite (SPZ) stage of the Plasmodium falciparum parasite. This was shown by direct binding of radiolabeled purified C4bp to live SPZs as well as by binding of C4bp from human serum to SPZs in indirect immunofluorescence assays. Using a membrane-bound peptide array, peptides from the N-terminal domain (NTD) of P. falciparum circumsporozoite protein (CSP) were found to bind C4bp. Soluble biotinylated peptide covering the same region on the NTD and a recombinantly expressed NTD also bound C4bp in a dose-dependent manner. NTD-binding site on C4bp was mapped to the CCP1-2 of the C4bp α-chain, a common binding site for many pathogens. Native CSP was also co-immunoprecipitated with C4bp from human serum. Preventing C4bp binding to the SPZ surface negatively affected the SPZs gliding motility in the presence of functional complement and malaria hyperimmune IgG confirming the protective role of C4bp in controlling complement activation through the classical pathway on the SPZ surface. Incorporating the CSP-C4bp binding region into a CSP-based vaccine formulation could induce vaccine-mediated immunity that neutralizes this immune evasion region and increases the vaccine efficacy.
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Affiliation(s)
- Ayman Khattab
- Department of Bacteriology and Immunology, Haartman Institute, and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland,Department of Nucleic Acid Research, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria, Egypt,*Correspondence: Ayman Khattab,
| | - Mikel Rezola
- Department of Bacteriology and Immunology, Haartman Institute, and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Marta Barroso
- Department of Bacteriology and Immunology, Haartman Institute, and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Mikael Kyrklund
- Department of Bacteriology and Immunology, Haartman Institute, and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland,Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Tero Pihlajamaa
- Department of Clinical Chemistry, HUSLAB, Helsinki University Hospital, HUS Diagnostic Center, Helsinki, Finland
| | - Tobias L. Freitag
- Department of Bacteriology and Immunology, Haartman Institute, and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Teun Bousema
- Department of Medical Microbiology, Radboudumc, Nijmegen, Netherlands
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Ossi Turunen
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland,School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | | | | | - Seppo Meri
- Department of Bacteriology and Immunology, Haartman Institute, and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland,HUSLAB Diagnostic Center, Helsinki University Central Hospital, Helsinki, Finland,Department of Biomedical Sciences, Humanitas University, Milan, Italy
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5
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Singh PP, Gupta V, Prakash B. Recent advancement in functional properties and toxicity assessment of plant-derived bioactive peptides using bioinformatic approaches. Crit Rev Food Sci Nutr 2021:1-19. [PMID: 34783283 DOI: 10.1080/10408398.2021.2002807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nowadays, biopeptides have gained considerable interest by the food industries, given their potent biological effect on health. BPs, when released from the sequence of their precursors by proteolytic enzymes, improved the various physiological functions of the body. Diabetic and hypertension are the two most common life-threatening diseases linked to dietary patterns. Angiotensin-converting enzyme (ACE) (hypertension-responsible glycoprotein) and dipeptidyl peptidase IV (DPP-IV) (proline-specific dimeric aminopeptidase) have been widely used as molecular target sites of action of bioactive compounds possessing antihypertensive and antidiabetic effects. Although, BPs possess considerable biological properties (antioxidant, antimicrobial, antiviral, immunomodulating, antiproliferative, antidiabetic, and antihypertensive effects), most of them possess inherent lacunae such as toxicity, allergenicity, bitterness, and lack of detailed mechanistic investigation, limiting their commercial application. The present review provides an overview on various sources of bioactive peptides, conventional and modern methods of extraction, and challenges that need to be addressed before its commercial application. In addition, bioinformatics' role in exploring the functional properties of biopeptides (ACE and DPP-IV inhibitory effects) toxicity, the target site of action with special reference to plant-based peptides, and recent burgeoning proficiencies in biopeptide research have been discussed.
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Affiliation(s)
- Prem Pratap Singh
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Vishal Gupta
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Bhanu Prakash
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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6
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Wilhelm M, Zolg DP, Graber M, Gessulat S, Schmidt T, Schnatbaum K, Schwencke-Westphal C, Seifert P, de Andrade Krätzig N, Zerweck J, Knaute T, Bräunlein E, Samaras P, Lautenbacher L, Klaeger S, Wenschuh H, Rad R, Delanghe B, Huhmer A, Carr SA, Clauser KR, Krackhardt AM, Reimer U, Kuster B. Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nat Commun 2021; 12:3346. [PMID: 34099720 PMCID: PMC8184761 DOI: 10.1038/s41467-021-23713-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of non-tryptic peptides presents substantial computational challenges. To address these, we synthesized and analyzed >300,000 peptides by multi-modal LC-MS/MS within the ProteomeTools project representing HLA class I & II ligands and products of the proteases AspN and LysN. The resulting data enabled training of a single model using the deep learning framework Prosit, allowing the accurate prediction of fragment ion spectra for tryptic and non-tryptic peptides. Applying Prosit demonstrates that the identification of HLA peptides can be improved up to 7-fold, that 87% of the proposed proteasomally spliced HLA peptides may be incorrect and that dozens of additional immunogenic neo-epitopes can be identified from patient tumors in published data. Together, the provided peptides, spectra and computational tools substantially expand the analytical depth of immunopeptidomics workflows.
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Affiliation(s)
- Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.
| | - Daniel P Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Michael Graber
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Siegfried Gessulat
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | - Celina Schwencke-Westphal
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich; and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Philipp Seifert
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Niklas de Andrade Krätzig
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | | | | | - Eva Bräunlein
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Ludwig Lautenbacher
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Roland Rad
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | | | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Angela M Krackhardt
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich; and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, Germany.
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7
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Holenya P, Lange PJ, Reimer U, Woltersdorf W, Panterodt T, Glas M, Wasner M, Eckey M, Drosch M, Hollidt J, Naumann M, Kern F, Wenschuh H, Lange R, Schnatbaum K, Bier FF. Peptide microarray-based analysis of antibody responses to SARS-CoV-2 identifies unique epitopes with potential for diagnostic test development. Eur J Immunol 2021; 51:1839-1849. [PMID: 33772767 PMCID: PMC8250065 DOI: 10.1002/eji.202049101] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Humoral immunity to the Severe Adult Respiratory Syndrome (SARS) Coronavirus (CoV)-2 is not fully understood yet but is a crucial factor of immune protection. The possibility of antibody cross-reactivity between SARS-CoV-2 and other human coronaviruses (HCoVs) would have important implications for immune protection but also for the development of specific diagnostic ELISA tests. Using peptide microarrays, n = 24 patient samples and n = 12 control samples were screened for antibodies against the entire SARS-CoV-2 proteome as well as the Spike (S), Nucleocapsid (N), VME1 (V), R1ab, and Protein 3a (AP3A) of the HCoV strains SARS, MERS, OC43, and 229E. While widespread cross-reactivity was revealed across several immunodominant regions of S and N, IgG binding to several SARS-CoV-2-derived peptides provided statistically significant discrimination between COVID-19 patients and controls. Selected target peptides may serve as capture antigens for future, highly COVID-19-specific diagnostic antibody tests.
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Affiliation(s)
| | - Paul Joris Lange
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- KH Labor GmbHBernburgGermany
- Medical FacultyInstitute of Experimental Internal MedicineOtto von Guericke UniversityMagdeburgGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Ulf Reimer
- JPT Peptide Technologies GmbHBerlinGermany
| | | | | | | | | | | | | | - Jörg‐Michael Hollidt
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- in.vent GmbHHennigsdorfGermany
| | - Michael Naumann
- Medical FacultyInstitute of Experimental Internal MedicineOtto von Guericke UniversityMagdeburgGermany
| | - Florian Kern
- JPT Peptide Technologies GmbHBerlinGermany
- Department of Clinical and Experimental MedicineBrighton and Sussex Medical SchoolBrightonUK
| | | | - Robert Lange
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- KH Labor GmbHBernburgGermany
| | | | - Frank F. Bier
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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8
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Hernandez DP, Dittmar G. Peptide array-based interactomics. Anal Bioanal Chem 2021; 413:5561-5566. [PMID: 33942139 PMCID: PMC8092715 DOI: 10.1007/s00216-021-03367-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 01/16/2023]
Abstract
The analysis of protein-protein interactions (PPIs) is essential for the understanding of cellular signaling. Besides probing PPIs with immunoprecipitation-based techniques, peptide pull-downs are an alternative tool specifically useful to study interactome changes induced by post-translational modifications. Peptides for pull-downs can be chemically synthesized and thus offer the possibility to include amino acid exchanges and post-translational modifications (PTMs) in the pull-down reaction. The combination of peptide pull-down and analysis of the binding partners with mass spectrometry offers the direct measurement of interactome changes induced by PTMs or by amino acid exchanges in the interaction site. The possibility of large-scale peptide synthesis on a membrane surface opened the possibility to systematically analyze interactome changes for mutations of many proteins at the same time. Short linear motifs (SLiMs) are amino acid patterns that can mediate protein binding. A significant number of SLiMs are located in regions of proteins, which are lacking a secondary structure, making the interaction motifs readily available for binding reactions. Peptides are particularly well suited to study protein interactions, which are based on SLiM-mediated binding. New technologies using arrayed peptides for interaction studies are able to identify SLIM-based interaction and identify the interaction motifs.
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Affiliation(s)
- Daniel Perez Hernandez
- Proteomics of Cellular Signalling, Department of Infection and Immunity, Luxembourg Institute of Health, 1 A Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signalling, Department of Infection and Immunity, Luxembourg Institute of Health, 1 A Rue Thomas Edison, 1445, Strassen, Luxembourg. .,Department of Life Sciences and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg.
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9
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Benchtop holdup assay for quantitative affinity-based analysis of sequence determinants of protein-motif interactions. Anal Biochem 2020; 603:113772. [PMID: 32428443 DOI: 10.1016/j.ab.2020.113772] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 11/22/2022]
Abstract
Many protein-protein interactions are mediated by short linear peptide motifs binding to cognate proteins or protein domains. Such interactions often display affinities in the mid-micromolar range that are challenging to quantify accurately, especially when the motifs harbor single-point mutations. Here, we present a manual benchtop assay for determining affinities of weak interactions between a purified protein and a peptide array representing mutants of a target motif. The assay is based on the "holdup" principle, a chromatographic approach allowing sensitive detection of weak interactions at equilibrium and accurate estimation of their binding free energy. We tested two alternative setups using, as a readout, either capillary electrophoresis or fluorescence. Using this approach, we studied the amino acid sequence determinants of the interactions between HPV16 E6 viral oncoprotein and single-point mutants of its prototypical target LXXLL motif from the E3 ubiquitin ligase E6AP. Comparing SPOT peptide array and holdup approaches revealed a good agreement for most interactions except the weakest ones, which were only detected by holdup assay. In addition, the strongest interactions were validated by Surface-Plasmon Resonance. The manual holdup procedure proposed here can be readily adapted for accurate evaluation of a wide variety of protein-motif interactions displaying low to medium affinities.
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10
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Abstract
Peptide libraries are a highly useful tool for drug development. While most preparations of peptide libraries are laborious during either the synthesis or its screening, the SPOT synthesis offers the possibility of directly synthesizing large numbers of peptides on a planar surface. As a positionally addressable, multiple solid-phase synthesis technique, the synthesis allows a very convenient handling during the screening of that peptide library in a form of an array. This publication will provide protocols for the basic procedures of the SPOT synthesis and references to some important literature regarding that technique and its application.
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11
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Sereikaite V, Fritzius T, Kasaragod VB, Bader N, Maric HM, Schindelin H, Bettler B, Strømgaard K. Targeting the γ-Aminobutyric Acid Type B (GABA B) Receptor Complex: Development of Inhibitors Targeting the K + Channel Tetramerization Domain (KCTD) Containing Proteins/GABA B Receptor Protein-Protein Interaction. J Med Chem 2019; 62:8819-8830. [PMID: 31509708 DOI: 10.1021/acs.jmedchem.9b01087] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Targeting multiprotein receptor complexes, rather than receptors directly, is a promising concept in drug discovery. This is particularly relevant to the GABAB receptor complex, which plays a prominent role in many brain functions and diseases. Here, we provide the first studies targeting a key protein-protein interaction of the GABAB receptor complex-the interaction with KCTD proteins. By employing the μSPOT technology, we first defined the GABAB receptor-binding epitope mediating the KCTD interaction. Subsequently, we developed a highly potent peptide-based inhibitor that interferes with the KCTD/GABAB receptor complex and efficiently isolates endogenous KCTD proteins from mouse brain lysates. X-ray crystallography and SEC-MALS revealed inhibitor induced oligomerization of KCTD16 into a distinct hexameric structure. Thus, we provide a template for modulating the GABAB receptor complex, revealing a fundamentally novel approach for targeting GABAB receptor-associated neuropsychiatric disorders.
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Affiliation(s)
- Vita Sereikaite
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Thorsten Fritzius
- Department of Biomedicine , University of Basel , CH-4056 Basel , Switzerland
| | - Vikram B Kasaragod
- Rudolf Virchow Center for Experimental Biomedicine , University of Würzburg , 97080 Würzburg , Germany
| | - Nicole Bader
- Rudolf Virchow Center for Experimental Biomedicine , University of Würzburg , 97080 Würzburg , Germany
| | - Hans M Maric
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine , University of Würzburg , 97080 Würzburg , Germany
| | - Bernhard Bettler
- Department of Biomedicine , University of Basel , CH-4056 Basel , Switzerland
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
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12
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Expression of programmed death ligand (PD-L1) in different tumors. Comparison of several current available antibody clones and antibody profiling. Ann Diagn Pathol 2019; 41:24-37. [DOI: 10.1016/j.anndiagpath.2019.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/11/2019] [Indexed: 12/11/2022]
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13
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Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat Methods 2019; 16:509-518. [DOI: 10.1038/s41592-019-0426-7] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/18/2019] [Indexed: 11/08/2022]
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14
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Identification of B cell epitopes enhanced by protein unfolding and aggregation. Mol Immunol 2018; 105:181-189. [PMID: 30550980 PMCID: PMC6344229 DOI: 10.1016/j.molimm.2018.11.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/16/2018] [Accepted: 11/30/2018] [Indexed: 12/21/2022]
Abstract
Aggregation of an exemplar therapeutic antibody fragment (scFv) enhances immunogenicity in vivo. Epitope mapping reveals immunogenicity is directed to a specific epitope in aggregate species. Molecular simulation demonstrates biophysical stress enhances epitope presentation. Protein aggregates have distinct immunological profiles to their native counterparts.
Aggregation of therapeutic proteins is a key factor in the generation of unwanted immunogenicity, and can result in reduced serum half-life, neutralization of function and adverse health effects. There is currently little information regarding how aggregates interact with B-cell receptors or cognate antibodies at the protein sequence level, or whether non-native, aggregate-induced epitopes predominate in these interactions. Using an antibody fragment (single chain antibody variable fragment; scFv) that forms aggregates readily at low temperature, anti-scFv IgG antibody responses were generated by intraperitoneal injection of BALB/c strain mice with monomer or aggregate preparations. Aggregate-specific immunosignatures were identified by oligo-peptide microarray fine epitope mapping, using overlapping 15mer peptides based on the linear sequence of scFv, printed onto glass slides. IgG antibodies from mice immunized with aggregated scFv preferentially recognized a patch of overlapping peptides. This region mapped to a β-strand located at the interface between the VH and VL domains. Molecular dynamics simulations indicated that the VL domain is less stable than the VH domain, suggesting the interface region between the two domains becomes exposed during partial unfolding of the scFv during aggregate formation. These data are consistent with the hypothesis that epitopes from partially unfolded states are revealed, or are more fully exposed, in the aggregated state, and that this can augment the IgG antibody response. This observation offers the theoretical possibility that epitopes preferentially associated with aggregates can be identified from the anti-drug antibody serum IgG response which may, in turn, lead to better methods for detection of anti-drug antibody responses, and improved design of therapeutic proteins to control immunogenicity.
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15
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Zolg DP, Wilhelm M, Schmidt T, Médard G, Zerweck J, Knaute T, Wenschuh H, Reimer U, Schnatbaum K, Kuster B. ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides. Mol Cell Proteomics 2018; 17:1850-1863. [PMID: 29848782 PMCID: PMC6126394 DOI: 10.1074/mcp.tir118.000783] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/21/2018] [Indexed: 11/06/2022] Open
Abstract
The analysis of the post-translational modification (PTM) state of proteins using mass spectrometry-based bottom-up proteomic workflows has evolved into a powerful tool for the study of cellular regulatory events that are not directly encoded at the genome level. Besides frequently detected modifications such as phosphorylation, acetylation and ubiquitination, many low abundant or less frequently detected PTMs are known or postulated to serve important regulatory functions. To more broadly understand the LC-MS/MS characteristics of PTMs, we synthesized and analyzed ∼5,000 peptides representing 21 different naturally occurring modifications of lysine, arginine, proline and tyrosine side chains and their unmodified counterparts. The analysis identified changes in retention times, shifts of precursor charge states and differences in search engine scores between modifications. PTM-dependent changes in the fragmentation behavior were evaluated using eleven different fragmentation modes or collision energies. We also systematically investigated the formation of diagnostic ions or neutral losses for all PTMs, confirming 10 known and identifying 5 novel diagnostic ions for lysine modifications. To demonstrate the value of including diagnostic ions in database searching, we reprocessed a public data set of lysine crotonylation and showed that considering the diagnostic ions increases confidence in the identification of the modified peptides. To our knowledge, this constitutes the first broad and systematic analysis of the LC-MS/MS properties of common and rare PTMs using synthetic peptides, leading to direct applicable utility for bottom-up proteomic experiments.
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Affiliation(s)
- Daniel Paul Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tobias Schmidt
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Guillaume Médard
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | | | | | - Ulf Reimer
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
- ¶Center for Integrated Protein Science Munich, Freising, Germany
- ‖Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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16
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Jiang K, Faltova L, Hua S, Capitani G, Prota AE, Landgraf C, Volkmer R, Kammerer RA, Steinmetz MO, Akhmanova A. Structural Basis of Formation of the Microtubule Minus-End-Regulating CAMSAP-Katanin Complex. Structure 2018; 26:375-382.e4. [DOI: 10.1016/j.str.2017.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/28/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022]
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17
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Zolg DP, Wilhelm M, Yu P, Knaute T, Zerweck J, Wenschuh H, Reimer U, Schnatbaum K, Kuster B. PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration. Proteomics 2017; 17. [PMID: 28872757 DOI: 10.1002/pmic.201700263] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/23/2017] [Indexed: 11/06/2022]
Abstract
Beyond specific applications, such as the relative or absolute quantification of peptides in targeted proteomic experiments, synthetic spike-in peptides are not yet systematically used as internal standards in bottom-up proteomics. A number of retention time standards have been reported that enable chromatographic aligning of multiple LC-MS/MS experiments. However, only few peptides are typically included in such sets limiting the analytical parameters that can be monitored. Here, we describe PROCAL (ProteomeTools Calibration Standard), a set of 40 synthetic peptides that span the entire hydrophobicity range of tryptic digests, enabling not only accurate determination of retention time indices but also monitoring of chromatographic separation performance over time. The fragmentation characteristics of the peptides can also be used to calibrate and compare collision energies between mass spectrometers. The sequences of all selected peptides do not occur in any natural protein, thus eliminating the need for stable isotope labeling. We anticipate that this set of peptides will be useful for multiple purposes in individual laboratories but also aiding the transfer of data acquisition and analysis methods between laboratories, notably the use of spectral libraries.
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Affiliation(s)
- Daniel Paul Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Peng Yu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | | | | | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Center for Integrated Protein Science Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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18
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Short Linear Sequence Motif LxxPTPh Targets Diverse Proteins to Growing Microtubule Ends. Structure 2017; 25:924-932.e4. [DOI: 10.1016/j.str.2017.04.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/06/2017] [Accepted: 04/28/2017] [Indexed: 11/23/2022]
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19
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López-Pérez PM, Grimsey E, Bourne L, Mikut R, Hilpert K. Screening and Optimizing Antimicrobial Peptides by Using SPOT-Synthesis. Front Chem 2017; 5:25. [PMID: 28447030 PMCID: PMC5388751 DOI: 10.3389/fchem.2017.00025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/29/2017] [Indexed: 11/14/2022] Open
Abstract
Peptide arrays on cellulose are a powerful tool to investigate peptide interactions with a number of different molecules, for examples antibodies, receptors or enzymes. Such peptide arrays can also be used to study interactions with whole cells. In this review, we focus on the interaction of small antimicrobial peptides with bacteria. Antimicrobial peptides (AMPs) can kill multidrug-resistant (MDR) human pathogenic bacteria and therefore could be next generation antibiotics targeting MDR bacteria. We describe the screen and the result of different optimization strategies of peptides cleaved from the membrane. In addition, screening of antibacterial activity of peptides that are tethered to the surface is discussed. Surface-active peptides can be used to protect surfaces from bacterial infections, for example implants.
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Affiliation(s)
| | - Elizabeth Grimsey
- Institute for Infection and Immunity, St. George's University of LondonLondon, UK
| | - Luc Bourne
- Institute for Infection and Immunity, St. George's University of LondonLondon, UK
| | - Ralf Mikut
- Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science (IAI)Eggenstein-Leopoldshafen, Germany
| | - Kai Hilpert
- TiKa Diagnostics LtdLondon, UK
- Institute for Infection and Immunity, St. George's University of LondonLondon, UK
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20
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Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B. Building ProteomeTools based on a complete synthetic human proteome. Nat Methods 2017; 14:259-262. [PMID: 28135259 DOI: 10.1038/nmeth.4153] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/20/2016] [Indexed: 01/02/2023]
Abstract
We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquid chromatography-tandem mass spectrometry analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products, and we exemplify the utility of these data in several applications. The resource (available at http://www.proteometools.org) will be extended to >1 million peptides, and all data will be shared with the community via ProteomicsDB and ProteomeXchange.
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Affiliation(s)
- Daniel P Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | | | | | | | | | - Siegfried Gessulat
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,SAP SE, Potsdam, Germany
| | | | - Maximilian Weininger
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Peng Yu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Karl Kramer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zürich, Switzerland.,Faculty of Science, University of Zürich, Zürich, Switzerland
| | | | | | | | | | | | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Center for Integrated Protein Science Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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21
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Tinti M, Panni S, Cesareni G. Profiling Phosphopeptide-Binding Domain Recognition Specificity Using Peptide Microarrays. Methods Mol Biol 2017; 1518:177-193. [PMID: 27873207 DOI: 10.1007/978-1-4939-6584-7_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cellular organization and response to internal and external stimuli are mediated by an intricate web of protein interactions. Some of these interactions are regulated by covalent posttranslational modifications such as phosphorylation and acetylation. These modifications can change the chemical nature of the interaction interfaces and modulate the binding affinity of the interacting partners. In signal transduction, the most frequent modification is reversible phosphorylation of tyrosine, serine or threonine residues. Protein phosphorylation may modulate the activity of enzymes by modifying their conformation, or regulate the formation of complexes by creating docking sites to recruit downstream effectors. Families of modular domains, such as SH2, PTB, and 14-3-3, act as "readers" of the modification event. Specificity between closely related domains of the same family is mediated by the chemical properties of the domain binding surface that, aside from offering a hydrophilic pocket for the phosphorylated residue, shows preference for specific sequences. Although the protein structure and the cell context are also important to ensure specificity, the amino acid sequence flanking the phosphorylation site defines the accuracy of the recognition process, and it is therefore essential to define the binding specificity of phosphopeptide binding domains in order to understand and to infer the interaction web mediated by phosphopeptides. Methods commonly used to discover new interactions (such as yeast two hybrid and phage display) are not suited to study interactions with phosphorylated proteins. On the other hand, peptide arrays are a powerful approach to precisely identify the binding preference of phosphopeptide recognition domains. Here we describe a detailed protocol to assemble arrays of hundreds to thousands phospho-peptides and to screen them with any modular domain of interest.
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Affiliation(s)
- Michele Tinti
- Division of Biochemical Chemistry and Drug Discovery, College of Life Science, Dundee University, Dow Street, Dundee, DD1 4HN, UK.
| | - Simona Panni
- Department of Biology, Ecology and Earth Science, DiBEST, University of Calabria, Rende, Italy.
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.,Istituto Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia, Rome, Italy
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22
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Manatschal C, Farcas AM, Degen MS, Bayer M, Kumar A, Landgraf C, Volkmer R, Barral Y, Steinmetz MO. Molecular basis of Kar9-Bim1 complex function during mating and spindle positioning. Mol Biol Cell 2016; 27:mbc.E16-07-0552. [PMID: 27682587 PMCID: PMC5170556 DOI: 10.1091/mbc.e16-07-0552] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 11/17/2022] Open
Abstract
The Kar9 pathway promotes nuclear fusion during mating and spindle alignment during metaphase in budding yeast. How Kar9 supports the different outcome of these two divergent processes is an open question. Here, we show that three sites in the C-terminal disordered domain of Kar9 mediate tight Kar9 interaction with the C-terminal dimerization domain of Bim1 (EB1 orthologue). Site1 and Site2 contain SxIP motifs; however, Site3 defines a novel type of EB1-binding site. Whereas Site2 and Site3 mediate Kar9 recruitment to microtubule tips, nuclear movement and karyogamy, solely Site2 functions in spindle positioning during metaphase. Site1 in turn plays an inhibitory role during mating. Additionally, the Kar9-Bim1 complex is involved in microtubule-independent activities during mating. Together, our data reveal how multiple and partially redundant EB1-binding sites provide a microtubule-associated protein with the means to modulate its biochemical properties to promote different molecular processes during cell proliferation and differentiation.
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Affiliation(s)
- Cristina Manatschal
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Ana-Maria Farcas
- Institute of Biochemistry, Biology Department, ETH Zürich, Zürich, Switzerland
| | - Miriam Steiner Degen
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Mathias Bayer
- Institute of Biochemistry, Biology Department, ETH Zürich, Zürich, Switzerland
| | - Anil Kumar
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Christiane Landgraf
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yves Barral
- Institute of Biochemistry, Biology Department, ETH Zürich, Zürich, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
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23
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Schlemm L, Giess RM, Rasche L, Pfuhl C, Wakonig K, Behrens JR, Scheibenbogen C, Bellmann-Strobl J, Paul F, Reimer U, Ruprecht K. Fine specificity of the antibody response to Epstein-Barr nuclear antigen-2 and other Epstein-Barr virus proteins in patients with clinically isolated syndrome: A peptide microarray-based case-control study. J Neuroimmunol 2016; 297:56-62. [PMID: 27397076 DOI: 10.1016/j.jneuroim.2016.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/20/2016] [Accepted: 05/11/2016] [Indexed: 01/14/2023]
Abstract
We analyzed the fine specificity of antibodies to Epstein-Barr nuclear antigen-2 (EBNA-2) and other Epstein-Barr virus (EBV) proteins in 29 patients with clinically isolated syndrome (CIS, the first clinical manifestation of multiple sclerosis [MS]) and 29 controls with a peptide microarray containing 117 overlapping peptides representing the full-length EBNA-2 protein and 71 peptides from 8 further EBV proteins. While EBV peptide antibodies were elevated in CIS, suggesting that EBV contributes to MS early during disease development, they discriminated groups only slightly better than EBNA-1 antibodies. Thus, the additional value of EBV peptide antibodies as diagnostic biomarkers for CIS appears moderate.
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Affiliation(s)
- Ludwig Schlemm
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - René Markus Giess
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Clinical and Experimental Multiple Sclerosis Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; NeuroCure Clinical Research Center, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ludwig Rasche
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Clinical and Experimental Multiple Sclerosis Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; NeuroCure Clinical Research Center, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Catherina Pfuhl
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Clinical and Experimental Multiple Sclerosis Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; NeuroCure Clinical Research Center, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Wakonig
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Clinical and Experimental Multiple Sclerosis Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; NeuroCure Clinical Research Center, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Janina Ruth Behrens
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Clinical and Experimental Multiple Sclerosis Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; NeuroCure Clinical Research Center, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Judith Bellmann-Strobl
- NeuroCure Clinical Research Center, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany; Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Friedemann Paul
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Clinical and Experimental Multiple Sclerosis Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; NeuroCure Clinical Research Center, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany; Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Klemens Ruprecht
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Clinical and Experimental Multiple Sclerosis Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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24
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Abstract
On a past volume of this monograph we have reviewed general aspects of the varied technologies available to generate peptide arrays. Hallmarks in the development of the technology and a main sketch of preparative steps and applications in binding assays were used to walk the reader through details of peptide arrays. In this occasion, we resume from that work and bring in some considerations on quantitative evaluation of measurements as well as on selected reports applying the technology.
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Affiliation(s)
| | - Rudolf Volkmer
- Institute of Medical Immunology, Charité-Universitätsmedizin zu Berlin, Hessische Str. 3-4, Berlin, 10115, Germany
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25
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Abstract
The automated SPOT (synthetic peptide arrays on membrane support technique) synthesis technology has entrenched as a rapid and robust method to generate peptide libraries on cellulose membrane supports. The synthesis method is based on conventional Fmoc chemistry building up peptides with free N-terminal amino acids starting at their cellulose-coupled C-termini. Several hundreds of peptide sequences can be assembled with this technique on one membrane comprising a strong binding potential due to high local peptide concentrations. Peptide orientation on SPOT membranes qualifies this array type for assaying substrate specificities of N-recognins, the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Pioneer studies described binding capability of mammalian and yeast enzymes depending on a peptide's N-terminus. SPOT arrays have been successfully used to describe substrate specificity of N-recognins which are the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Here, we describe the implementation of SPOT binding assays with focus on the identification of N-recognin substrates, applicable also for plant NERD enzymes.
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Affiliation(s)
- Maria Klecker
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany. .,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany.
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26
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Rohe A, Platzer C, Masch A, Greiner S, Henze C, Ihling C, Erdmann F, Schutkowski M, Sippl W, Schmidt M. Identification of peptidic substrates for the human kinase Myt1 using peptide microarrays. Bioorg Med Chem 2015; 23:4936-4942. [DOI: 10.1016/j.bmc.2015.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 01/25/2023]
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27
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Malešević M, Migge A, Hertel TC, Pietzsch M. A fluorescence-based array screen for transglutaminase substrates. Chembiochem 2015; 16:1169-74. [PMID: 25940638 DOI: 10.1002/cbic.201402709] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 01/05/2023]
Abstract
Transglutaminases (EC 2.3.2.13) form an enzyme family that catalyzes the formation of isopeptide bonds between the γ-carboxamide group of glutamine and the ε-amine group of lysine residues of peptides and proteins. Other primary amines can be accepted in place of lysine. Because of their important physiological and pathophysiological functions, transglutaminases have been studied for 60 years. However, the substrate preferences of this enzyme class remain largely elusive. In this study, we used focused combinatorial libraries of 400 peptides to investigate the influence of the amino acids adjacent to the glutamine and lysine residues on the catalysis of isopeptide bond formation by microbial transglutaminase. Using the peptide microarray technology we found a strong positive influence of hydrophobic and basic amino acids, especially arginine, tyrosine, and leucine. Several tripeptide substrates were synthesized, and enzymatic kinetic parameters were determined both by microarray analysis and in solution.
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Affiliation(s)
- Miroslav Malešević
- Institute of Biochemistry and Biotechnology, Department of Enzymology, Project Group gFP5, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany)
| | - Andreas Migge
- Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Faculty of Sciences I, Biosciences, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany)
| | - Thomas C Hertel
- Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Faculty of Sciences I, Biosciences, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany)
| | - Markus Pietzsch
- Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Faculty of Sciences I, Biosciences, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany).
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28
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Schönberg A, Bergner E, Helm S, Agne B, Dünschede B, Schünemann D, Schutkowski M, Baginsky S. The peptide microarray "ChloroPhos1.0" identifies new phosphorylation targets of plastid casein kinase II (pCKII) in Arabidopsis thaliana. PLoS One 2014; 9:e108344. [PMID: 25295873 PMCID: PMC4189921 DOI: 10.1371/journal.pone.0108344] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
We report the development of a peptide microarray based on previously determined phosphorylation sites in chloroplast proteins. Altogether, 905 peptides were spotted as 15mers in nine replicates onto glass slides. We used the microarray for in vitro phosphorylation experiments and specifically assessed the peptide substrate spectrum of chloroplast casein kinase II (pCKII). To this end, native pCKII from Arabidopsis thaliana and Sinapis alba chloroplasts was enriched by Heparin-Sepharose chromatography and its activity on the microarray was compared to the activity of a recombinant Arabidopsis pCKII. All three kinase preparations phosphorylated a similar set of peptides that were clearly distinct from those phosphorylated by bovine heart protein kinase A (PKA) in control experiments. The majority of the pCKII phosphorylation targets are involved in plastid gene expression, supporting the earlier denomination of pCKII as plastid transcription kinase (PTK). In addition we identified Alb3 as pCKII substrate that is essential for the integration of light-harvesting complex subunits (LHC) into the thylakoid membrane. Plastid CKII phosphorylation activity was characterized in greater detail in vitro with recombinant wildtype Alb3 and phosphorylation site mutants as substrates, establishing S424 as the pCKII phosphorylation site. Our data show that the peptide microarray ChloroPhos1.0 is a suitable tool for the identification of new kinase downstream targets in vitro that can be validated subsequently by in vivo experiments.
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Affiliation(s)
- Anna Schönberg
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Elena Bergner
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Bochum, Germany
| | - Mike Schutkowski
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- Steinbeis-Forschungszentrum, Peptide Microarrays, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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29
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Ruprecht K, Wunderlich B, Gieß R, Meyer P, Loebel M, Lenz K, Hofmann J, Rosche B, Wengert O, Paul F, Reimer U, Scheibenbogen C. Multiple sclerosis: The elevated antibody response to Epstein–Barr virus primarily targets, but is not confined to, the glycine–alanine repeat of Epstein–Barr nuclear antigen-1. J Neuroimmunol 2014; 272:56-61. [DOI: 10.1016/j.jneuroim.2014.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/05/2014] [Accepted: 04/08/2014] [Indexed: 01/14/2023]
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30
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Maiolica A, de Medina-Redondo M, Schoof EM, Chaikuad A, Villa F, Gatti M, Jeganathan S, Lou HJ, Novy K, Hauri S, Toprak UH, Herzog F, Meraldi P, Penengo L, Turk BE, Knapp S, Linding R, Aebersold R. Modulation of the chromatin phosphoproteome by the Haspin protein kinase. Mol Cell Proteomics 2014; 13:1724-40. [PMID: 24732914 DOI: 10.1074/mcp.m113.034819] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Recent discoveries have highlighted the importance of Haspin kinase activity for the correct positioning of the kinase Aurora B at the centromere. Haspin phosphorylates Thr(3) of the histone H3 (H3), which provides a signal for Aurora B to localize to the centromere of mitotic chromosomes. To date, histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin-associated proteins and identified a Haspin protein-protein interaction network. We determined the Haspin consensus motif and the co-crystal structure of the kinase with the histone H3 tail. The structure revealed a unique bent substrate binding mode positioning the histone H3 residues Arg(2) and Lys(4) adjacent to the Haspin phosphorylated threonine into acidic binding pockets. This unique conformation of the kinase-substrate complex explains the reported modulation of Haspin activity by methylation of Lys(4) of the histone H3. In addition, the identification of the structural basis of substrate recognition and the amino acid sequence preferences of Haspin aided the identification of novel candidate Haspin substrates. In particular, we validated the phosphorylation of Ser(137) of the histone variant macroH2A as a target of Haspin kinase activity. MacroH2A Ser(137) resides in a basic stretch of about 40 amino acids that is required to stabilize extranucleosomal DNA, suggesting that phosphorylation of Ser(137) might regulate the interactions of macroH2A and DNA. Overall, our data suggest that Haspin activity affects the phosphorylation state of proteins involved in gene expression regulation and splicing.
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Affiliation(s)
- Alessio Maiolica
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Maria de Medina-Redondo
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Erwin M Schoof
- ¶Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Apirat Chaikuad
- ‖Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, United Kingdom
| | - Fabrizio Villa
- **Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Marco Gatti
- ‡‡Department of Pharmaceutical Sciences, University of Piemonte Orientale "A. Avogadro" Novara, Italy
| | - Siva Jeganathan
- §§Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Hua Jane Lou
- ¶¶Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut 06520, USA
| | - Karel Novy
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Simon Hauri
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Umut H Toprak
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Franz Herzog
- ‖‖Gene Center Munich Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Meraldi
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lorenza Penengo
- ‡‡Department of Pharmaceutical Sciences, University of Piemonte Orientale "A. Avogadro" Novara, Italy
| | - Benjamin E Turk
- ¶¶Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut 06520, USA
| | - Stefan Knapp
- ‖Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, United Kingdom
| | - Rune Linding
- ¶Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
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31
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Lisson M, Novak N, Erhardt G. Immunoglobulin E epitope mapping by microarray immunoassay reveals differences in immune response to genetic variants of caseins from different ruminant species. J Dairy Sci 2014; 97:1939-54. [DOI: 10.3168/jds.2013-7355] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/08/2013] [Indexed: 12/25/2022]
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32
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Rauh D, Fischer F, Gertz M, Lakshminarasimhan M, Bergbrede T, Aladini F, Kambach C, Becker CFW, Zerweck J, Schutkowski M, Steegborn C. An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms. Nat Commun 2014; 4:2327. [PMID: 23995836 DOI: 10.1038/ncomms3327] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 07/19/2013] [Indexed: 12/22/2022] Open
Abstract
Sirtuin enzymes regulate metabolism and aging processes through deacetylation of acetyl-lysines in target proteins. More than 6,800 mammalian acetylation sites are known, but few targets have been assigned to most sirtuin isoforms, hampering our understanding of sirtuin function. Here we describe a peptide microarray system displaying 6,802 human acetylation sites for the parallel characterisation of their modification by deacetylases. Deacetylation data for all seven human sirtuins obtained with this system reveal isoform-specific substrate preferences and deacetylation substrate candidates for all sirtuin isoforms, including Sirt4. We confirm malate dehydrogenase protein as a Sirt3 substrate and show that peroxiredoxin 1 and high-mobility group B1 protein are deacetylated by Sirt5 and Sirt1, respectively, at the identified sites, rendering them likely new in vivo substrates. Our microarray platform enables parallel studies on physiological acetylation sites and the deacetylation data presented provide an exciting resource for the identification of novel substrates for all human sirtuins.
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Affiliation(s)
- David Rauh
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University, Kurt-Mothes-Staße 3, 06120 Halle (Saale), Germany
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33
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OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 2014; 32:219-23. [DOI: 10.1038/nbt.2841] [Citation(s) in RCA: 547] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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34
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Schnatbaum K, Schmoldt HU, Daneschdar M, Plum LM, Jansong J, Zerweck J, Kühne Y, Masch A, Wenschuh H, Fiedler M, Türeci Ö, Sahin U, Reimer U. Peptide microarrays enable rapid mimotope optimization for pharmacokinetic analysis of the novel therapeutic antibody IMAB362. Biotechnol J 2014; 9:545-54. [DOI: 10.1002/biot.201300456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/06/2013] [Accepted: 02/04/2014] [Indexed: 01/27/2023]
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35
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Tinti M, Kiemer L, Costa S, Miller ML, Sacco F, Olsen JV, Carducci M, Paoluzi S, Langone F, Workman CT, Blom N, Machida K, Thompson CM, Schutkowski M, Brunak S, Mann M, Mayer BJ, Castagnoli L, Cesareni G. The SH2 domain interaction landscape. Cell Rep 2013; 3:1293-305. [PMID: 23545499 DOI: 10.1016/j.celrep.2013.03.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 01/23/2023] Open
Abstract
Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells.
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Affiliation(s)
- Michele Tinti
- Department of Biology, University of Rome Tor Vergata, I-00133 Rome, Italy
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36
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Ho MC, Wilczek C, Bonanno JB, Xing L, Seznec J, Matsui T, Carter LG, Onikubo T, Kumar PR, Chan MK, Brenowitz M, Cheng RH, Reimer U, Almo SC, Shechter D. Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity. PLoS One 2013; 8:e57008. [PMID: 23451136 PMCID: PMC3581573 DOI: 10.1371/journal.pone.0057008] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/16/2013] [Indexed: 01/07/2023] Open
Abstract
The arginine methyltransferase PRMT5-MEP50 is required for embryogenesis and is misregulated in many cancers. PRMT5 targets a wide variety of substrates, including histone proteins involved in specifying an epigenetic code. However, the mechanism by which PRMT5 utilizes MEP50 to discriminate substrates and to specifically methylate target arginines is unclear. To test a model in which MEP50 is critical for substrate recognition and orientation, we determined the crystal structure of Xenopus laevis PRMT5-MEP50 complexed with S-adenosylhomocysteine (SAH). PRMT5-MEP50 forms an unusual tetramer of heterodimers with substantial surface negative charge. MEP50 is required for PRMT5-catalyzed histone H2A and H4 methyltransferase activity and binds substrates independently. The PRMT5 catalytic site is oriented towards the cross-dimer paired MEP50. Histone peptide arrays and solution assays demonstrate that PRMT5-MEP50 activity is inhibited by substrate phosphorylation and enhanced by substrate acetylation. Electron microscopy and reconstruction showed substrate centered on MEP50. These data support a mechanism in which MEP50 binds substrate and stimulates PRMT5 activity modulated by substrate post-translational modifications.
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Affiliation(s)
- Meng-Chiao Ho
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
| | - Carola Wilczek
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Jeffrey B. Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Li Xing
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
| | | | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Lester G. Carter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Takashi Onikubo
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - P. Rajesh Kumar
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Man K. Chan
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - R. Holland Cheng
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
| | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
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37
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Hüttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J, Rinner O, Kusebauch U, Hajdúch M, Moritz RL, Wollscheid B, Aebersold R. N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol Cell Proteomics 2013; 12:1005-16. [PMID: 23408683 DOI: 10.1074/mcp.o112.026617] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein biomarkers have the potential to transform medicine as they are clinically used to diagnose diseases, stratify patients, and follow disease states. Even though a large number of potential biomarkers have been proposed over the past few years, almost none of them have been implemented so far in the clinic. One of the reasons for this limited success is the lack of technologies to validate proposed biomarker candidates in larger patient cohorts. This limitation could be alleviated by the use of antibody-independent validation methods such as selected reaction monitoring (SRM). Similar to measurements based on affinity reagents, SRM-based targeted mass spectrometry also requires the generation of definitive assays for each targeted analyte. Here, we present a library of SRM assays for 5568 N-glycosites enabling the multiplexed evaluation of clinically relevant N-glycoproteins as biomarker candidates. We demonstrate that this resource can be utilized to select SRM assay sets for cancer-associated N-glycoproteins for their subsequent multiplexed and consistent quantification in 120 human plasma samples. We show that N-glycoproteins spanning 5 orders of magnitude in abundance can be quantified and that previously reported abundance differences in various cancer types can be recapitulated. Together, the established N-glycoprotein SRMAtlas resource facilitates parallel, efficient, consistent, and sensitive evaluation of proposed biomarker candidates in large clinical sample cohorts.
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Affiliation(s)
- Ruth Hüttenhain
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
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38
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Habermann K, Mirgorodskaya E, Gobom J, Lehmann V, Müller H, Blümlein K, Deery MJ, Czogiel I, Erdmann C, Ralser M, von Kries JP, Lange BMH. Functional analysis of centrosomal kinase substrates in Drosophila melanogaster reveals a new function of the nuclear envelope component otefin in cell cycle progression. Mol Cell Biol 2012; 32:3554-69. [PMID: 22751930 PMCID: PMC3422010 DOI: 10.1128/mcb.00814-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 06/25/2012] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation is one of the key mechanisms that regulate centrosome biogenesis, spindle assembly, and cell cycle progression. However, little is known about centrosome-specific phosphorylation sites and their functional relevance. Here, we identified phosphoproteins of intact Drosophila melanogaster centrosomes and found previously unknown phosphorylation sites in known and unexpected centrosomal components. We functionally characterized phosphoproteins and integrated them into regulatory signaling networks with the 3 important mitotic kinases, cdc2, polo, and aur, as well as the kinase CkIIβ. Using a combinatorial RNA interference (RNAi) strategy, we demonstrated novel functions for P granule, nuclear envelope (NE), and nuclear proteins in centrosome duplication, maturation, and separation. Peptide microarrays confirmed phosphorylation of identified residues by centrosome-associated kinases. For a subset of phosphoproteins, we identified previously unknown centrosome and/or spindle localization via expression of tagged fusion proteins in Drosophila SL2 cells. Among those was otefin (Ote), an NE protein that we found to localize to centrosomes. Furthermore, we provide evidence that it is phosphorylated in vitro at threonine 63 (T63) through Aurora-A kinase. We propose that phosphorylation of this site plays a dual role in controlling mitotic exit when phosphorylated while dephosphorylation promotes G(2)/M transition in Drosophila SL2 cells.
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Affiliation(s)
- Karin Habermann
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Ekaterina Mirgorodskaya
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Johan Gobom
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Verena Lehmann
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Hannah Müller
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Katharina Blümlein
- University of Cambridge, Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge, United Kingdom
| | - Michael J. Deery
- University of Cambridge, Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge, United Kingdom
| | - Irina Czogiel
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Christoph Erdmann
- Leibniz Institute for Molecular Pharmacology (FMP), Screening Unit, Berlin, Germany
| | - Markus Ralser
- University of Cambridge, Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge, United Kingdom
| | - Jens Peter von Kries
- Leibniz Institute for Molecular Pharmacology (FMP), Screening Unit, Berlin, Germany
| | - Bodo M. H. Lange
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
- Alacris Theranostics GmbH, Berlin, Germany
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39
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Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med 2012; 4:142ra94. [PMID: 22786679 PMCID: PMC3766734 DOI: 10.1126/scitranslmed.3003989] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The rigorous testing of hypotheses on suitable sample cohorts is a major limitation in translational research. This is particularly the case for the validation of protein biomarkers; the lack of accurate, reproducible, and sensitive assays for most proteins has precluded the systematic assessment of hundreds of potential marker proteins described in the literature. Here, we describe a high-throughput method for the development and refinement of selected reaction monitoring (SRM) assays for human proteins. The method was applied to generate such assays for more than 1000 cancer-associated proteins, which are functionally related to candidate cancer driver mutations. We used the assays to determine the detectability of the target proteins in two clinically relevant samples: plasma and urine. One hundred eighty-two proteins were detected in depleted plasma, spanning five orders of magnitude in abundance and reaching below a concentration of 10 ng/ml. The narrower concentration range of proteins in urine allowed the detection of 408 proteins. Moreover, we demonstrate that these SRM assays allow reproducible quantification by monitoring 34 biomarker candidates across 83 patient plasma samples. Through public access to the entire assay library, researchers will be able to target their cancer-associated proteins of interest in any sample type using the detectability information in plasma and urine as a guide. The generated expandable reference map of SRM assays for cancer-associated proteins will be a valuable resource for accelerating and planning biomarker verification studies.
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Affiliation(s)
- Ruth Hüttenhain
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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40
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Buey RM, Sen I, Kortt O, Mohan R, Gfeller D, Veprintsev D, Kretzschmar I, Scheuermann J, Neri D, Zoete V, Michielin O, de Pereda JM, Akhmanova A, Volkmer R, Steinmetz MO. Sequence determinants of a microtubule tip localization signal (MtLS). J Biol Chem 2012; 287:28227-42. [PMID: 22696216 DOI: 10.1074/jbc.m112.373928] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubule plus-end-tracking proteins (+TIPs) specifically localize to the growing plus-ends of microtubules to regulate microtubule dynamics and functions. A large group of +TIPs contain a short linear motif, SXIP, which is essential for them to bind to end-binding proteins (EBs) and target microtubule ends. The SXIP sequence site thus acts as a widespread microtubule tip localization signal (MtLS). Here we have analyzed the sequence-function relationship of a canonical MtLS. Using synthetic peptide arrays on membrane supports, we identified the residue preferences at each amino acid position of the SXIP motif and its surrounding sequence with respect to EB binding. We further developed an assay based on fluorescence polarization to assess the mechanism of the EB-SXIP interaction and to correlate EB binding and microtubule tip tracking of MtLS sequences from different +TIPs. Finally, we investigated the role of phosphorylation in regulating the EB-SXIP interaction. Together, our results define the sequence determinants of a canonical MtLS and provide the experimental data for bioinformatics approaches to carry out genome-wide predictions of novel +TIPs in multiple organisms.
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Affiliation(s)
- Rubén M Buey
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
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41
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Maiolica A, Jünger MA, Ezkurdia I, Aebersold R. Targeted proteome investigation via selected reaction monitoring mass spectrometry. J Proteomics 2012; 75:3495-513. [PMID: 22579752 DOI: 10.1016/j.jprot.2012.04.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 04/27/2012] [Accepted: 04/29/2012] [Indexed: 12/20/2022]
Abstract
Due to the enormous complexity of proteomes which constitute the entirety of protein species expressed by a certain cell or tissue, proteome-wide studies performed in discovery mode are still limited in their ability to reproducibly identify and quantify all proteins present in complex biological samples. Therefore, the targeted analysis of informative subsets of the proteome has been beneficial to generate reproducible data sets across multiple samples. Here we review the repertoire of antibody- and mass spectrometry (MS) -based analytical tools which is currently available for the directed analysis of predefined sets of proteins. The topics of emphasis for this review are Selected Reaction Monitoring (SRM) mass spectrometry, emerging tools to control error rates in targeted proteomic experiments, and some representative examples of applications. The ability to cost- and time-efficiently generate specific and quantitative assays for large numbers of proteins and posttranslational modifications has the potential to greatly expand the range of targeted proteomic coverage in biological studies. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Alessio Maiolica
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
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42
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Volkmer R, Tapia V, Landgraf C. Synthetic peptide arrays for investigating protein interaction domains. FEBS Lett 2012; 586:2780-6. [PMID: 22576123 DOI: 10.1016/j.febslet.2012.04.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 11/28/2022]
Abstract
Synthetic peptide array technology was first developed in the early 1990s by Ronald Frank. Since then the technique has become a powerful tool for high throughput approaches in biology and biochemistry. Here, we focus on peptide arrays applied to investigate the binding specificity of protein interaction domains such as WW, SH3, and PDZ domains. We describe array-based methods used to reveal domain networks in yeast, and briefly review rules as well as ideas about the synthesis and application of peptide arrays. We also provide initial results of a study designed to investigate the nature and evolution of SH3 domain interaction networks in eukaryotes.
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Affiliation(s)
- Rudolf Volkmer
- Institut für Medizinische Immunologie Berlin, Molecular Libraries and Recognition Group, Charité-Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany.
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43
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Rezaei Araghi R, Mahrenholz CC, Volkmer R, Koksch B. Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique. Beilstein J Org Chem 2012; 8:640-9. [PMID: 22563362 PMCID: PMC3343290 DOI: 10.3762/bjoc.8.71] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 04/03/2012] [Indexed: 12/01/2022] Open
Abstract
We screened a randomized library and identified natural peptides that bound selectively to a chimeric peptide containing α-, β- and γ-amino acids. The SPOT arrays provide a means for the systematic study of the possible interaction space accessible to the αβγ-chimera. The mutational analysis reveals the dependence of the binding affinities of α-peptides to the αβγ-chimera, on the hydrophobicity and bulkiness of the side chains at the corresponding hydrophobic interface. The stability of the resulting heteroassemblies was further confirmed in solution by CD and thermal denaturation.
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Affiliation(s)
- Raheleh Rezaei Araghi
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Carsten C Mahrenholz
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Rudolf Volkmer
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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44
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Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
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Volkmer R, Kretzschmar I, Tapia V. Mapping receptor–ligand interactions with synthetic peptide arrays: Exploring the structure and function of membrane receptors. Eur J Cell Biol 2012; 91:349-56. [DOI: 10.1016/j.ejcb.2011.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/15/2011] [Accepted: 03/17/2011] [Indexed: 11/25/2022] Open
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Maksimov P, Zerweck J, Maksimov A, Hotop A, Groß U, Spekker K, Däubener W, Werdermann S, Niederstrasser O, Petri E, Mertens M, Ulrich RG, Conraths FJ, Schares G. Analysis of clonal type-specific antibody reactions in Toxoplasma gondii seropositive humans from Germany by peptide-microarray. PLoS One 2012; 7:e34212. [PMID: 22470537 PMCID: PMC3314601 DOI: 10.1371/journal.pone.0034212] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 02/28/2012] [Indexed: 11/18/2022] Open
Abstract
Background Different clonal types of Toxoplasma gondii are thought to be associated with distinct clinical manifestations of infections. Serotyping is a novel technique which may allow to determine the clonal type of T. gondii humans are infected with and to extend typing studies to larger populations which include infected but non-diseased individuals. Methodology A peptide-microarray test for T. gondii serotyping was established with 54 previously published synthetic peptides, which mimic clonal type-specific epitopes. The test was applied to human sera (n = 174) collected from individuals with an acute T. gondii infection (n = 21), a latent T. gondii infection (n = 53) and from T. gondii-seropositive forest workers (n = 100). Findings The majority (n = 124; 71%) of all T. gondii seropositive human sera showed reactions against synthetic peptides with sequences specific for clonal type II (type II peptides). Type I and type III peptides were recognized by 42% (n = 73) or 16% (n = 28) of the human sera, respectively, while type II–III, type I–III or type I–II peptides were recognized by 49% (n = 85), 36% (n = 62) or 14% (n = 25) of the sera, respectively. Highest reaction intensities were observed with synthetic peptides mimicking type II-specific epitopes. A proportion of the sera (n = 22; 13%) showed no reaction with type-specific peptides. Individuals with acute toxoplasmosis reacted with a statistically significantly higher number of peptides as compared to individuals with latent T. gondii infection or seropositive forest workers. Conclusions Type II-specific reactions were overrepresented and higher in intensity in the study population, which was in accord with genotyping studies on T. gondii oocysts previously conducted in the same area. There were also individuals with type I- or type III-specific reactions. Well-characterized reference sera and further specific peptide markers are needed to establish and to perform future serotyping approaches with higher resolution.
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Affiliation(s)
- Pavlo Maksimov
- Federal Research Institute for Animal Health, Institute of Epidemiology, Friedrich-Loeffler-Institut, Wusterhausen, Germany
- * E-mail: (PM); (GS)
| | | | - Aline Maksimov
- Federal Research Institute for Animal Health, Institute of Epidemiology, Friedrich-Loeffler-Institut, Wusterhausen, Germany
| | - Andrea Hotop
- German National Consulting Laboratory for Toxoplasmosis, Department of Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Groß
- German National Consulting Laboratory for Toxoplasmosis, Department of Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Katrin Spekker
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Walter Däubener
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | | | | | | | - Marc Mertens
- Federal Research Institute for Animal Health, Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Rainer G. Ulrich
- Federal Research Institute for Animal Health, Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Franz J. Conraths
- Federal Research Institute for Animal Health, Institute of Epidemiology, Friedrich-Loeffler-Institut, Wusterhausen, Germany
| | - Gereon Schares
- Federal Research Institute for Animal Health, Institute of Epidemiology, Friedrich-Loeffler-Institut, Wusterhausen, Germany
- * E-mail: (PM); (GS)
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Florea M, Kudithipudi S, Rei A, González-Álvarez MJ, Jeltsch A, Nau WM. A Fluorescence-Based Supramolecular Tandem Assay for Monitoring Lysine Methyltransferase Activity in Homogeneous Solution. Chemistry 2012; 18:3521-8. [DOI: 10.1002/chem.201103397] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Indexed: 11/06/2022]
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Barros SC, Martins JA, Marcos JC, Cavaco-Paulo A. Characterization of potential elastase inhibitor-peptides regulated by a molecular switch for wound dressings applications. Enzyme Microb Technol 2012; 50:107-14. [DOI: 10.1016/j.enzmictec.2011.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 10/27/2011] [Accepted: 10/31/2011] [Indexed: 11/24/2022]
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Abstract
A crucial part of optimization of metabolically engineered organisms is producing balanced levels of pathway proteins. Typically, protein levels are monitored by Western blot analysis; however, application to multiple enzyme pathways can be difficult without unique antibodies for each enzyme in the pathway. Furthermore, it can be time consuming, and cost prohibitive during exploratory stages of pathway design when many different proteins must be monitored simultaneously. We present here a targeted proteomics approach that uses selected-reaction monitoring (SRM) mass spectrometry to quantify multiple proteins in a sample. SRM methods provide high selectivity and high sensitivity to enable rapid quantification of multiple proteins in an engineered pathway regardless of sequence or organism of origin.
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Affiliation(s)
- Tanveer S Batth
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Joint BioEnergy Institute (JBEI), Berkeley, CA, USA
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Adams R, Worth CL, Guenther S, Dunkel M, Lehmann R, Preissner R. Binding sites in membrane proteins--diversity, druggability and prospects. Eur J Cell Biol 2011; 91:326-39. [PMID: 21872966 DOI: 10.1016/j.ejcb.2011.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 06/22/2011] [Accepted: 06/22/2011] [Indexed: 11/27/2022] Open
Abstract
The identification of novel drug targets is one of the major challenges in proteomics. Computational methods developed over the last decade have enhanced the process of drug design in both terms of time and quality. The main task is the design of selective compounds, which bind targets more specifically, dependent on the desired mode of action of the particular drug. This makes it necessary to create compounds, which either exhibit their functions on one single protein to exclude undesired cross-reactivity or to use the advantageous effect of less selective drugs that target numerous proteins and therefore exhibit their functions on whole protein classes. Main aspects in the assignment of interactions between ligands and putative targets involve the amino acid composition of the binding site, evolutionary conservation and similarity in sequence and structure of known targets. Similarities or differences within classified protein families can be the key to their function and give first hints to functional drug design. Hereby, binding site-based classification outnumbers sequence-based classifications since similar binding sites can also be found in more distant proteins. Membrane proteins are 'difficult targets', because of their special physicochemical characteristics and the general lack of structural information. Here, we describe recent advances in modeling methods dedicated to membrane proteins. Different descriptors of similarity between compounds and the similarity between binding sites are under development and elucidate important aspects like dynamics or entropy. The importance of computational drug design is undisputable. Nevertheless, the process of design is complicated by increasing complexity, which underlines the importance of accurate knowledge about the addressed target class(es) and particularly their binding sites. One main objective by considering named topics is to predict putative side effects and errant functions (off-target effects) of novel drugs, which requires a holistic (systems biology) view on drug-target-pathway relations. In the following, we give a brief summary about the recent discussion on drug-target interactions with emphasis on membrane proteins.
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Affiliation(s)
- Robert Adams
- Charité-Universitätsklinikum Berlin, Structural Bioinformatics Group, Lindenberger Weg 80, 13125 Berlin, Germany
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