Molecular tools for functional proteomics and interactomics


The vast amount of data originating from the different genome initiatives in the context of systems biology require more and more emphasis to be placed on the elucidation of the different levels of dynamic processes present in the living cell.
Beyond the transcription level (transcriptome), systematic analysis of the proteins expressed by a cell at a certain time and under certain condition (proteome) is of eminent importance, as they are the major players in biological processes. Despite the fact, that many technological advances are currently involved in proteome analysis, there is still a great need for the development of novel molecular tools for genome-wide proteome analysis or tailored creation and analysis of proteome subsets. A modular, universally applicable method has been established to enable the identification of protein families via suitable ligands and their detection by reporter groups (e.g. fluorophores). In case of reversibly binding ligands, the covalent linkage of the ligand-fluorophor conjugates with the protein is a main prerequisite. Hence, the conjugates are attached to a photoreactive group which irreversibly ligates protein and the modified ligand.
This method is generally applicable, since it is not based on irreversibly binding ligands (suicide inhibitors). This modular concept can be widely extended to many relevant protein families. The method presented herein primarily serves as a diagnostic tool in proteome research. For the systematic analysis of enzymatic families in cellular compartments it also holds its potential in pharmaceutical research, e.g. for target validation as well as for biotechnology.
In this project, 2D-gel electrophoresis, MALDI-ToF MS, ESI-MS and surface plasmon resonance (SPR, BIAcore) are applied in order to detect new, hitherto unknown, members of protein families.
Retrieval of biomolecular interaction partners from the proteome results in the interactome of a class of proteins or other biomolecules. The scientific goal of the project is the development and application of novel engineered chemical probes for proteomics and interactomics. Focus is placed on the interaction of integrins and matrix metalloproteinases with each other and with other proteins, as both are potential targets in tumour therapy. Small-molecule integrin ligands (RGD peptides) and matrix metalloproteinases (hydroxamate inhibitors), respectively, will be chemically modified to allow for the immobilisation of the ligands to magnetic beads or affinity chromatography materials. Proteins will be detected together with their native interaction partners because of the non-denaturing conditions.



Mechanism-Based Tagging of Protein Families – A New Concept in Functional Proteomics
M. C. Hagenstein, J. H. Mussgnug, K. Lotte, R. Plessow, A. Brockhinke, O. Kruse, N. Sewald
Angew. Chem., 115 (2003) 5793-5796; Angew. Chem. Int. Ed. Engl., 42 (2003) 5635-5638.




Synthesis of Marimastat and a Marimastat Conjugate for Affnity Chromatography and Surface Plasmon Resonance Studies
K. Jenssen, K. Sewald, N. Sewald
Bioconj. Chem., 15 (2004) 594-600.




Molekulare Werkzeuge für die funktionelle Proteomanalyse
N. Sewald
BIOforum, 7-8 (2005), 40-41.



People involved:
Dr. Magalie Collet, Dr. Miriam C. Hagenstein, Dr. Kai Jenssen, Dr. Janina Lenger, Dr. Patrik Plattner


Collaborations:
Dr. Olaf Kruse, Bielefeld; Dr. Dominique Alfandari, Amherst


Info

Here you find Information about the projects of the workgroup Organic Chemistry III.