Proteins are the chief actors within all living systems
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Prof. Dr. Matthias Selbach
Proteins are the chief actors within all living systems: They are major structural components of all cells, catalyze almost all biochemical reactions and mediate virtually all signal transduction processes. Despite their paramount importance there is still little information about proteins at the global scale. Recent developments in mass spectrometry have dramatically improved the analytical power of this technology. Particularly, quantitative approaches have been developed to comprehensively identify and quantify proteins in complex samples. We are using mass spectrometry-based quantitative proteomics to analyze biological systems at the protein level. This allows us to gather data with direct functional relevance not attainable with other technologies. We focus on posttranscriptional regulation of gene expression, protein-protein interaction and cell signaling.
Regulation of gene expression occurs at all stages from mRNA transcription to protein synthesis. While most research in the past has concentrated on transcriptional regulation it is now clear that translation itself is a regulated process with a central role in cellular physiology and therefore in a growing catalogue of human diseases. We developed a novel quantitative proteomics approach, pSILAC, to measure changes in protein production on a global scale (Schwanhaeusser et al, in press). We are using pSILAC to investigate post-transcriptional regulation of gene expression by microRNAs. In a proof of principle paper we were able to show that individual microRNAs directly repress production of hundreds of proteins (Selbach et al, 2008). We are continuing to employ pSILAC to unravel the principles of microRNA mediated regulation of gene expression. By combining state of the art mass spectrometry-based proteomics with deep sequencing technology we will obtain a comprehensive picture of gene expression.
Another central and frequently missed aspect of biological systems is the dynamic regulation of protein-protein interaction. A useful method to study protein-protein interactions in mammalian cells is affinity purification combined with mass spectrometry. However, like all other biochemical purification procedures this method suffers from the trade-off between sensitivity and specificity: Stringent purification conditions remove contaminants but may also eliminate specific interaction partners with weak affinities and/or low abundance. Quantitative proteomics solves this problem by comparing the abundance of proteins identified in a pull-down experiment with a suitable internal control. This allows the development of assays that can directly lead to understanding of biological systems (Selbach and Mann, 2006). We are using this method to detect interaction partners of proteins involved in neurological disorders. In addition, we are using quantitative mass spectrometry to study signalling by Rho-GTPases, an important family of signalling molecules thought to regulate or be regulated by as much as 1 % of all proteins encoded in the human genome.