Sfinx: Cool acronym, more accurate protein analysis
The labs of Jan Tavernier, Kris Gevaert and Sven Eyckerman from the VIB Medical Biotechnology Center, UGent tackle some of the most fundamental life sciences questions in their research into the detection and analysis of protein-protein interaction. This kind of analysis helps scientists come up with new hypotheses for the functions of proteins. Unfortunately, good data analysis in this area is tricky. Until now: Jan, Kris and Sven developed SFINX, a powerful online tool that does away with the hassle.
Sven: “High-end mass spectrometry instruments are incredibly sensitive. Since they are capable of identifying huge numbers of proteins, finding the relevant ones is quite an analytical challenge. PhD student Kevin Titeca developed an intuitive and powerful tool to filter out the relevant proteins that can be applied to a number of different approaches and techniques. In collaboration with Lennart Martens from our department and researchers from the University of Antwerp, he developed the Straightforward Filtering INdeX, or simply SFINX.”
Harder, better, faster, stronger
There are already software solutions that separate false from true positives in these protein-protein interaction datasets, but none of them combine accuracy, speed and user-friendliness without the need for external data.
Kevin: “SFINX outperforms other techniques. It’s stronger, faster and highly intuitive. Unlike the other solutions out there, it doesn’t need any external resources, which makes its results more objective and reproducible. SFINX’s algorithm and web interface are user-friendly and produce immediate visual results.”
Anybody can easily access SFINX via its web interface at sfinx.ugent.be
Trapping mammalian protein complexes in viral particles
The VIB/UGent research team led by Sven Eyckerman has developed Virotrap, a generic platform for characterizing protein complexes under native conditions. Virotrap catches a bait protein together with its associated protein partners in virus-like particles that bud from mammalian cells. In this way, cell lysis is not needed and protein complexes are preserved during purification. Virotrap is already successfully being used in collaboration with other VIB teams. The development and application of this pioneering technique is described in a paper in Nature Communications.
Publication: Eyckerman et al., Nature Communications 2016
Discovering more about proteins created by genes
Even though the human genome was sequenced a decade ago, figuring out which DNA regions create which proteins remains a challenge. Recent research suggests that current knowledge of protein creation sites on genes is incomplete, pointing to the possibility that 10-20% are created at alternative sites. In their new project, Petra Van Damme of the of VIB Medical Biotechnology Center, UGent and her team studied newly discovered N-terminal proteoforms (protein “bits” created by a single gene). She’s happy to tell us all about it.
Petra, can you tell us more about protein stability?
Petra: “Protein stability has a big impact on gene expression, which determines which types of cells our bodies make. Ours is the first large-scale study of protein stability that can see differences between multiple N-terminal protein forms that are produced by a single gene. Using the method we developed in our lab, we confirmed that N-Terminal proteoforms come from alternative start sites on the same gene, and that they can vary widely in stability.”
How will these findings be put to use?
Petra: “It’s important for us to expand our current understanding of proteoforms – and the human genome – by exploring alternative start sites of proteomes. Overlooked in the past, alternative proteoforms can cause problems in biomedical research because of their effects on antibodies and gene expression.”
What are your plans moving forward in terms of proteomics research?
Petra: “There’s a real lack of scientific literature in this area, and N-terminal proteoforms are still poorly-understood. Our future goals center around identifying where and why certain proteoforms are generated within genes. We also want to expand scientific awareness of the processes that drive alternative translation events, and increase our understanding of translation regulation and the creation of these protein forms.”