top of page
Peter Nagy's Research Group
Quantitative Receptor Analysis
Department of Biophysics and Cell Biology
University of Debrecen
On this page you can find a brief description of projects that are currently undertaken. For a background of these project, please refer to the "Interests" page.
1. Membrane dependent effects on growth factor binding and ligand-induced cellular responses
Growth factor binding is usually regarded as a simple event and the complexity of biological responses only unfolds after "simple" binding has been completed. However, binding is a complex equilibrium that is influenced by the presence of the membrane, membrane curvature, nonspecific binding and endocytosis. Currently, we are studying, both experimentally and using simulations, how these parameters bear on binding of EGF to its receptor.
2. Clustering of and transmembrane signaling mediated by different isoforms of ErbB4 and transmembrane-domain mutated ErbB2
While the general principles of how receptor tyrosine kinases are activated are quite well defined, there are still many open question. From among these problems we are currently studying
how the four different isoforms of ErbB4 dimerize and transmit signals. The JM-a juxtamembrane domain variant is processed by the TACE protease, while the JM-b variant is not. The Cyt-1 variant can bind PI3K and the Itch ubiquitin ligase, while the Cyt-2 variant cannot. In collaboration with Mario Brameshuber from the Technical University of Vienna we are looking at the clustering and signaling propensities of these variants.
how ErbB2 mutants, isolated from human sperm, differ from each other in terms of dimerization and their ability to stimulate proliferation. In collaboration with Irene Tiemann-Boege from the Johannes Kepler University Linz we would like to find out if these mutations have anything to do with the paternal age effect.
3. Characterization of the interactions of penetratin in the membrane from a biophysical perspective
Penetratin is a cell penetrating peptide that can get into the cytosol of cells with intact plasma membranes. It can achieve this feat even when loaded with cargo, i.e. when drugs are conjugated to it. Although it can get into cells either by direct membrane penetration or by endocytosis, both mechanisms include crossing the membrane. Therefore, it is of utmost importance what happens with penetratin in the membrane. We are characterizing the mobility and oligomerization of penetratin in different cellular compartments. In collaboration with István Mándity from the Semmelweis University we would like to design new penetratin derivatives and correlate their biophysical properties with their structure and cell-penetrating potential. We would also like to test targeted penetratin derivatives in vitro and in vivo.
4. The membrane dipole potential in different cellular compartments
The dipole potential is a strong, intramembrane potential whose magnitude is influenced by the composition and order of the membrane. The dipole potential influences the oligomerization and conformation of membrane proteins and the interaction of substances with the membrane. We would like to measure the dipole potential in different cellular compartments and to correlate these findings with the behavior of membrane proteins in these compartments.
5. The effect of CH4 on the biophysical properties of the membrane
Our collaboration partners from the Institute of Surgical Research, University of Szeged have shown that methane can significantly alleviate the consequences of hypoxia-reperfusion injury. Although methane is a potential therapeutic gas for its aforementioned effects, its mechanism of action is largely unknown. We are studying how methane affects membrane structure, and how these effects could explain its effect on free radical-induced cell death. A model is beginning to emerge in which membrane domains take a central role in the mechanism of action of methane.
6. Effect of membrane composition on the formation of membrane nanotubes and extracellular vesicles
We have shown previously that accumulation of glycosphingolipids substantially alters the domain structure and the biophysical properties of the membrane that include a higher number of membrane tethers artificially generated by the tip of an atomic force microscope. We believe that the accumulation of glycosphingolipids in the extracellular leaflet of the membrane increases its tendency to be positively curved (figure on the left). We are currently investigating if the generation of membraneous structures with different curvatures can indeed be explained by the aforementioned hypothesis. In particular, we are comparing the formation of tunneling nanotubes and extracellular vesicles in control cells and in those in which the amount of glycosphingolipids is high. Tunneling nanotubes are spontaneously formed membrane tubes that can extend several micrometers from cells and they can mediate intercellular communication (image on the right).
7. Calibration of intensity-based FRET measurements
Calculation of FRET values in intensity-based measurements hinges upon the accurate determination of a calibration factor, alpha, characterizing the detection efficiency of the system for excited acceptors vs. excited donors. In a method aimed at determining alpha, the intensities of two samples are compared:
one of them is labeled by donor-tagged antibodies
and the other one is labeled by the acceptor-conjugated version of the same kind of antibody.
When comparing the intensities of these two samples, it is assumed that cells with equal numbers of bound antibodies are compared. In microscopy, when relatively few cells are measured, this condition is not necessarily met. Therefore, we are using calibration beads with a known, narrow distribution of antibody binding sites to perform this calibration. In addition, we are trying to find ways to get around the problem of the bound and unbound antibody fractions having different degrees of labeling, as described on the "Interests" page, that could also lead to systematic misestimation of alpha.
bottom of page