Protein Structure and Bioinformatics



Research Interests


Bioinformatics of genomes and proteomes, folding and disease, protein/DNA interactions, intercellular communication, NOTCH signaling, network models, systems biology.


Description of Research


The Group is interested in the principles of macromolecular stability and specificity, with special regard to intercellular communication. Both the structural organization and the molecular interactions of proteins can be described as specific and robust networks. A better knowledge of the underlying principles is important for theoretical and practical purposes such as understanding the cellular mechanisms or the design of better pharmacons. The lab uses the approaches of bioinformatics, peptide chemistry, NMR, mass spectrometry and recombinant DNA technologies. It studies the proteins of the Notch signalling network and its involvement in genetic diseases. In particular, it looks at the formation of disulfide bonds in proteins; evolution of network stability and systems biology; prediction of protein structure and function using machine learning approaches, and aspects of protein chemistry including synthesis of modified peptides and pharmaceutical applications.

Selected Publications


Kuzniar, A., van Ham, R.C.H.J., Pongor, S., Leunissen, J.A.M. 2008. The Quest for Orthologs: Finding Gene Correspondences across Genomes, Trends Genet, In press

De Biasio, A., Guarnaccia, C., Popovic, M., Uversky, V.N., Pintar, A., Pongor, S. 2008. Prevalence of Intrinsic Disorder in the Intracellular Region of Human Single-Pass Type I Proteins: The Case of the Notch Ligand Delta-4. J Proteome Res. 7, 2496-2506

Popovic, M., De Biasio, A., Pintar, A., Pongor, S. 2007. The intracellular region of the Notch ligand Jagged-1 gains partial structure upon binding to synthetic membranes. FEBS J 274, 5325-5336

Sonego, P., Pacurar, M., Dhir, S., Kertész-Farkas, A, Kocsor, A., Gáspári, Z., Leunissen, J.A.M., Pongor, S. 2007. A Protein Classification Benchmark collection for machine learning. Nucl. Acids. Res. D232-236

Zahariev, S., Guarnaccia, C., Zanuttin, F., Pintar, A., Esposito, G., Maravic, G., Krust, B., Hovanessian, A.G., Pongor, S. 2005. Efficient synthesis and comparative studies of the arginine and Nomega,Nomega-dimethylarginine forms of the human nucleolin glycine/arginine rich domain. J Pept Sci. 11, 17-28

Csermely, P., Ágoston, V., Pongor S. 2005. The efficiency of multi-target drugs: The network approach may help drug design. Trends Pharmacol Sciences, 26, 178-182


Cemazar, M., Zakhariev, S., Lopez, J.J., Carugo, O., Jones, J.A., Hore, P.J. and Pongor, S. (2002) Oxidative folding intermediates with non-native disulfide bridges between adjacent cystein residues, Proc. Natl. Acad. Sci., USA. 100, 5754-5759.

 

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