Wykład doktora Mieczysława Torchały

Szanowni Państwo;

Zapraszamy serdecznie na wykład dr Mieczysława Torchały poświęcony oddziaływaniom białko-białko.

Prelegent: dr Mieczysław Torchała - Biomolecular Modelling Laboratory, Cancer Research UK, London

Wykład odbędzie się w dniu: 15 kwietnia 2015 roku (środa) o godz. 12:00 w sali D102, Budynek Wydziału Chemii, Gdańsk-Oliwa, ul. Wita Stwosza 63

Temat wystąpienia:

"Application of SwarmDock Server and RaTrav to understand protein-protein binding funnels"

Organizowane przez: Wydział Chemii Uniwersytetu Gdańskiego, Gdański Oddział Polskiego Towarzystwa Chemicznego oraz Wydział III Gdańskiego Towarzystwa Naukowego (Komisja Chemii).

Abstract: Protein-protein interactions drive many of the biological functions of the cell. Any two proteins have the potential to interact; however, whether the interactions are of biological significance is dependent on a number of complicated factors. Thus, modelling the three-dimensional structure of protein-protein complexes is still considered to be a complex endeavour. In addition to correct protein-protein complex 3D structure returned by the algorithm, equally important is dynamics of binding, i.e., how proteins find their binding partners in the multidimensional space of conformational transitions and how their binding partners, upon complex formation, sample binding funnels, i.e. what is the structure of conformational states space and in which manner proteins change their conformations when traversing this network. We released two freely available tools: SwarmDock Server (a web service for the flexible modelling of protein-protein complexes) [1,2] and RaTrav (a tool for calculating mean first-passage times and node occupancies) [3]. In this talk we share our experience related to conformational state network generation, its structure and dynamics. We successfully applied occupancy probabilities to distinguish between false positive and true positive protein-protein binding funnels [4] and mean first-passage times to find the favourable path and limiting transitions in the true positive protein-protein binding funnel [3].

[1] M. Torchala, I.H. Moal, R.A.G. Chaleil, J. Fernandez-Recio, P.A. Bates, 'SwarmDock: a server for flexible protein-protein docking', Bioinformatics 29,   807-809 (2013).
[2] M. Torchala, P. A. Bates, 'Predicting the Structure of Protein-Protein Complexes Using the SwarmDock Web Server', in: Protein Structure Prediction 3rd Edition (Methods in Molecular Biology, Vol. 1137), Humana Press, 2014
[3] M. Torchala, P. Chelminiak, M. Kurzynski, P.A. Bates, 'RaTrav: a tool for calculating mean first-passage times on biochemical networks', BMC Syst. Biol. 7, 130 (2013).
[4] M. Torchala, I.H. Moal, R.A.G. Chaleil, R. Agius, P.A. Bates, 'A Markov-chain model description of binding funnels to enhance the ranking of docked solutions', Proteins: Structure, Function, and Bioinformatics 81, 2143-2149 (2013).