Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session II

49 – POS Board 21 Multiscale Flexible Docking of Troponin I to Troponin C Jacek Wabik , Mateusz Kurcinski, Andrzej Kolinski. Warsaw University, Warsaw, Poland.

Most of the current protein-protein docking procedures fail to reproduce large-scale motions of a modeled complex. Our approach based on the coarse-grained modeling of flexible proteins overcomes this limitation. The CABSDock procedure used in this work employs a coarse- grained CABS model, an efficient and versatile tool for modeling protein structure, dynamics and interactions [1-4]. In this work CABSDock was used to model the assembly process of troponin C (TnC) with the N-terminal helix of troponin I (TnI). TnC/TnI binding was investigated for both cardiac and skeletal troponin. The TnI fragment was modeled as fully flexible protein chain, without any restraints. The entire structure of the TnC was also treated as flexible, although each domain was restricted to near-native conformation. Our simulations show that binding of TnI fragment changes orientation between N-terminal and C-terminal domain of TnC. The obtained picture of the binding process provides a valuable insight into the mechanistic description of troponin function. [1] S. Kmiecik, D. Gront, M. Kouza, A. Kolinski, J Phys. Chem. B., 2012, 116 (23), 7026–7032 [2] S. Kmiecik,A. Kolinski, Biophys. J., 2008, 94, 726-736 [3] J. Wabik, S. Kmiecik, D. Gront, M. Kouza, A. Koliński, Int. J. Mol. Sci.,2013, 14, 9893-9905 [4] A. Kolinski, J.M. Bujnicki, Proteins, 2005, 61, 84-90

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