Disordered Motifs and Domains in Cell Control - October 11-15, 2014

Disordered Motifs and Domains in Cell Control

Poster Session II

35-POS Board 11 The Mechanism of pKID-KIX Complex Formation Studied by Molecular Dynamics Simulations Rainer Bomblies , Manuel Luitz, Martin Zacharias. TU Muenchen, Garching, Germany. The intrinsically disordered kinase inducible domain (KID) of the transcription cofactor CREB forms a kinked two-alpha-helices motif upon serine phosphorylation and subsequent binding to the transcription factor CBP. The effect of phosphorylation and the contribution of individual amino acid residues to the coupled folding and binding process are still not fully understood. An exhaustive sampling of the accessible conformational space of the unbound disordered state is difficult by unrestraint continuous molecular dynamics (cMD) simulations since substates are stable for hundreds of nanoseconds. We thus determined the conformational preferences of the unbound phosphorylated and non-phosphorylated KID with a novel method of sampling where the root mean square deviation (RMSD) of a set of chosen distances (dRMSD) is used as the reaction coordinate. Hamilton-Replica Exchange MD umbrella sampling (US) with this reaction coordinate allows sampling of a significantly larger fraction of the conformational space than cMD. Our dRMSD-US simulations show that KID phosphorylation promotes a more helical structure, mainly around the phosphorylation site, in turn facilitating pKID binding to KIX. To identify key binding residues in pKID we performed computational alanine-scanning with free energy calculations in explicit water. The major contributions arise from the hydrophobic residues of both helices, most importantly Leu141 in helix B and Leu128 in helix A each contributing more than 10 kJ/mol to the binding affinity. These residues might form initial key contacts prior to the structural transition into the bound state.

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