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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