3D-modeling of Ssn6 fragments.

(A) Modeling of Δ45: (Left) Cartoon representation of the initial 3D-model used for the explicit MD simulation. (Right) Average structure obtained from the last 10ns of the 100 ns MD trajectory, colored according to estimated atomic B-factors: from blue to red for low and high atomic fluctuations, respectively. (B) Modeling of NTpolyQ_TPR1-3: (Left) Cartoon representation of the initial 3D-model of a NTpolyQ_TPRs2.5 fragment used for the REMD simulations. (Right) (a) Average structures obtained from the last 10ns of the solvated 100 ns MD trajectories of the two REMD models (see “Materials & Methods”). Coloring is according to estimated B-factors, as in A. (b), (c) and (d) Average structures obtained from the last 10ns of the second set of solvated 100 ns MD trajectories of the two NTpolyQ_TPR1-3 models colored according to B-factor values for the entire NTpolyQ_TPR1-3, NTpolyQ and TPR domains, respectively, for clarity. Various domains discussed in the text are labeled. Arrows point to susceptible to proteolysis sites of Ssn6, as described in [11] (also shown in Fig 1C).