Folding PDZ2 domain using the Molecular Transfer Model

Abstract

A major challenge in molecular simulations is to describe denaturant-dependent folding of proteins order to make direct comparisons with in vitro experiments. We use the molecular transfer model, which is currently the only method that accomplishes this goal albeit phenomenologically, to quantitatively describe urea-dependent folding of PDZ domain, which plays a significant role in molecular recognition and signaling. Experiments show that urea-dependent unfolding rates of the PDZ2 domain exhibit a downward curvature at high urea concentrations, which has been interpreted by invoking the presence of a sparsely populated high energy intermediate. Simulations using the MTM and a coarse-grained model of PDZ2 are used to show that the intermediate, which has some native-like character, is present in equilibrium both in the presence and absence of urea. The free energy profiles show that there are two barriers separating the folded and unfolded states. Structures of the transition state ensembles, (TSE1 separating the unfolded and I_EQ and TSE2 separating I_EQ and the native state), determined using the P_fold method, show that TSE1 is expanded; TSE2 and native-like. Folding trajectories reveal that PDZ2 folds by parallel routes. In one pathway folding occurs exclusively through I_1, which resembles I_EQ. In a fraction of trajectories, constituting the second pathway, folding occurs through a combination of I_1 and a kinetic intermediate. The radius of gyration (R_g^U) of the unfolded state is more compact (by 9\%) under native conditions. Decrease in R_g^U occurs on the time scale on the order of utmost 20 s. The modest decrease in R_g^U and the rapid collapse suggest that high spatial and temporal resolution are needed to detect compaction in finite-sized proteins.

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