A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Abstract

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins. Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For the Trp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap. Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the and chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

Sampling the equilibrium kinetic network of Trp-cage in explicit solvent

“…In addition, these findings corroborate with the recent IR experiment of Meuzelaar et al 19 Interestingly enough, we found that the intermediate I state, consisting of a formed α-helix with a solvated and 24,28 We can solve this paradox, by constructing the free energy landscape.…”

“…They found Trp-cage folding paths that formed tertiary contacts and the salt bridge before formation of the helix, as well as paths that first formed the helix. These two folding routes were also observed by Marinelli et al 24 using bias exchange metadynamics simulations. These authors calculated that the folding process takes ∼2.3 ± 0.7 μs.…”

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

“…3A). Specifically, we employed the bias-exchange metadynamics (BE) method (26)(27)(28), to derive quantitative information on the conformational freedom of the protein, in the form of free-energy landscapes (see Materials and Methods). BE simulations were thus carried out for wild-type TeaA, in the apo and substrate-bound states.…”

Two-state dynamics of the SH3–SH2 tandem of Abl kinase and the allosteric role of the N-cap

“…The probability of the on state is the integral of this 2D function for 0 < RMSD 2 < 4 Å and 6 < RMSD 1 < 10 Å, whereas for the off state is 0 < RMSD 1 < 4 Å and 6 < RMSD 2 < 10 Å. Error estimates were computed as described previously (52).…”