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High temperature unfolding simulations of the TRPZ1 peptide.

Settanni G, Fersht AR - Biophys. J. (2008)

Bottom Line: But, the speed of the folding process is mainly determined by the transition from the completely unfolded state to the intermediate and specifically by the closure of the hairpin loop driven by formation of two native backbone hydrogen bonds and hydrophobic contacts between tryptophan residues.The temperature dependence of the unfolding time provides an estimate of the unfolding activation enthalpy that is in agreement with experiments.The unfolding time extrapolated to room temperature is in agreement with the experimental data as well, thus providing a further validation to the analysis reported here.

View Article: PubMed Central - PubMed

Affiliation: Centre for Protein Engineering, Cambridge, United Kingdom. gs@mrc-lmb.cam.ac.uk

ABSTRACT
We report high temperature molecular dynamics simulations of the unfolding of the TRPZ1 peptide using an explicit model for the solvent. The system has been simulated for a total of 6 mus with 100-ns minimal continuous stretches of trajectory. The populated states along the simulations are identified by monitoring multiple observables, probing both the structure and the flexibility of the conformations. Several unfolding and refolding transition pathways are sampled and analyzed. The unfolding process of the peptide occurs in two steps because of the accumulation of a metastable on-pathway intermediate state stabilized by two native backbone hydrogen bonds assisted by nonnative hydrophobic interactions between the tryptophan side chains. Analysis of the un/folding kinetics and classical commitment probability calculations on the conformations extracted from the transition pathways show that the rate-limiting step for unfolding is the disruption of the ordered native hydrophobic packing (Trp-zip motif) leading from the native to the intermediate state. But, the speed of the folding process is mainly determined by the transition from the completely unfolded state to the intermediate and specifically by the closure of the hairpin loop driven by formation of two native backbone hydrogen bonds and hydrophobic contacts between tryptophan residues. The temperature dependence of the unfolding time provides an estimate of the unfolding activation enthalpy that is in agreement with experiments. The unfolding time extrapolated to room temperature is in agreement with the experimental data as well, thus providing a further validation to the analysis reported here.

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Conformations form two transition pathways of the simulations run at 450 K. (a) Conformations with  (b) Conformations with  (c) Conformations with  The N-terminal strand is located on the left of each picture. Closure of the loop between Thr3 and Thr10 and the Trp residues is rate-limiting in this case. This can occur either as a zipping process starting from the proximal part of the hairpin (right column) or as a process driven by diffusion of the termini, starting from the distal part of the hairpin (left column). Please note that, in the transition state conformation on the left, no intervening water molecule is present between the Trp2 and Trp11 side chains and between the methyl groups of the Thr3 and Thr10 side chains, which, for simplicity, were not shown. Thus, even in that case, the loop closure is taking place at the rate-limiting step.
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fig8: Conformations form two transition pathways of the simulations run at 450 K. (a) Conformations with (b) Conformations with (c) Conformations with The N-terminal strand is located on the left of each picture. Closure of the loop between Thr3 and Thr10 and the Trp residues is rate-limiting in this case. This can occur either as a zipping process starting from the proximal part of the hairpin (right column) or as a process driven by diffusion of the termini, starting from the distal part of the hairpin (left column). Please note that, in the transition state conformation on the left, no intervening water molecule is present between the Trp2 and Trp11 side chains and between the methyl groups of the Thr3 and Thr10 side chains, which, for simplicity, were not shown. Thus, even in that case, the loop closure is taking place at the rate-limiting step.

Mentions: The validated transition pathways for the I→D transition show that, in this case, the loss of the backbone hydrogen bond between Thr3 and Thr10 is the rate-limiting step (Figs. 8 and 9). This process is concurrent with the loss of nonnative unspecific hydrophobic interactions between the side chains of Trp residues on the opposite sides of the hairpin. Conversely, the degree of nativeness of the turn region (residues 5–7) as measured by its backbone RMSD is less correlated to the (data not shown). Taken together, these data indicate that loop closure is rate-determining in the D→I transition. Namely, the transition can occur either as a zipping process initiating in the turn region or by diffusional encounter of the termini (Fig. 8).


High temperature unfolding simulations of the TRPZ1 peptide.

Settanni G, Fersht AR - Biophys. J. (2008)

Conformations form two transition pathways of the simulations run at 450 K. (a) Conformations with  (b) Conformations with  (c) Conformations with  The N-terminal strand is located on the left of each picture. Closure of the loop between Thr3 and Thr10 and the Trp residues is rate-limiting in this case. This can occur either as a zipping process starting from the proximal part of the hairpin (right column) or as a process driven by diffusion of the termini, starting from the distal part of the hairpin (left column). Please note that, in the transition state conformation on the left, no intervening water molecule is present between the Trp2 and Trp11 side chains and between the methyl groups of the Thr3 and Thr10 side chains, which, for simplicity, were not shown. Thus, even in that case, the loop closure is taking place at the rate-limiting step.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2480669&req=5

fig8: Conformations form two transition pathways of the simulations run at 450 K. (a) Conformations with (b) Conformations with (c) Conformations with The N-terminal strand is located on the left of each picture. Closure of the loop between Thr3 and Thr10 and the Trp residues is rate-limiting in this case. This can occur either as a zipping process starting from the proximal part of the hairpin (right column) or as a process driven by diffusion of the termini, starting from the distal part of the hairpin (left column). Please note that, in the transition state conformation on the left, no intervening water molecule is present between the Trp2 and Trp11 side chains and between the methyl groups of the Thr3 and Thr10 side chains, which, for simplicity, were not shown. Thus, even in that case, the loop closure is taking place at the rate-limiting step.
Mentions: The validated transition pathways for the I→D transition show that, in this case, the loss of the backbone hydrogen bond between Thr3 and Thr10 is the rate-limiting step (Figs. 8 and 9). This process is concurrent with the loss of nonnative unspecific hydrophobic interactions between the side chains of Trp residues on the opposite sides of the hairpin. Conversely, the degree of nativeness of the turn region (residues 5–7) as measured by its backbone RMSD is less correlated to the (data not shown). Taken together, these data indicate that loop closure is rate-determining in the D→I transition. Namely, the transition can occur either as a zipping process initiating in the turn region or by diffusional encounter of the termini (Fig. 8).

Bottom Line: But, the speed of the folding process is mainly determined by the transition from the completely unfolded state to the intermediate and specifically by the closure of the hairpin loop driven by formation of two native backbone hydrogen bonds and hydrophobic contacts between tryptophan residues.The temperature dependence of the unfolding time provides an estimate of the unfolding activation enthalpy that is in agreement with experiments.The unfolding time extrapolated to room temperature is in agreement with the experimental data as well, thus providing a further validation to the analysis reported here.

View Article: PubMed Central - PubMed

Affiliation: Centre for Protein Engineering, Cambridge, United Kingdom. gs@mrc-lmb.cam.ac.uk

ABSTRACT
We report high temperature molecular dynamics simulations of the unfolding of the TRPZ1 peptide using an explicit model for the solvent. The system has been simulated for a total of 6 mus with 100-ns minimal continuous stretches of trajectory. The populated states along the simulations are identified by monitoring multiple observables, probing both the structure and the flexibility of the conformations. Several unfolding and refolding transition pathways are sampled and analyzed. The unfolding process of the peptide occurs in two steps because of the accumulation of a metastable on-pathway intermediate state stabilized by two native backbone hydrogen bonds assisted by nonnative hydrophobic interactions between the tryptophan side chains. Analysis of the un/folding kinetics and classical commitment probability calculations on the conformations extracted from the transition pathways show that the rate-limiting step for unfolding is the disruption of the ordered native hydrophobic packing (Trp-zip motif) leading from the native to the intermediate state. But, the speed of the folding process is mainly determined by the transition from the completely unfolded state to the intermediate and specifically by the closure of the hairpin loop driven by formation of two native backbone hydrogen bonds and hydrophobic contacts between tryptophan residues. The temperature dependence of the unfolding time provides an estimate of the unfolding activation enthalpy that is in agreement with experiments. The unfolding time extrapolated to room temperature is in agreement with the experimental data as well, thus providing a further validation to the analysis reported here.

Show MeSH
Related in: MedlinePlus