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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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Related in: MedlinePlus

Eyring plot based on the data coming from the simulations (solid circles). The linear fit of the log(ku/T) as a function of 1/T is shown (solid line). The slope provides an estimate for the unfolding activation enthalpy ΔH‡ = 14.0 ± 1.2 Kcal/mol. The fit is extrapolated to room temperature. The 95% credibility interval for the extrapolation is provided (dashed lines). The available experimental data (open circle) correspond to an unfolding time of 18.3 ± 3.1 μs at T = 296 K (2). The unfolding time as extrapolated from the fit is 62 μs.
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fig5: Eyring plot based on the data coming from the simulations (solid circles). The linear fit of the log(ku/T) as a function of 1/T is shown (solid line). The slope provides an estimate for the unfolding activation enthalpy ΔH‡ = 14.0 ± 1.2 Kcal/mol. The fit is extrapolated to room temperature. The 95% credibility interval for the extrapolation is provided (dashed lines). The available experimental data (open circle) correspond to an unfolding time of 18.3 ± 3.1 μs at T = 296 K (2). The unfolding time as extrapolated from the fit is 62 μs.

Mentions: The kinetics of unfolding was sampled sufficiently to construct an Eyring plot for the reaction (Fig. 5), which shows that unfolding follows the Arrhenius law, as expected (43). The slope of the regression line gives an activation enthalpy for unfolding as ΔH‡ = 14.0 ± 1.2 Kcal/mol. The extrapolation of the unfolding time to room temperature gives an estimate for the unfolding rate constant ku = (62 μs)−1. Limited sampling, especially at 373 K and 400 K, prevents the same analysis for the folding process. Estimate of the population of I with respect to all the other states needs a precise knowledge of all the transition rates; thus, we cannot reliably measure it at the lower temperatures or, worse, extrapolate it to room temperature.


High temperature unfolding simulations of the TRPZ1 peptide.

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

Eyring plot based on the data coming from the simulations (solid circles). The linear fit of the log(ku/T) as a function of 1/T is shown (solid line). The slope provides an estimate for the unfolding activation enthalpy ΔH‡ = 14.0 ± 1.2 Kcal/mol. The fit is extrapolated to room temperature. The 95% credibility interval for the extrapolation is provided (dashed lines). The available experimental data (open circle) correspond to an unfolding time of 18.3 ± 3.1 μs at T = 296 K (2). The unfolding time as extrapolated from the fit is 62 μs.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Eyring plot based on the data coming from the simulations (solid circles). The linear fit of the log(ku/T) as a function of 1/T is shown (solid line). The slope provides an estimate for the unfolding activation enthalpy ΔH‡ = 14.0 ± 1.2 Kcal/mol. The fit is extrapolated to room temperature. The 95% credibility interval for the extrapolation is provided (dashed lines). The available experimental data (open circle) correspond to an unfolding time of 18.3 ± 3.1 μs at T = 296 K (2). The unfolding time as extrapolated from the fit is 62 μs.
Mentions: The kinetics of unfolding was sampled sufficiently to construct an Eyring plot for the reaction (Fig. 5), which shows that unfolding follows the Arrhenius law, as expected (43). The slope of the regression line gives an activation enthalpy for unfolding as ΔH‡ = 14.0 ± 1.2 Kcal/mol. The extrapolation of the unfolding time to room temperature gives an estimate for the unfolding rate constant ku = (62 μs)−1. Limited sampling, especially at 373 K and 400 K, prevents the same analysis for the folding process. Estimate of the population of I with respect to all the other states needs a precise knowledge of all the transition rates; thus, we cannot reliably measure it at the lower temperatures or, worse, extrapolate it to room temperature.

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