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Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

Radford IH, Fersht AR, Settanni G - J Phys Chem B (2011)

Bottom Line: The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach.The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis.The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

View Article: PubMed Central - PubMed

Affiliation: MRC-Centre for Protein Engineering, Cambridge, UK.

ABSTRACT
Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

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Conformations of the four stable macrostates identified by the Markov state model analysis (D1, D2, I, and N) and the transition state identified by the commitment probability (T) at (a) 300 K, (b) 330 K, and (c) 360 K. The unstructured random coil is shown in gray, turn sequence in tan, extended β-sheet structure in red, and β-bridge structure in blue. Several backbone conformations for each state are superimposed to illustrate the conformational variability within the state, and representative positions of the four tryptophan side chains are shown. The Cα atoms of the conformations were aligned using the first NMR conformation as a reference.
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fig6: Conformations of the four stable macrostates identified by the Markov state model analysis (D1, D2, I, and N) and the transition state identified by the commitment probability (T) at (a) 300 K, (b) 330 K, and (c) 360 K. The unstructured random coil is shown in gray, turn sequence in tan, extended β-sheet structure in red, and β-bridge structure in blue. Several backbone conformations for each state are superimposed to illustrate the conformational variability within the state, and representative positions of the four tryptophan side chains are shown. The Cα atoms of the conformations were aligned using the first NMR conformation as a reference.

Mentions: A structural comparison of the various states of the peptide is provided in Figure 6. The secondary structure of the peptide according to STRIDE(42) was computed along the trajectories using VMD(43) for the macrostates D1, D2, I, N, and T. For the compact denatured state D1 (Figure 6, column 1), the hairpin is quite “open”, and with the H-bonds between residues E5 and K8 only loosely formed (HB < 0.01), the shape of the backbone fluctuates significantly within this state. The turn sequence extends from residues W4 to N7 at the three simulation temperatures, while the rest of the residues are in the coil region. The four tryptophan side-chains appear to stabilize this state. In this case, the tryptophan residues appear to minimize their exposed surface area by packing between the backbones of the two strands. The second denatured state D2 (Figure 6, column 2) has, on average, a greatly extended turn sequence from residues W2 to T10 at 300, 330, and 360 K, though the secondary structure is less homogeneous than for the other macrostates. The hairpin is more open with much higher fluctuation in both backbone shape and the positions of the tryptophan side-chains. The I state (Figure 6, column 3), in which the native G6–N7 turn sequence is preserved, features β-bridge structure at residues E5 and K8 and additional turn structure for residue W4 at 300, 330, and 360 K. The rest of the peptide is random coil. The hairpin remains relatively “closed”, and the tryptophan residues form a disordered hydrophobic core on one side of the hairpin. The shape of the backbone shows slightly less variation within this macrostate, primarily toward the terminal residues, since the turn sequence is stabilized by a strong H-bond between residues E5 and K8. The N state conformations (Figure 6, column 4) at all three temperatures are characterized by the preservation of the G6–N7 turn sequence and the presence of extended β-sheet structure in the four residues on either side of the turn, residues W2–E5 and K8–W11. Stabilized by the presence of five strongly formed backbone H-bonds, the ensemble of conformations shows very little variation in the shape of the backbone within the N state, and the tryptophan residues are regularly packed in the center of the hairpin.


Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

Radford IH, Fersht AR, Settanni G - J Phys Chem B (2011)

Conformations of the four stable macrostates identified by the Markov state model analysis (D1, D2, I, and N) and the transition state identified by the commitment probability (T) at (a) 300 K, (b) 330 K, and (c) 360 K. The unstructured random coil is shown in gray, turn sequence in tan, extended β-sheet structure in red, and β-bridge structure in blue. Several backbone conformations for each state are superimposed to illustrate the conformational variability within the state, and representative positions of the four tryptophan side chains are shown. The Cα atoms of the conformations were aligned using the first NMR conformation as a reference.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3106446&req=5

fig6: Conformations of the four stable macrostates identified by the Markov state model analysis (D1, D2, I, and N) and the transition state identified by the commitment probability (T) at (a) 300 K, (b) 330 K, and (c) 360 K. The unstructured random coil is shown in gray, turn sequence in tan, extended β-sheet structure in red, and β-bridge structure in blue. Several backbone conformations for each state are superimposed to illustrate the conformational variability within the state, and representative positions of the four tryptophan side chains are shown. The Cα atoms of the conformations were aligned using the first NMR conformation as a reference.
Mentions: A structural comparison of the various states of the peptide is provided in Figure 6. The secondary structure of the peptide according to STRIDE(42) was computed along the trajectories using VMD(43) for the macrostates D1, D2, I, N, and T. For the compact denatured state D1 (Figure 6, column 1), the hairpin is quite “open”, and with the H-bonds between residues E5 and K8 only loosely formed (HB < 0.01), the shape of the backbone fluctuates significantly within this state. The turn sequence extends from residues W4 to N7 at the three simulation temperatures, while the rest of the residues are in the coil region. The four tryptophan side-chains appear to stabilize this state. In this case, the tryptophan residues appear to minimize their exposed surface area by packing between the backbones of the two strands. The second denatured state D2 (Figure 6, column 2) has, on average, a greatly extended turn sequence from residues W2 to T10 at 300, 330, and 360 K, though the secondary structure is less homogeneous than for the other macrostates. The hairpin is more open with much higher fluctuation in both backbone shape and the positions of the tryptophan side-chains. The I state (Figure 6, column 3), in which the native G6–N7 turn sequence is preserved, features β-bridge structure at residues E5 and K8 and additional turn structure for residue W4 at 300, 330, and 360 K. The rest of the peptide is random coil. The hairpin remains relatively “closed”, and the tryptophan residues form a disordered hydrophobic core on one side of the hairpin. The shape of the backbone shows slightly less variation within this macrostate, primarily toward the terminal residues, since the turn sequence is stabilized by a strong H-bond between residues E5 and K8. The N state conformations (Figure 6, column 4) at all three temperatures are characterized by the preservation of the G6–N7 turn sequence and the presence of extended β-sheet structure in the four residues on either side of the turn, residues W2–E5 and K8–W11. Stabilized by the presence of five strongly formed backbone H-bonds, the ensemble of conformations shows very little variation in the shape of the backbone within the N state, and the tryptophan residues are regularly packed in the center of the hairpin.

Bottom Line: The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach.The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis.The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

View Article: PubMed Central - PubMed

Affiliation: MRC-Centre for Protein Engineering, Cambridge, UK.

ABSTRACT
Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

Show MeSH