Seminarium z fizyki biologicznej i bioinformatyki
Thermodynamics and kinetics of GB1 hairpin folding from replica-exchange and molecular dynamics simulations
Abstract
We have performed molecular dynamics (MD) and replica-exchange (REMD) simulations of folding for the 16-residue GB1 hairpin peptide in explicit solvent. REMD predicts a folded hairpin fraction of 39-41% at 320 K and a statistical folding pathway consistent with a zipper model. Based on 120 microseconds of MD trajectories at 320 K, the two slowest relaxation times were 1,800 and 170 ns, with the slower one assigned to global folding. MD trajectories also followed the zipper mechanism, with nucleation at the central turn followed by consecutive hydrogen bond formation/breaking in a highly cooperative manner. Backbone and hydrophobic sidechain aggregation were highly correlated as well. We also constructed coarse-grained kinetic models with the Optimal Dimensionality Reduction (ODR) approach. Besides the 1,800 ns folding process, additional relaxation times in the 130-170 ns range could be assigned to formation/decay of the transition state and off-path intermediates. The ‘coil’ state was the most highly populated and also most heterogenous, including primarily extended and turn structures. The ‘hairpin’ state was also heterogenous, , involving fully folded and partially folded in-register hairpins along the zipper pathway. The transition state corresponded to the nucleated hairpin. Overall, our simulations were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. Additionally, the kinetic modeling allowed identification of a nascent hairpin as a transition state for folding and a faster relaxation time of ~100 ns related to formation of off-path intermediates and the transition state.
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Bogdan Lesyng (UW)
Anna Niedźwiecka (IF PAN)
Piotr Zielenkiewicz (IBB)