GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction

Abstract

We have performed molecular dynamics (MD) and replica-exchange (REMD) simulations of folding of the GB1 hairpin peptide in aqueous solution. REMD results were consistent with a cooperative zipper folding model. 120 $\mu s$ MD trajectories at 320 K yielded relaxation times of 1.8 $\mu s$ and 100 ns, with the slower assigned to global folding. The MD folding/unfolding transitions also followed the cooperative zipper model, specifying nucleation at the central turn followed by consecutive hydrogen bond formation. Formation of hydrogen bonds and hydrophobic contacts were highly correlated. Coarse-grained kinetic models constructed with the Optimal Dimensionality Reduction (ODR) approach found a folding time of 3.3 $\mu s$ and unfolding time of 4.0 $\mu s.$ Additionally, relaxation times in the 130–170 ns range could be assigned to formation of the transition state and off-path intermediates. The unfolded state was the most highly populated and, significantly, most heterogenous, assembling the largest number of microstates, primarily composed of extended and turn structures. The folded state was also heterogenous, but a to a lesser degree, involving the fully folded and partially folded in-register hairpins at early stages of the zipper pathway. The transition state corresponded to the nucleated hairpin, with central turn and first beta-sheet hydrogen bond, while the off-path intermediates were off-register partial hairpins. Our simulation results were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. The new findings from this work suggest a highly cooperative zipper folding mechanism, nascent hairpin transition state and ∼100 ns relaxation related to intermediate formation.

Communicated by Ramaswamy H. Sarma

Keywords:

• GB1 hairpin peptide
• molecular dynamics
• replica-exchange molecular dynamics
• kinetic modeling
• folding pathways

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

Molecular dynamics simulations were carried out on the University of California San Diego Comet system (as part of XSEDE grant TG-MCB 16009), as well as on computer clusters at the University of Kansas Center for Research Computing and at the Warsaw University Center for Biological and Chemical Research. Trajectory analyses were performed on computer workstations supported by the General Research Fund at the University of Kansas. The work of KK and GSJ on this project was supported by NSF (National Science Foundation Division of Chemistry) grant CHE1807852. The work of RS was supported by the National Science Center, Poland, grant no. 2018/30/M/ST4/00005.