Turn-directed folding dynamics of β-hairpin-forming de novo decapeptide Chignolin

Abstract

Realistic mechanistic pictures of β-hairpin formation, offering valuable insights into some of the key early events in protein folding, are accessible through short designed polypeptides as they allow atomic-level scrutiny through simulations. Here, we present a detailed picture of the dynamics and mechanism of β-hairpin formation of Chignolin, a de novo decapeptide, using extensive, unbiased molecular dynamics simulations. The results provide clear evidence for turn-directed broken-zipper folding and reveal details of turn nucleation and cooperative progression of turn growth, hydrogen-bond formations, and eventual packing of the hydrophobic core. Further, we show that, rather than driving folding through hydrophobic collapse, cross-strand side-chain packing could in fact be rate-limiting as packing frustrations can delay formation of the native hydrophobic core prior to or during folding and even cause relatively long-living misfolded or partially folded states that may nucleate aggregative events in more complex situations. The results support the increasing evidence for turn-centric folding mechanisms for β-hairpin formation suggested recently for GB1 and Peptide 1 based on experiments and simulations but also point to the need for similar examinations of polypeptides with larger numbers of cross-strand hydrophobic residues.

WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm

“…From this graph we can see that only the two native-like states have low C α -C α distances for the 1–10 pair. This implies that these residues are the last to come together when folding, and the first to come apart when unfolding, which is in direct conflict with the results of Enemark et al 34 It is possible that the OPLS-AA force field used in their work demonstrates different behavior than the CHARMM22 force field used here. As we move higher up the stem, nodes change from red to blue in a monotonic fashion, indicating a zipper-like mechanism.…”

“…30 It has served as an excellent system for theoretical study 34–37 since it is the one of the smallest molecules that exhibits stable secondary structure. The folded structure of the molecule consists of a central turn region (residues 4–7) flanked by three amino acids on each side, which form the stem of the hairpin, which is stabilized by hydrogen bonding interactions.…”

“…Two main folding mechanisms for hairpins of this type have been proposed: the “zipper” model, 38 where the turn region forms first, and stem residues come into contact successively, moving outward from the turn; and, the “hydrophobic collapse” model, 39 where there is an initial, fast collapse to a compact structure, followed by slow rearrangements resulting in the hairpin structure. Enemark and Rajagopalan 34 observed the folding of chignolin in ten 1 μ s trajectories, and found folding to occur predominantly by a “broken-zipper” mechanism, where stem residues come into contact out-of-order; residues 1 and 10 come into contact earliest. Suenaga et al, 36 in contrast, observed that interactions between the aromatic rings of Tyr2 and Typ9 initiates the folding process.…”

β-hairpin forms by rolling up from C-terminal: Topological guidance of early folding dynamics

“…For chignolin, we have recently shown that formation of the native turn (NT) region (Pro4-Gly7) drives folding and marks the beginning of the downhill zipping stage of the folding cascade19. Other recent studies of different β-hairpins have also reported turn-directed mechanisms, providing support for a general turn-centric folding scenario1315.…”

“…For example, given that turns exist at Thr8 and Trp9 only, propagation to turns at Thr6 and Gly7 typically occurs on the order of a few ns, while further propagation to Glu5 and Pro4 occurs about 2 orders of magnitude more slowly. As folding is driven by NT formation19, the timescale of turn propagation to Pro4 thus provides a lower bound for the overall folding time, estimated to be ~1 μs1720.…”