Coiled-Coil Response to Mechanical Force: Global Stability and Local Cracking

Abstract

Coiled coils are important structural motifs formed by two or more amphipathic α-helices that twist into a supercoil. These motifs are found in a wide range of proteins, including motor proteins and structural proteins, that are known to transmit mechanical loads. We analyze atomically detailed simulations of coiled-coil cracking under load with Milestoning. Milestoning is an approach that captures the main features of the process in a network, quantifying kinetics and thermodynamics. A 112-residue segment of the β-myosin S2 domain was subjected to constant-magnitude (0-200 pN) and constant-direction tensile forces in molecular dynamics simulations. Twenty 20 ns straightforward simulations at several load levels revealed that initial single-residue cracking events (Ψ > 90°) at loads <100 pN were accompanied by rapid refolding without either intra- or interhelix unfolding propagation. Only initial unfolding events at the highest load (200 pN) regularly propagated along and between helices. Analysis of hydrophobic interactions and of interhelix hydrogen bonds did not show significant variation as a function of load. Unfolding events were overwhelmingly located in the vicinity of E929, a charged residue in a hydrophobic position of the heptad repeat. Milestoning network analysis of E929 cracking determined that the mean first-passage time ranges from 20 ns (200 pN) to 80 ns (50 pN), which is ∼20 times the mean first-passage time of an isolated helix with the same sequence.

Computational study of peptide permeation through membrane: searching for hidden slow variables

“…Anchors can be determined by prior thermodynamic sampling (e.g. by replica exchange[41,42]), by reaction path calculations [43,44], or by chemical intuition[34,45]. For example, studies of peptide folding and unfolding in an explicit solvent use only the backbone dihedral angles of the peptide as the coarse variables [42,46].…”

“…If their corresponding relaxation times are long compared to typical MD simulations of membranes (a few to hundreds of nanoseconds) then their sampling must be explicitly enhanced, or longer simulations must be conducted. The sampling of more than a single variable can be enhanced by methods such as TAMD [31], TAMC [32], Metadynamics [33] and Milestoning [34]. Milestoning has the advantage that it makes it possible to compute the kinetics.…”

Harnessing the Unique Structural Properties of Isolated α-Helices

“…As the heptad is repeated, it forms a continuous hydrophobic patch located along a single face of the ␣-helix compatible with a tight intermolecular interaction between polypeptides with the same or similar heptad pattern (2). However, often polar or charged residues occupy the a and d positions, leading to local destabilization of the coiled-coil motif (2)(3)(4). By extension, when most or all of the a and d sites in consecutive heptads are occupied by polar residues, individual ␣-helices cannot be mutually stabilized through hydrophobic packing.…”

“…In a parallel vein, helix formation through E-K interactions, independent of alanine, was examined by Lyu et al (17) with 18-amino acid peptides with either (E 2 K 2 ) 4 or (E 4 K 4 ) 4 repeats. Although the composition was exactly the same for both peptides, CD and 1 H NMR data showed that the E 4 K 4 peptide has 65% helical content, whereas the E 2 K 2 peptide is essentially a random coil.…”

Analyzing milestoning networks for molecular kinetics: Definitions, algorithms, and examples

“…It has been used previously with methods like Hyper-Dynamics, 11 MSM, 4 and Milestoning. 9 The advantage of frequent exchanges of information between networks and continuous space is the ability to identify "on-the-fly," regions that are poorly or oversampled. For example, the network analysis may identify an important transition (or an edge) for which only a few successful events were recorded.…”