Stability and growth mechanism of self-assembling putative antifreeze cyclic peptides

Abstract

Cyclic peptides (CPs) that self-assemble in nanotubes can be candidates for use as antifreeze proteins. Based on the cyclic peptide sequence cyclo-[(l-LYS-d-ALA-l-LEU-d-ALA)], which can stack into nanotubes, we propose a putative antifreeze cyclic peptide (AFCP) sequence, cyclo-[(l-LYS-d-ALA)-(l-THR-d-ALA)], containing THR-ALA-THR ice binding motifs. Using molecular dynamics simulations we investigate the stability of these cyclic peptides and their growth mechanism. Both nanotube sequences get more stable as a function of size. The relative stability of the AFCP sequence CPNT increases at sizes greater than a dimer by forming intermolecular THR side chain H-bonds. We find that, like the naturally occurring AF protein from spruce budworm (Choristoneura fumiferana), the THR distances of the AFCP's ice binding motif match the ice prism plane O-O distances, thus making the AFCP a suitable AF candidate. In addition, we investigated the nanotube growth process, i.e. the association/dissociation of a single CP to an existing AFCP nanotube, by Transition Path Sampling. We found a general dock-lock mechanism, in which a single CP first docks loosely before locking into place. Moreover, we identified several qualitatively different mechanisms for association, involving different metastable intermediates, including a state in which the peptide was misfolded inside the hydrophobic core of the tube. Finally, we find evidence for a mechanism involving non-specific association followed by 1D diffusion. Under most conditions, this will be the dominant pathway. The results yield insights into the mechanisms of peptide assembly, and might lead to an improved design of self-assembling antifreeze proteins.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

“…TPS has been used, for instance, to study dissociation pathways of tube-forming cyclic peptides with the all-atom AMBER force field. 155 The study revealed multiple possible dissociation pathways ( Fig. 7 ).…”

Molecular modelling of supramolecular polymers

“…The group of Balasubramanian studied the polymerization process of BTAbased supramolecular polymers in nonane at AA and CG level [45,72]. The group of Bolhuis recently used transition path sampling to monitor the stability and growth mechanism of cyclic peptide nanotubes in water at atomistic level [79]. Explicit-water CG models (see above) for BTA monomers also allowed to follow supramolecular polymerization in time, monitoring the growth of the aggregates and the amplification of order (core-core coordination, see Figure 4) inside them during the cooperative polymerization process [29].…”

“…In the last years, enhanced sampling computational techniques have been proven very effective to tackle this issue [81][82][83][84][85][86]. For example, Botzakis et al recently used transition path sampling simulations to identify the pathway of incorporation (polymerization) in tubules of peptide macrocycles [79]. Particularly interesting, infrequent well-tempered metadynamics (WT-MetaD) [81] simulations were recently proven an efficient tool to explore rare exchange events, providing information on the pathway, rate limiting steps and their relative kinetics in once [82].…”

Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook

“…Note that these kind of TPS applications have only become possible with the development of the spring shooting algorithm. [ 67 ]…”