Investigating Stereochemically-Driven Peptide Assembly Via Molecular Dynamics Simulations

Injectable hydrogels that utilize short, self-assembling sequences of peptides mimic neural physiology and provide a delivery mechanism to the brain for neural stem cells. These gels are applied with the goal of promoting tissue repair following damage due to injury, stroke or neurodegenerative disease. We investigated the amino acid sequence lysine (K), tyrosine (Y), phenylalanine (F), isoleucine (I) and leucine (L), (KYFIL). This peptide is one of a class of rapidly assembling pentapeptides for injectable delivery (RAPID) hydrogels developed by the Lampe group at UVA. We observed that racemic mixtures of KYFIL exhibit lower stiffness and distinct morphology compared to the enantiomerically pure peptide hydrogels.

Methods

In order to investigate the mechanisms of stereochemically driven gel assembly, we conducted molecular dynamics simulations through Nanoscale Molecular Dynamics (NAMD) and performed analysis through Visual Molecular Dynamics (VMD). We modeled 64 amidated KYFIL peptides, varying the ratio of ÊŸ:á´…-form peptides solvated with explicit water containing physiological concentrations of ions. Under constant pressure and temperature conditions, we followed the trajectory of KYFIL in NAMD for 200 ns.

Results

Qualitative visualization in VMD focused on clusters, subgroups of peptides close together. The simulation’s trajectory revealed clusters smaller in size but larger in quantity in racemic mixtures compared to simulations with only pure ʟ or ᴅ peptides. Enantiomerically pure ʟ and ᴅ peptides formed larger clusters in smaller quantities. We observed that in enantiomeric mixtures ʟ-KYFIL and ᴅ-KYFIL cluster together, rather than in enantiomerically pure clusters. Further, hydrogen bonding data suggest that the average number of hydrogen bonds after 200 ns decreases in racemic mixtures. This suggests stereochemically driven cluster assembly.

Conclusions

We conclude that in stereocomplexed peptide hydrogels, enantiomeric ratio plays a role in the assembly mechanism of gels through the size and enantiomeric composition of clusters. This difference in cluster assembly seems to be directly connected to experimental observations of change in morphology of these gels. Further investigating the mechanism behind assembly will reveal more information about RAPID gels and their potential clinical applications in neural tissues.

Acknowledgements

We’d like to thank Professor Kyle Lampe, Professor Rachel Letteri, and the members of each of their groups for their continued support, as well as the Center for Advanced Biomanufacturing at UVA for the opportunity to explore this project through their summer internship program. Finally, we would like to thank the Rivanna Computing Cluster at UVA for their guidance in high performance computing.