2022 Annual Meeting

Investigating the Role of Amino Acid Stereochemistry in the Assembly of Fibrous Peptide Hydrogels for Tissue Engineering

Objectives: Biomaterials provide environments for stem cell assembly into functional tissues, thus repairing injury. For effective repair in various applications, biomaterials must be easily tunable to mimic the properties of the tissue they seek to heal. A peptide hydrogel made of the pentapeptide KYFIL (lysine, tyrosine, phenylalanine, isoleucine, leucine) is stereochemically tunable and designed to mimic the stiffness and morphology of neural tissue. When made of purely ʟ- or ᴅ- peptides, KYFIL forms a stiff, fibrous, self-healing hydrogel. However, when made from a racemic mixture of ʟ- and ᴅ- peptides, the resulting material is less stiff with plate-like morphology.

Understanding how stereochemistry affects peptide assembly will provide control over this tunable property. Molecular dynamics simulations (MD) can probe the role of individual amino acid residue's stereochemistry in hydrogel assembly. By varying the position of a single stereochemically opposite ᴅ-amino acid into an otherwise ʟ-form peptide (pure ʟ- and ᴅ- KYFIL, dKYFIL, KdYFIL, KYdFIL, KYFdIL, and KYFIdL), we determined the effect of ᴅ-stereochemistry on assembly and developed computational quantification methods.

Methods: In silico, we placed 27 peptides in a 3x3x3 grid within a water box under benchtop environmental conditions. Initial peptide configuration was determined through minimization, and then assembly was simulated in solution for 200 ns using Nanoscale MD (NAMD). Analysis of the atomic trajectory in Visual MD (VMD), its plugin Residue Interactions in Protein - MD (RIP-MD), and in-house scripts probed hydrogen bonding and pi-pi stacking, interactions contributing to peptide assembly. Through this analysis, we quantified individual residues' roles in these interactions. Another in-house script determined the number of peptides per assembled cluster, groups of peptide pairs within 15 Å of each other.

Results: Preliminary analysis demonstrated clustering of peptides and an increasing hydrogen bond and pi-pi interaction quantity over time. Hydrogen bond formation rate varied with the position of the inverted residue. The inversion of leucine led to the lowest hydrogen bond quantity among the peptides studied. Inversion of aromatic tyrosine and phenylalanine increased pi-pi stacking, with phenylalanine-tyrosine and phenylalanine-phenylalanine interactions favored over tyrosine-tyrosine interactions.

Conclusions: We successfully developed analysis scripts to quantify intermolecular interactions involving individual residues. While inverting one residue in KYFIL can affect the assembly of clusters by modulating intermolecular interactions, the peptides behave similarly to pure ʟ- and ᴅ- KYFIL, though some variation arises. Further work will focus on pairing favorability and how this changes due to stereochemical inversions.