Sequence Dependence of Folding and Self-Assembly of Glycine-X Repeat Peptides on Graphite

Abstract Cyclic peptides consisting of glycine-X repeats have been shown in simulation and experiment to fold at the graphite–water interface into beta-hairpins, which then self-assemble by intermolecular hydrogen bonding. In this contribution, we investigate the role of the hairpin turn sequence, strand length, and the X amino acid on folding and self-assembly. Simulations of relatively large systems with 9 initially unfolded peptides allow us to observe spontaneous folding, which, together with free energy profiles as a function of RMSD, enable comparison of folding thermodynamics and kinetics among sequences and identification of metastable misfolded conformations. Likewise, spontaneous assembly also occurs in these simulations, which, together with absolute binding free energy calculations, enable comparison of assembly kinetics and preferences for different intermolecular alignments. We find that the GPGG sequence best enforces folding with the desired hairpin turn compared to GGGG and GDGG sequences. While our previous peptide design was head-to-tail cyclized, here, we demonstrate that disulfide cyclization is a viable alternative. Peptides having strands with GT, GA, GG, GS, and GD repeats, as well as those with charge-complementary GE/GZ pairs (where Z is diaminobutyric acid), can fold correctly, but vary in their folding free energy, tendency to adopt misfolded conformations, folding cooperativity, and preference for different intermolecular alignments. GT-repeat strands most favor folding into the desired beta-strands; however, they yield the weakest intermolecular assembly. GG-repeats yield the strongest intermolecular assembly, but peptides with all GG repeats show a greater tendency to misfold. GA-repeat strands exhibit strong folding cooperativity─folding becomes more favorable in the presence of other folded peptides. A peptide with GE repeats on one strand and GZ on the other yields assemblies with alternating negative and positive strands.