Experimental and Computational Studies Reveal an Alternative Supramolecular Structure for Fmoc-Dipeptide Self-Assembly

Abstract

We have investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dialanine (Fmoc-AA) molecules using combined computational and experimental approaches. Fmoc-AA gels were characterized using TEM, circular dichroism, FTIR, and WAXS. Computationally, we simulated the assembly of Fmoc-AA using molecular dynamics techniques. All simulations converged to a condensed fibril structure in which the Fmoc groups stack mostly within in the center of the fibril. However, the Fmoc groups are partially exposed to water, creating an amphiphilic surface, which may be responsible for aggregation of fibrils into nano-scale fibers observed in TEM. From the fibril models, radial distribution calculations agree with d-spacings observed in WAXS for the fibril diameter and π-stacking interactions. Our analyses show that dialanine, despite its short length, adopts a mainly extended polyproline II conformation. In contrast to previous hypotheses, these results indicate that β-sheet-like hydrogen bonding is not prevalent. Rather, stacking of Fmoc groups, inter-residue hydrogen bonding and hydrogen bonding with water play the important roles in stabilizing the fibril structure of supramolecular assemblies of short conjugated peptides.

Computational Amphiphilic Materials for Drug Delivery

“…The formation of fibrils with Fmoc groups at the center was observed; nevertheless, the partial exposure of Fmoc groups to water caused the fibrils to aggregate into nanoscale fibers. The radial distribution calculations agreed well with the d-spacings measured by wide angle X-ray scattering for the fibril diameter and π-stacking interactions (Mu et al, 2012). Similarly, Lopez-Perez et al found Fmoc conjugated tetrapeptides (Fmoc-RGDS and Fmoc-GRDS) retained pre-assembled β-sheet parallel conformations under low concentrations, which were dominated by the interactions among Fmoc units.…”

Structural determinants in a library of low molecular weight gelators

“…38,39 Similar values have been found elsewhere for Fmoc-dipeptides, and have been ascribed to either distances between ß-sheets or distances between the Fmoc groups. 32,[40][41][42] The interstrand separation in Å, indicated by the strongest meridional signals, are generally grouped by the identity of the naphthalene group since HNap-AA and H-Nap-AV show a meridional repeat of 4.68 -4.70 Å whilst the peptides containing Br or CN have shorter repeats closer to 4.55 Å (Table S3). Reflection positions, relative intensity and axial alignment of reflections for each fXRD pattern must arise from the molecular packing of the dipeptides in the self-assembled fibres.…”

“…Reflections at approximately 26 Å have been found for Fmoc-dipeptides and ascribed to the fibre widths. 32,40,42 This data has been used to build a model for the assembly, although it is not clear to us that this model can be directly translated to our systems. Further, the reflections with the greatest relative intensity are matched in Br-Nap and CN-Nap systems.…”

“…For related Fmoc-dipeptide systems, it has been suggested that the driving force is assembly of the aromatic rings. 32,[40][41][42] Related work on a system where one amino acid was replaced with lactic acid showed that the formation of beta-sheets is not a pre-requisite for gelation (and also makes the point that interpretation of IR data is difficult for such short peptides). 40 In general, dipeptides such as those described here form micellar aggregates at high pH (i.e.…”

Charge and sequence effects on the self-assembly and subsequent hydrogelation of Fmoc-depsipeptides

“…16 Our group has previously demonstrated both experimentally and computationally that while the stacking of the Fmoc group of Fmoc-Ala-Ala was critical in fiber formation and subsequent gelation, the formation of β-sheet-like hydrogen bonds between molecules was not prevalent. 23 …”