Computationally designed coiled coil peptides for the solution assembly of nanostructured materials
Date
2018
Authors
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Journal ISSN
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Publisher
University of Delaware
Abstract
The de novo design of peptides enables the creation of highly specific solution self-assembled structures. Coiled coils are excellent candidates for the building blocks of these assemblies due to their robust and simple architecture that allows for the precise placement of amino acid residues at bundle interfaces within a design. The ability to design from first principles their oligomerization and subsequent higher order assembly offers their expanded use in producing new materials. Toward these ends, homo-tetrameric, antiparallel, coiled-coil, peptide bundles have been designed computationally, synthesized via solid-phase methods, and their solution behavior characterized. Two different bundle-forming peptides were designed and found to be extremely stable with respect to temperature and remained soluble in solution even at high (millimolar) peptide concentrations. The coiled-coil tetramer was confirmed to be the dominant species in solution by analytical sedimentation studies and by small-angle neutron scattering, where the scattering form factor is well represented by a cylinder model with the dimensions of the targeted coiled coil. At higher concentrations evidence of interbundle structure was observed via neutron scattering that was well-modeled by a structure factor for soluble aggregates of the bundles. The behavior of the dispersed bundles is similar to that observed for natural proteins. ☐ Furthering this work, peptide sequences were computationally designed to self-assemble in solution to create lattices with defined spacings and symmetry. These computationally designed sequences are incredibly similar. However, they create vastly different assemblies in solution determined by minor changes in their primary structure. Rational modification of a designed sequence illustrates the importance of single amino acids in the hierarchical assembly process. These sequences are characterized using circular dichroism to confirm the coiled-coil design as well as transmission electron microscopy to illustrate the microstructure and nanostructure of the assembled peptides. The sequences each create unique assemblies with specific underlying lattice symmetries and spacings, the differences in which can be attributed to differences in their primary structures. ☐ Five additional peptide sequences were found to assemble into coiled-coils that subsequently assembled into a variety of different microstructures. The sequences were previously designed to assemble to form 2D lattices. However, they were originally screened out as not viable candidates for lattice formation by an analysis of their interfacial interactions. The five peptide sequences all assembled into nanostructures with unique lattices. However, the lattice nanostructures differ from the originally predicted symmetry designed for the 2D sheets. The importance of subtle changes in the primary sequence, especially the impact of arginine over lysine, are illustrated through comparisons of the microstructure, nanostructure, and assembly kinetics of these sequences. The TEM analysis of these peptide assemblies under different pH and ionic strength conditions helps to elucidate the possible interactions responsible for the resulting morphologies as well as to expand our understanding of these sequences and other similar computationally designed coiled coil sequences. ☐ Combining the observations made for the specific impact of amino acid identity and placement in the coiled-coil bundle, trends imipacting the assembly of the originally intended 2D lattice can be inferred such as: the total number and position of charged residues, the number and position of arginine residues in particular, and the placement of aromatic residues.