Abstract
Self-assembled cyclic peptide nanotubes have attracted much attention because of their antimicrobial properties. Here, we present calculations on the formation of cyclic peptide dimers using basin-hopping and discrete path sampling. We present an analysis of the basin-hopping move sets that most efficiently explore the conformations of cyclic peptides. Group rotation moves, in which sections of the ring are rotated as a rigid body, are the most effective for cyclic peptides containing up to 20 residues. For cyclic peptide dimers, we find that a combination of group rotation intramolecular moves and rigid body intermolecular moves performs well. Discrete path sampling calculations on the cyclic peptide dimers show significant differences in the dimerization of hexa- and octapeptides.
Highlights
Self-assembly is the process by which small molecules aggregate to form large, ordered structures
Cyclic peptide nanotubes have been observed to form across lipid bilayers.[3,8,9]
The hydrogenbonding arrangement of cyclic peptide nanotubes is similar to that seen in amyloid fibrils, and it has been shown that cyclic peptides can disrupt amyloid formation.[10]
Summary
Self-assembly is the process by which small molecules aggregate to form large, ordered structures. Self-assembling cyclic peptides have sequences comprising alternating D- and L-peptide residues because this arrangement places the side-chains equatorial to the peptide rings with the peptide groups aligned axially to hydrogen bond to other cyclic peptides. Cyclic octapeptides are the most widely studied because they have the highest tendency to form nanotubes.[1−4] dimerization of cyclic hexapeptides has been observed,[13] and nanotubes of larger cyclic peptides are known.[9,14] Nanotubes with antiparallel hydrogen bonding arrangements are more stable than those with parallel hydrogen bonds.[15]
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