Journal of Physical Chemistry B, Vol.112, No.26, 7956-7966, 2008
Structure and stability of short beta-peptide nanotubes: A non-natural representative of collagen?
Since secondary structure elements are known to play a key role in stabilizing the 3D-fold of proteins for the design of non-natural proteins composed of beta-amino acid residues, the construction of suitable secondary structural elements is mandatory. Folding analogues of alpha-helices and P-strands of beta-polypeptides were already described (Chem. Biodiversity 2004, 1, 11111). Here, we present several collagen-like folds composed exclusively of beta-Ala(s). Unlike their natural counterpart, these tubular nanostructures can be composed of more than three polypeptide chains aligned parallel and/or antiparallel. By using ab initio and DFT calculations we have optimized a large number of versatile collagen-like antiparallel nanostructures. In these tubular systems, oligopeptide strands are interconnected by i -> (i) type H-bonds, except for the "closing" set. This latter is called "the H-bond zipper" and is either (i) -> i, (i + 1) -> i, or (i + 2) -> i type. Antiparallel, tubular foldamers composed of I number of strands, each of k number of P-amino acid residues (e.g., ap(beta-T-i+l(l))(k), ap(beta-T-i+1(l))(k), or ap(beta-T-i+2(l))(k)) are unexpectedly stable supramolecular complexes. Independent of k and l, the local backbone fold of the amino acid residues is usually spiral, abbreviated as "SP" or "S*p". Nevertheless, in contrast to parallel, in antiparallel nanotubes the backbone fold can occasionally twist out from Sp or S*p type into an alternative local structure. However, the more the local geometry of the strands resembles to Sp or S*p, the higher the stability is. Besides the backbone twisting, the overall stability is determined by the type and the geometrical properties of the constituent H-bonds. Interestingly, higher number of total H-bonds can provide a lower overall stability, when H-bond parameters are inferior. In general, the increase of both the number of strands and their length stabilize the supramolecular complex. Now that, for P-peptides, collagenlike overall folds with their stability were determined, their POG- or PPG-like sequence specificity has to be revealed.