106
A. Bagaria and S. Ramakumar
dipeptides (Gorbitz 2001). The stacked aromatic rings in the dehydrodipeptide
are held by intermolecular C–H · π interactions, contributing to the overall stability of the assembled structure. The centroid of the dehydrophenylalanine ring
acts as the acceptor and the C1E1 acts as the donor. The donor to acceptor distance is
3.942 Å, the hydrogen to acceptor distance is 3.07 Å while the angle D-HLA (where
D is donor and A is acceptor) is 156° (Brandl et al. 2001).
3.1.6 Discussions About Dipeptide I (FF)
Self-assembly has recently become a major thrust for material scientists. This process
of self-assembly ultimately would give us the potential to create artificial molecules
whose architecture and function is not limited by the paradigms found in nature but
only by the creativity of the chemist. In this context, small peptides like dipeptides
have gained much attention in displaying a myriad of structures and their potential
applications. Recent work by Reches and Gazit (2003) showing the supramolecular assembly in a Phe-Phe dipeptide motif and the crystallographic detail realized
by Gorbitz (2001), earlier, has led us to investigate the potential of conformation
constraining residue Phe in the dipeptide motif.
The tubular structure is formed by the aggregation of four dipeptide
molecules (Figs. 8 and 9) resulting in a rectangular channel having van der
Waals dimension of 6.0 × 4.5 Å. In contrast, the saturated analogue, Phe–Phe,
exhibits nearly circular channels formed by the assembly of 6 peptide molecules
(Gorbitz 2001), with a diameter of 24 Å. Further differences in the two structures, Phe–Phe and Phe–Phe, are seen in their molecular conformations. A
simplified description of a dipeptide can be made by calculating a torsion angle θ
= C
β
1 –C
α
1 … C
α
2 –C
β
2 , proposed by Gorbitz (2001). It defines the relative position of
the two side chains with respect to the peptide plane. Gorbitz et al. have shown that
for zwitterionic L -Xaa- L -Xaa dipeptides (Xaa is neither Gly nor Pro), the side chains
usually point in the almost opposite direction with |θ| usually being >135. According
to this torsion angle description, Phe–Phe occurs in the most unusual conformation with θ being 40.2°. The side chains are thus located on the same side
of the peptide bond plane and appear to emanate out from the channel core.
However, for Phe–Phe this torsion angle |θ| has a value of 149.70° suggesting
the side chains being present on both sides of the peptide bond plane, imparting
an amphipathic nature to the channel. The acetic acid molecules trapped in the
channel formed by Phe–Phe is crystallographically detected (Gupta et al. 2007).
Self-assembly of the dehydrodipeptide was investigated under acidic, neutral and
basic conditions by varying the pH of the medium used, and it was interesting to note
that the morphology of the fundamental tubular unit remains unchanged (27–30 nm)
over the range of pH used. The characteristic lateral association of the tubes observed
under different pH conditions might arise due to contributions from hydrophobic
interactions. This lateral association was absent in Phe–Phe dipeptide with both the
side chains located at the same side of the plane defined by the peptide bond.
A. Bagaria and S. Ramakumar
dipeptides (Gorbitz 2001). The stacked aromatic rings in the dehydrodipeptide
are held by intermolecular C–H · π interactions, contributing to the overall stability of the assembled structure. The centroid of the dehydrophenylalanine ring
acts as the acceptor and the C1E1 acts as the donor. The donor to acceptor distance is
3.942 Å, the hydrogen to acceptor distance is 3.07 Å while the angle D-HLA (where
D is donor and A is acceptor) is 156° (Brandl et al. 2001).
3.1.6 Discussions About Dipeptide I (FF)
Self-assembly has recently become a major thrust for material scientists. This process
of self-assembly ultimately would give us the potential to create artificial molecules
whose architecture and function is not limited by the paradigms found in nature but
only by the creativity of the chemist. In this context, small peptides like dipeptides
have gained much attention in displaying a myriad of structures and their potential
applications. Recent work by Reches and Gazit (2003) showing the supramolecular assembly in a Phe-Phe dipeptide motif and the crystallographic detail realized
by Gorbitz (2001), earlier, has led us to investigate the potential of conformation
constraining residue Phe in the dipeptide motif.
The tubular structure is formed by the aggregation of four dipeptide
molecules (Figs. 8 and 9) resulting in a rectangular channel having van der
Waals dimension of 6.0 × 4.5 Å. In contrast, the saturated analogue, Phe–Phe,
exhibits nearly circular channels formed by the assembly of 6 peptide molecules
(Gorbitz 2001), with a diameter of 24 Å. Further differences in the two structures, Phe–Phe and Phe–Phe, are seen in their molecular conformations. A
simplified description of a dipeptide can be made by calculating a torsion angle θ
= C
β
1 –C
α
1 … C
α
2 –C
β
2 , proposed by Gorbitz (2001). It defines the relative position of
the two side chains with respect to the peptide plane. Gorbitz et al. have shown that
for zwitterionic L -Xaa- L -Xaa dipeptides (Xaa is neither Gly nor Pro), the side chains
usually point in the almost opposite direction with |θ| usually being >135. According
to this torsion angle description, Phe–Phe occurs in the most unusual conformation with θ being 40.2°. The side chains are thus located on the same side
of the peptide bond plane and appear to emanate out from the channel core.
However, for Phe–Phe this torsion angle |θ| has a value of 149.70° suggesting
the side chains being present on both sides of the peptide bond plane, imparting
an amphipathic nature to the channel. The acetic acid molecules trapped in the
channel formed by Phe–Phe is crystallographically detected (Gupta et al. 2007).
Self-assembly of the dehydrodipeptide was investigated under acidic, neutral and
basic conditions by varying the pH of the medium used, and it was interesting to note
that the morphology of the fundamental tubular unit remains unchanged (27–30 nm)
over the range of pH used. The characteristic lateral association of the tubes observed
under different pH conditions might arise due to contributions from hydrophobic
interactions. This lateral association was absent in Phe–Phe dipeptide with both the
side chains located at the same side of the plane defined by the peptide bond.