Peptide Nanotubes: A Crystallographic Approach
119
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 solved
by Gorbitz (2001), earlier, has led us to investigate the potential of conformation
constraining residue Phe in the dipeptide motif. In a minimalist approach towards
examining the role of Phe residue towards self-assembly, Phe–Phe, Val-Phe
and AlaPhe dipeptides have been investigated.
The peptide L -Phenylalanyl-α, β-dehydrophenylalanine (FF) forms selfassembly by the aggregation of four dipeptide molecules. The self-assembly has
been depicted in all the methods by which the peptide was characterized. The
rectangular channel thus formed is amphipathic in nature and holds an amphipathic, acetic acid molecule. The introduction of Phe that introduces a restriction on account of a double bond between C α and C β atoms seem to provide
order and directionality needed for the formation of well-ordered supramolecular structures and can be potentially utilized in fine-tuning the nature of other
molecular assemblies.
The two dipeptides L -Valyl-α, β-Dehydrophenylalanine (VF) and L Alanylα, β-Dehydrophenylalanine (AF) show different packing arrangements and
were studied together to investigate how the self-assembly behaves when the
molecular structure is modified. Here we have used two different hydrophobic
residues Ala and Val, Ala being less hydrophobic than Val. The conformations of
both the peptides are almost similar. VF forms hydrophobic columns having a
hydrophilic core while AF forms hydrophilic and hydrophobic layers with peptide
main chain moieties and peptide side chains, respectively.
A systematic survey carried by Gorbitz 2004 (Helle et al. 2004) reveals that
dipeptides constructed from two amino acid residues with large hydrophobic side
chains may give porous structures with hydrophilic inner surfaces. This structural
family is referred to as FF class after L -Phe- L -Phe and includes Leu-Leu, Leu-Phe,
Ile-Phe, Ile-Leu. The absolute value of the torsion angle θ for this class is less than
90°, meaning thereby that both side chains lie on the same side of the peptide bond
plane. In an attempt to understand the effect of change in molecular structures on selfassembly, we have compared the solid-state structures of VF and AF. VF falls
under FF class fulfilling both the criteria and being more hydrophobic prefers channel
formation tracing helicity. Albeit, for AF |θ| < 90°, but it being less hydrophobic,
prefers extended layer formation. It is clear that the introduction of the hydrophobicity
parameter brings about changes in packing. Even though the confirmation of these
two peptides is quite similar, both exhibit remarkably different packing arrangements.
Thus we can say that changes in molecular structure by altering the hydrophobicity
of the dipeptide in the dehydro peptides studied here alter the self-assembly.
π-stacking is considered as one of the major determinants in self-assembly process. The present peptide structures however revealed that it is just not the
π-stacking but also the overall hydrophobicity of the molecule that dictates
self-assembly. Phe has a high hydrophobicity index than Ala. The absence of
tubular assembly in Ala-Phe as compared to Phe-Phe substantiates the above
119
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 solved
by Gorbitz (2001), earlier, has led us to investigate the potential of conformation
constraining residue Phe in the dipeptide motif. In a minimalist approach towards
examining the role of Phe residue towards self-assembly, Phe–Phe, Val-Phe
and AlaPhe dipeptides have been investigated.
The peptide L -Phenylalanyl-α, β-dehydrophenylalanine (FF) forms selfassembly by the aggregation of four dipeptide molecules. The self-assembly has
been depicted in all the methods by which the peptide was characterized. The
rectangular channel thus formed is amphipathic in nature and holds an amphipathic, acetic acid molecule. The introduction of Phe that introduces a restriction on account of a double bond between C α and C β atoms seem to provide
order and directionality needed for the formation of well-ordered supramolecular structures and can be potentially utilized in fine-tuning the nature of other
molecular assemblies.
The two dipeptides L -Valyl-α, β-Dehydrophenylalanine (VF) and L Alanylα, β-Dehydrophenylalanine (AF) show different packing arrangements and
were studied together to investigate how the self-assembly behaves when the
molecular structure is modified. Here we have used two different hydrophobic
residues Ala and Val, Ala being less hydrophobic than Val. The conformations of
both the peptides are almost similar. VF forms hydrophobic columns having a
hydrophilic core while AF forms hydrophilic and hydrophobic layers with peptide
main chain moieties and peptide side chains, respectively.
A systematic survey carried by Gorbitz 2004 (Helle et al. 2004) reveals that
dipeptides constructed from two amino acid residues with large hydrophobic side
chains may give porous structures with hydrophilic inner surfaces. This structural
family is referred to as FF class after L -Phe- L -Phe and includes Leu-Leu, Leu-Phe,
Ile-Phe, Ile-Leu. The absolute value of the torsion angle θ for this class is less than
90°, meaning thereby that both side chains lie on the same side of the peptide bond
plane. In an attempt to understand the effect of change in molecular structures on selfassembly, we have compared the solid-state structures of VF and AF. VF falls
under FF class fulfilling both the criteria and being more hydrophobic prefers channel
formation tracing helicity. Albeit, for AF |θ| < 90°, but it being less hydrophobic,
prefers extended layer formation. It is clear that the introduction of the hydrophobicity
parameter brings about changes in packing. Even though the confirmation of these
two peptides is quite similar, both exhibit remarkably different packing arrangements.
Thus we can say that changes in molecular structure by altering the hydrophobicity
of the dipeptide in the dehydro peptides studied here alter the self-assembly.
π-stacking is considered as one of the major determinants in self-assembly process. The present peptide structures however revealed that it is just not the
π-stacking but also the overall hydrophobicity of the molecule that dictates
self-assembly. Phe has a high hydrophobicity index than Ala. The absence of
tubular assembly in Ala-Phe as compared to Phe-Phe substantiates the above