Peptide Nanotubes: A Crystallographic Approach
111
chains of Val and F. The crystal structure further revealed that the individual peptide columns are regularly aligned via intermolecular hydrogen bonds (Table 6) and
other non-covalent interactions to form higher ordered supramolecular arrays along
the crystallographic basis (Fig. 12). The interior of the channel is hydrophilic and
water molecules are crystallographically detected inside the channel. The channel
formed by VF is shown in Fig. 13. All side chains appear to emanate from the
channel core filled with water molecules. The structure can thus be visualized as
close packing of the hydrophobic tubes with the interior lined by many polar atoms.
This channel has van der Waals dimension of 4.0 × 5.0 Å.
These water molecules exhibit N–HLO hydrogen bonding with the NH 3
+ group.
The VF molecules depict a direct head-to-tail hydrogen-bond pattern similar
to that seen in other dipeptides consisting of coded amino acids. The pattern was
analysed on the graph set theory (Etter et al. 1990) (Fig. 14). The centroid of the
dehydrophenylalanine ring acts as the acceptor and the C1G1 acts as the donor in a
C-HLπ interaction (Brandl et al. 2001). The donor to acceptor distance is 3.929 Å,
Table 6 Hydrogen–bond parameters for L -Valyl-α, β-dehydrophenylalanine (VF)
D (donor)
A(acceptor)
DL.A (Å)
HLA (Å)
D-HLA (°)
Symmetry Code
N1A
O2B
3.413
2.56
161
−x, +y − 1, −z
N1A
O2 B
2.827
2.06
143
−x, +y − 1, −z
N1A
O1W
3.087
2.25
156
−x, +y, −z
N1A
O2B
2.824
2.00
135
−x, +y, −z
N2A
O2A
2.822
2.08
145
x, +y − 1, +z
N1B
O1W
3.045
2.33
138
x, +y − 1, +z
N1B
O2W
2.927
2.39
120
x, +y − 1, +z
N1B
O2 A
3.377
2.52
161
x, +y − 1, +z
N1B
O2A
2.802
2.05
142
x, +y − 1, +z
N1B
O2 A
2.808
2.09
138
x, y, z
N2B
O2 B
2.807
2.08
142
x, +y − 1, +z
C1A
O1 A
3.220
2.48
132
x, +y − 1, +z
C2D1
N2B
3.096
2.47
125
x, y, z
C1B
O1 B
3.225
2.45
135
x, +y − 1, +z
C2G2
O1’B
3.072
2.44
123
x, y, z
D (donor) A(acceptor) D …. A
(Å)
H … A (Å)
D-H … A (°)
Symmetry Code
O1W
O2W
3.430
–
–
x, +y − 1, +z
O1W
O2W
3.114
–
–
−x, +y − 1, −z
O1W
O2W
3.070
–
–
−x, +y, −z
O1W
O2 A
2.733
–
–
−x, +y, −z
O2W
O2W
2.809
–
–
−x, +y, −z
O1W
O1 A
3.347
–
–
−x, +y, −z
111
chains of Val and F. The crystal structure further revealed that the individual peptide columns are regularly aligned via intermolecular hydrogen bonds (Table 6) and
other non-covalent interactions to form higher ordered supramolecular arrays along
the crystallographic basis (Fig. 12). The interior of the channel is hydrophilic and
water molecules are crystallographically detected inside the channel. The channel
formed by VF is shown in Fig. 13. All side chains appear to emanate from the
channel core filled with water molecules. The structure can thus be visualized as
close packing of the hydrophobic tubes with the interior lined by many polar atoms.
This channel has van der Waals dimension of 4.0 × 5.0 Å.
These water molecules exhibit N–HLO hydrogen bonding with the NH 3
+ group.
The VF molecules depict a direct head-to-tail hydrogen-bond pattern similar
to that seen in other dipeptides consisting of coded amino acids. The pattern was
analysed on the graph set theory (Etter et al. 1990) (Fig. 14). The centroid of the
dehydrophenylalanine ring acts as the acceptor and the C1G1 acts as the donor in a
C-HLπ interaction (Brandl et al. 2001). The donor to acceptor distance is 3.929 Å,
Table 6 Hydrogen–bond parameters for L -Valyl-α, β-dehydrophenylalanine (VF)
D (donor)
A(acceptor)
DL.A (Å)
HLA (Å)
D-HLA (°)
Symmetry Code
N1A
O2B
3.413
2.56
161
−x, +y − 1, −z
N1A
O2 B
2.827
2.06
143
−x, +y − 1, −z
N1A
O1W
3.087
2.25
156
−x, +y, −z
N1A
O2B
2.824
2.00
135
−x, +y, −z
N2A
O2A
2.822
2.08
145
x, +y − 1, +z
N1B
O1W
3.045
2.33
138
x, +y − 1, +z
N1B
O2W
2.927
2.39
120
x, +y − 1, +z
N1B
O2 A
3.377
2.52
161
x, +y − 1, +z
N1B
O2A
2.802
2.05
142
x, +y − 1, +z
N1B
O2 A
2.808
2.09
138
x, y, z
N2B
O2 B
2.807
2.08
142
x, +y − 1, +z
C1A
O1 A
3.220
2.48
132
x, +y − 1, +z
C2D1
N2B
3.096
2.47
125
x, y, z
C1B
O1 B
3.225
2.45
135
x, +y − 1, +z
C2G2
O1’B
3.072
2.44
123
x, y, z
D (donor) A(acceptor) D …. A
(Å)
H … A (Å)
D-H … A (°)
Symmetry Code
O1W
O2W
3.430
–
–
x, +y − 1, +z
O1W
O2W
3.114
–
–
−x, +y − 1, −z
O1W
O2W
3.070
–
–
−x, +y, −z
O1W
O2 A
2.733
–
–
−x, +y, −z
O2W
O2W
2.809
–
–
−x, +y, −z
O1W
O1 A
3.347
–
–
−x, +y, −z