Peptide Nanotubes: A Crystallographic Approach
113
the hydrogen to acceptor distance is 3.11 Å while the angle D-HLA (where D is the
donor and A is the acceptor) is 145°.
3.2.6 Discussions About Dipeptide II (VF)
In VF, four peptide molecules constitute the circumference of the rectangular
channel of dimension 5.0 × 4.0 Å. The interior of this channel is hydrophilic due
to the presence of CONH moieties and NH 3 + and −OOC groups, while the exterior
is hydrophobic as it is occupied by the side chains of Val and F.
The crystal structure of the dipeptide L -Valyl- L -Phenylalanyl (VF) was solved by
Gorbitz (2002a, b). VF does not reveal the presence of channel structures. The crystal
packing of VF in one of the crystal form depicts a hydrogen-bond cage formation
around the hydrophobic groups by co-crystallized water molecules.
3.3 Characterization of Dipeptide III (AΔF)
3.3.1 Crystallization and Data Collection
Crystals of peptide III were grown by slow evaporation of peptide solution in
methanol and toluene mixture (1:1 v/v). Rod-shaped crystals suitable for x-ray
diffraction, appeared within 4–5 days. The suitable crystal was mounted on the glass
fibre and X-ray diffraction data were collected on a Bruker AXS SMART APEX CCD
diffractometer equipped with Mo K α radiation. Unit cell parameters and orientation
matrix were determined initially by collecting three sets of data collected at three
different settings (set1 ϕ = 0°, 2θ = −28°, ω = −28°; set2 ϕ = 90°, 2θ = −28°, ω =
−28°; set3 ϕ = 0°, 2θ = 28°, ω = 28°), each data set consists of 50 frames with ω-scan
width of 0.3°. The diffraction data were acquired over a hemisphere of reciprocal
lattice space by three different settings of ϕ (ϕ = 0°, 90°, 180°) and keeping detector
at an angle of 2θ = −25°, with detector to crystal distance of 6.07 cm. For each
setting of ϕ, 606 diffraction image frames with ω-width of 0.3° and exposure time of
20 s per fame were obtained. The data processing was done by reducing the image
frames to obtain the integrated intensities for each reflection and intensities were
corrected for Lorentz and polarization factors. The data processing was done using
the software SAINTV6.1 (Bruker 1998). The data sets were corrected for absorption
effect by using software SADABS (Sheldrick 1996). Finally, the corrected intensity
data were used for the structure solution and refinement.
3.3.2 Structure Determination and Refinement
The structure solution was obtained by using direct methods employed in SHELXS97
software (Sheldrick 1997). All the non-hydrogen atoms were located in the E-map
113
the hydrogen to acceptor distance is 3.11 Å while the angle D-HLA (where D is the
donor and A is the acceptor) is 145°.
3.2.6 Discussions About Dipeptide II (VF)
In VF, four peptide molecules constitute the circumference of the rectangular
channel of dimension 5.0 × 4.0 Å. The interior of this channel is hydrophilic due
to the presence of CONH moieties and NH 3 + and −OOC groups, while the exterior
is hydrophobic as it is occupied by the side chains of Val and F.
The crystal structure of the dipeptide L -Valyl- L -Phenylalanyl (VF) was solved by
Gorbitz (2002a, b). VF does not reveal the presence of channel structures. The crystal
packing of VF in one of the crystal form depicts a hydrogen-bond cage formation
around the hydrophobic groups by co-crystallized water molecules.
3.3 Characterization of Dipeptide III (AΔF)
3.3.1 Crystallization and Data Collection
Crystals of peptide III were grown by slow evaporation of peptide solution in
methanol and toluene mixture (1:1 v/v). Rod-shaped crystals suitable for x-ray
diffraction, appeared within 4–5 days. The suitable crystal was mounted on the glass
fibre and X-ray diffraction data were collected on a Bruker AXS SMART APEX CCD
diffractometer equipped with Mo K α radiation. Unit cell parameters and orientation
matrix were determined initially by collecting three sets of data collected at three
different settings (set1 ϕ = 0°, 2θ = −28°, ω = −28°; set2 ϕ = 90°, 2θ = −28°, ω =
−28°; set3 ϕ = 0°, 2θ = 28°, ω = 28°), each data set consists of 50 frames with ω-scan
width of 0.3°. The diffraction data were acquired over a hemisphere of reciprocal
lattice space by three different settings of ϕ (ϕ = 0°, 90°, 180°) and keeping detector
at an angle of 2θ = −25°, with detector to crystal distance of 6.07 cm. For each
setting of ϕ, 606 diffraction image frames with ω-width of 0.3° and exposure time of
20 s per fame were obtained. The data processing was done by reducing the image
frames to obtain the integrated intensities for each reflection and intensities were
corrected for Lorentz and polarization factors. The data processing was done using
the software SAINTV6.1 (Bruker 1998). The data sets were corrected for absorption
effect by using software SADABS (Sheldrick 1996). Finally, the corrected intensity
data were used for the structure solution and refinement.
3.3.2 Structure Determination and Refinement
The structure solution was obtained by using direct methods employed in SHELXS97
software (Sheldrick 1997). All the non-hydrogen atoms were located in the E-map