April Journal-2009.p65 - Association of Biotechnology and Pharmacy

Current Trends in Biotechnology and Pharmacy
Vol. 3 (2) 210-218, April 2009. ISSN 0973-8916
215
classification (4,5). The predicted structure was
analyzed using VERIFY 3D (21,22) which
assessed and confirmed the quality of the
predicted structure of CtGH39 with acceptable
scores. The scores (from -1 to +1) were added
and plotted for individual residues. The residues
falling in the area where the blue line crosses 0.1
have low prediction accuracy and less stable
conformation whereas most of the residues fall
above 0.2-0.4 and so we can say that the model
is of good quality (Fig. 5).
Fig. 6. Ramachandran plot for CtGH39 from
Clostridium thermocellum using RC plot online
server available from IISc Bangalore (13). It shows
the left-handed as well as right-handed helices, beta
sheets and disallowed and allowed areas. Black areas
are allowed only for Gly residues.
Fig. 5. Three dimensional model testing for assessing
the quality of predicted 3-D model by VARIFY 3D
software (very few residues cross the red line having
negative value implying predicted model is good).
Ramachandran plot (24) reveals that the
repeating values of phi and psi angles along the
polypeptide chain results in regular structure, such
as repeating values of phi ~-57 and psi ~-47 give
a right-handed helix (the á-helix). The structure
of CtGH39 showed many segments of helix and
the Ramachandran plot showed a tight grouping
or clustering of (φ), (ψ) angles around -50, -50
(Fig. 6). The total number of residues in alpha
helix is 156 which have (φ)~ -50 and (ψ)~ -50,
these alpha helix residues are more clustered than
spread like clouds i.e. these structures are more
rigid than beta sheets and thus have less allowed
conformations. Similarly, repetitive values in the
region (Fig. 6) of φ = -110 to -140 and ψ = +110
to +135 gave extended chains with conformations
that allow interactions between closely folded
parallel segments (â-sheet structures). The
structure of CtGH39 is composed mostly of â-
sheets and the Ramachandran plot showed a
broad range of values in the -110, +130 regions
(Fig. 6). Repeating φ, ø angles always lead to a
regular structure provided it is sterically allowed.
There are total 22 residues in 3 10
helical regions,
which are present in first quadrant of
conformational map (Fig. 6). The total number of
residues in beta sheet is 188, which covers almost
all the region of second quadrant and extremities
of the 3rd quadrant (Fig. 6). The Ramachandran
plot for CtGH39 using RAMPAGE software (24),
revealed that among the 390 residues, 352 (90.7%)
were in favoured region, 26 (6.7%) were in
allowed region and 10 (2.6%) were in disallowed
region proving again that the predicted model is
acceptable (Fig. 7). Ramachandran plot for
general, glycine, pre-proline and proline was also
done and it showed the glycine, pre-Pro and proline
of CtGH39 falling under allowed regions and also
Ahmed et al