April Journal-2009.p65 - Association of Biotechnology and Pharmacy
April Journal-2009.p65 - Association of Biotechnology and Pharmacy
April Journal-2009.p65 - Association of Biotechnology and Pharmacy
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Current Trends in <strong>Biotechnology</strong> <strong>and</strong> <strong>Pharmacy</strong><br />
Vol. 3 (2) 210-218, <strong>April</strong> 2009. ISSN 0973-8916<br />
215<br />
classification (4,5). The predicted structure was<br />
analyzed using VERIFY 3D (21,22) which<br />
assessed <strong>and</strong> confirmed the quality <strong>of</strong> the<br />
predicted structure <strong>of</strong> CtGH39 with acceptable<br />
scores. The scores (from -1 to +1) were added<br />
<strong>and</strong> plotted for individual residues. The residues<br />
falling in the area where the blue line crosses 0.1<br />
have low prediction accuracy <strong>and</strong> less stable<br />
conformation whereas most <strong>of</strong> the residues fall<br />
above 0.2-0.4 <strong>and</strong> so we can say that the model<br />
is <strong>of</strong> good quality (Fig. 5).<br />
Fig. 6. Ramach<strong>and</strong>ran plot for CtGH39 from<br />
Clostridium thermocellum using RC plot online<br />
server available from IISc Bangalore (13). It shows<br />
the left-h<strong>and</strong>ed as well as right-h<strong>and</strong>ed helices, beta<br />
sheets <strong>and</strong> disallowed <strong>and</strong> allowed areas. Black areas<br />
are allowed only for Gly residues.<br />
Fig. 5. Three dimensional model testing for assessing<br />
the quality <strong>of</strong> predicted 3-D model by VARIFY 3D<br />
s<strong>of</strong>tware (very few residues cross the red line having<br />
negative value implying predicted model is good).<br />
Ramach<strong>and</strong>ran plot (24) reveals that the<br />
repeating values <strong>of</strong> phi <strong>and</strong> psi angles along the<br />
polypeptide chain results in regular structure, such<br />
as repeating values <strong>of</strong> phi ~-57 <strong>and</strong> psi ~-47 give<br />
a right-h<strong>and</strong>ed helix (the á-helix). The structure<br />
<strong>of</strong> CtGH39 showed many segments <strong>of</strong> helix <strong>and</strong><br />
the Ramach<strong>and</strong>ran plot showed a tight grouping<br />
or clustering <strong>of</strong> (φ), (ψ) angles around -50, -50<br />
(Fig. 6). The total number <strong>of</strong> residues in alpha<br />
helix is 156 which have (φ)~ -50 <strong>and</strong> (ψ)~ -50,<br />
these alpha helix residues are more clustered than<br />
spread like clouds i.e. these structures are more<br />
rigid than beta sheets <strong>and</strong> thus have less allowed<br />
conformations. Similarly, repetitive values in the<br />
region (Fig. 6) <strong>of</strong> φ = -110 to -140 <strong>and</strong> ψ = +110<br />
to +135 gave extended chains with conformations<br />
that allow interactions between closely folded<br />
parallel segments (â-sheet structures). The<br />
structure <strong>of</strong> CtGH39 is composed mostly <strong>of</strong> â-<br />
sheets <strong>and</strong> the Ramach<strong>and</strong>ran plot showed a<br />
broad range <strong>of</strong> values in the -110, +130 regions<br />
(Fig. 6). Repeating φ, ø angles always lead to a<br />
regular structure provided it is sterically allowed.<br />
There are total 22 residues in 3 10<br />
helical regions,<br />
which are present in first quadrant <strong>of</strong><br />
conformational map (Fig. 6). The total number <strong>of</strong><br />
residues in beta sheet is 188, which covers almost<br />
all the region <strong>of</strong> second quadrant <strong>and</strong> extremities<br />
<strong>of</strong> the 3rd quadrant (Fig. 6). The Ramach<strong>and</strong>ran<br />
plot for CtGH39 using RAMPAGE s<strong>of</strong>tware (24),<br />
revealed that among the 390 residues, 352 (90.7%)<br />
were in favoured region, 26 (6.7%) were in<br />
allowed region <strong>and</strong> 10 (2.6%) were in disallowed<br />
region proving again that the predicted model is<br />
acceptable (Fig. 7). Ramach<strong>and</strong>ran plot for<br />
general, glycine, pre-proline <strong>and</strong> proline was also<br />
done <strong>and</strong> it showed the glycine, pre-Pro <strong>and</strong> proline<br />
<strong>of</strong> CtGH39 falling under allowed regions <strong>and</strong> also<br />
Ahmed et al