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

More documents

Recommendations

Info

Current Trends in Biotechnology and Pharmacy Vol. 3 (2) 210-218, April 2009. ISSN 0973-8916 214 Fig. 4. Three dimensional structure of CtGH39 developed utilizing MODELLER 8v2 and visualized using RASWIN (RASMOL) software showing the characteristic (ß/á) 8 fold (alpha helix in red ribbons and beta sheets in yellow arrows) Fig. 3. Secondary structure of CtGH39 predicted using PSIPRED VIEW software (18) showing helix (shown as cylinders) and beta strands (shown as arrow region) and coils (as continuous line) with confidence level of prediction. The secondary structures of proteins are the regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the alpha-helix and beta-sheet. Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule. Protein secondary structure prediction of CtGH39 from its sequence using PSIPRED VIEW is shown in (Fig. 3). It revealed many helices, strands and coils present at various positions in the protein structure along with their confidence level for such occurrence. Tertiary structure is generally stabilized by non-local interactions, most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds and even post-translational modifications. The term “tertiary structure” is often used as synonymous with the term fold. The tertiary structure prediction of CtGH39 using the structures from PDB (27,28,29) as template was done (Fig. 4) by utilizing MODELLER 8v2 (9,10,11,12) a web service provided by Max-Planck Institute (20). The characteristic feature of CtGH39 showing a (ß/á) 8 fold was easily identified from the predicted 3-dimensional structure of CtGH39 as it also belonged to Clan ‘A’ according to the CAZy Homology modeling of family 39 glycoside hydrolase
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
Page 2 and 3:
Current Trends in Biotechnology and
Page 4 and 5:
Association of Biotechnology and Ph
Page 6 and 7:
Page 8 and 9:
Page 10 and 11:
Page 12 and 13:
Page 14 and 15:
Page 16 and 17:
Page 18 and 19:
Page 20 and 21:
Page 22 and 23:
Page 24 and 25:
Page 26 and 27:
Page 28 and 29:
Page 30 and 31:
Page 32 and 33:
Page 34 and 35:
Page 36 and 37:
Page 38 and 39:
Page 40 and 41:
Page 42 and 43:
Page 44 and 45:
Page 46 and 47:
Page 48 and 49:
Page 50:
Page 54 and 55:
Page 56 and 57:
Page 58 and 59:
Page 60 and 61:
Page 62 and 63: Current Trends in Biotechnology and
show all

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

Create successful ePaper yourself

Delete template?

Save as template?