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In silico modeling and functional interpretations of Cry1Ab15 toxin from Bacillus thuringiensis BtB-Hm-16.

Kashyap S - Biomed Res Int (2013)

Bottom Line: The novel structural differences found are the presence of β0 and α3, and the absence of α7b, β1a, α10a, α10b, β12, and α11a while α9 is located spatially downstream.Validation by SUPERPOSE and with the use of PROCHECK program showed folding of 98% of modeled residues in a favourable and stable orientation with a total energy Z-score of -6.56; the constructed model has an RMSD of only 1.15 Å.These increments of 3D structure information will be helpful in the design of domain swapping experiments aimed at improving toxicity and will help in elucidating the common mechanism of toxin action.

View Article: PubMed Central - PubMed

Affiliation: National Bureau of Agriculturally Important Microorganisms (ICAR), Kusmaur, Kaithauli, Maunath Bhanjan, Uttar Pradesh 275101, India.

ABSTRACT
The theoretical homology based structural model of Cry1Ab15 δ-endotoxin produced by Bacillus thuringiensis BtB-Hm-16 was predicted using the Cry1Aa template (resolution 2.25 Å). The Cry1Ab15 resembles the template structure by sharing a common three-domain extending conformation structure responsible for pore-forming and specificity determination. The novel structural differences found are the presence of β0 and α3, and the absence of α7b, β1a, α10a, α10b, β12, and α11a while α9 is located spatially downstream. Validation by SUPERPOSE and with the use of PROCHECK program showed folding of 98% of modeled residues in a favourable and stable orientation with a total energy Z-score of -6.56; the constructed model has an RMSD of only 1.15 Å. These increments of 3D structure information will be helpful in the design of domain swapping experiments aimed at improving toxicity and will help in elucidating the common mechanism of toxin action.

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Superimposed backbone 3D structure between Cry1Aa1 (green) and Cry1Ab15 (red) coordinates. The RMSD for backbone and alpha carbons is 1.15. The image was generated using the SUPERPOSE software (http://wishart.biology.ualberta.ca/SuperPose/).
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fig5: Superimposed backbone 3D structure between Cry1Aa1 (green) and Cry1Ab15 (red) coordinates. The RMSD for backbone and alpha carbons is 1.15. The image was generated using the SUPERPOSE software (http://wishart.biology.ualberta.ca/SuperPose/).

Mentions: Finally, the recognition of artefacts and errors in experimental and theoretical structures remains a problem in the field of structure modeling. A structural comparison of Cry1Aa toxin with the theoretical model of the Cry1Ab15 protein indicates correspondence with the general model for a Cry protein the superimposed backbone traces showed low RMS deviations (Figure 5). The comparison between the overall energy of developed structure and those of experimentally determined structures in PROSA database validated the developed model as folded near to experimentally determined, natural structures (Figure 6) while the Ramachandran plot analysis (Figure 7) supported the above conclusions by showing that most of the residue (98%) has φ and ψ angles in the core- and allowed-regions, except for nine residues which qualified for outlier region. Most bond lengths, bond angles, and torsion angles were in the range of values expected for a naturally folded protein (Figure 7).


In silico modeling and functional interpretations of Cry1Ab15 toxin from Bacillus thuringiensis BtB-Hm-16.

Kashyap S - Biomed Res Int (2013)

Superimposed backbone 3D structure between Cry1Aa1 (green) and Cry1Ab15 (red) coordinates. The RMSD for backbone and alpha carbons is 1.15. The image was generated using the SUPERPOSE software (http://wishart.biology.ualberta.ca/SuperPose/).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3818814&req=5

fig5: Superimposed backbone 3D structure between Cry1Aa1 (green) and Cry1Ab15 (red) coordinates. The RMSD for backbone and alpha carbons is 1.15. The image was generated using the SUPERPOSE software (http://wishart.biology.ualberta.ca/SuperPose/).
Mentions: Finally, the recognition of artefacts and errors in experimental and theoretical structures remains a problem in the field of structure modeling. A structural comparison of Cry1Aa toxin with the theoretical model of the Cry1Ab15 protein indicates correspondence with the general model for a Cry protein the superimposed backbone traces showed low RMS deviations (Figure 5). The comparison between the overall energy of developed structure and those of experimentally determined structures in PROSA database validated the developed model as folded near to experimentally determined, natural structures (Figure 6) while the Ramachandran plot analysis (Figure 7) supported the above conclusions by showing that most of the residue (98%) has φ and ψ angles in the core- and allowed-regions, except for nine residues which qualified for outlier region. Most bond lengths, bond angles, and torsion angles were in the range of values expected for a naturally folded protein (Figure 7).

Bottom Line: The novel structural differences found are the presence of β0 and α3, and the absence of α7b, β1a, α10a, α10b, β12, and α11a while α9 is located spatially downstream.Validation by SUPERPOSE and with the use of PROCHECK program showed folding of 98% of modeled residues in a favourable and stable orientation with a total energy Z-score of -6.56; the constructed model has an RMSD of only 1.15 Å.These increments of 3D structure information will be helpful in the design of domain swapping experiments aimed at improving toxicity and will help in elucidating the common mechanism of toxin action.

View Article: PubMed Central - PubMed

Affiliation: National Bureau of Agriculturally Important Microorganisms (ICAR), Kusmaur, Kaithauli, Maunath Bhanjan, Uttar Pradesh 275101, India.

ABSTRACT
The theoretical homology based structural model of Cry1Ab15 δ-endotoxin produced by Bacillus thuringiensis BtB-Hm-16 was predicted using the Cry1Aa template (resolution 2.25 Å). The Cry1Ab15 resembles the template structure by sharing a common three-domain extending conformation structure responsible for pore-forming and specificity determination. The novel structural differences found are the presence of β0 and α3, and the absence of α7b, β1a, α10a, α10b, β12, and α11a while α9 is located spatially downstream. Validation by SUPERPOSE and with the use of PROCHECK program showed folding of 98% of modeled residues in a favourable and stable orientation with a total energy Z-score of -6.56; the constructed model has an RMSD of only 1.15 Å. These increments of 3D structure information will be helpful in the design of domain swapping experiments aimed at improving toxicity and will help in elucidating the common mechanism of toxin action.

Show MeSH
Related in: MedlinePlus