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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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Amino acid sequence alignment of the Cry1Ab15 with Cry1Aa (1ciy: A). The residues highlighted in red color represent helix; those in blue represent strand; in green represent turn; and those in black represent coil, and alignment is generated using SAS software.
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fig1: Amino acid sequence alignment of the Cry1Ab15 with Cry1Aa (1ciy: A). The residues highlighted in red color represent helix; those in blue represent strand; in green represent turn; and those in black represent coil, and alignment is generated using SAS software.

Mentions: The possible outliers and side chains static constrain refinement of the developed model was performed on Summa Lab server [17] after the selected theoretical model were further subjected to a series of tests for evaluating its consistency and reliability. Backbone confirmation was evaluated by the inspection of the Psi/Phi Ramachandran plot from RAMPAGE web server [18]. The energy criterion was evaluated by ProSA web server [19], which compares the potential of mean forces derived from a large set of NMR and X-ray crystallographically derived protein structures of similar sizes. Potential deviations were calculated by SUPERPOSE web server [20] for root mean square deviations (RMSD) between target and template protein structure. The comparative analysis of generated model showed it to be superimposable. The secondary structure visualization was made using PDBsum [21], and amino acid sequence alignments are generated with SAS software [22] (Figure 1). The visualization of models was performed on UCF Chimera software [23] and PyMOL [24] loaded on a personal computer machine that has an Intel Quad core processor and four gigabytes of random accessed memory. Figures and electrostatic potential calculations were generated with PyMOL0.99rc6. The final model was submitted to the PMDB database [25] to obtain protein model databank (PMDB) identifier PM0076556.


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

Kashyap S - Biomed Res Int (2013)

Amino acid sequence alignment of the Cry1Ab15 with Cry1Aa (1ciy: A). The residues highlighted in red color represent helix; those in blue represent strand; in green represent turn; and those in black represent coil, and alignment is generated using SAS software.
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Related In: Results  -  Collection

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

fig1: Amino acid sequence alignment of the Cry1Ab15 with Cry1Aa (1ciy: A). The residues highlighted in red color represent helix; those in blue represent strand; in green represent turn; and those in black represent coil, and alignment is generated using SAS software.
Mentions: The possible outliers and side chains static constrain refinement of the developed model was performed on Summa Lab server [17] after the selected theoretical model were further subjected to a series of tests for evaluating its consistency and reliability. Backbone confirmation was evaluated by the inspection of the Psi/Phi Ramachandran plot from RAMPAGE web server [18]. The energy criterion was evaluated by ProSA web server [19], which compares the potential of mean forces derived from a large set of NMR and X-ray crystallographically derived protein structures of similar sizes. Potential deviations were calculated by SUPERPOSE web server [20] for root mean square deviations (RMSD) between target and template protein structure. The comparative analysis of generated model showed it to be superimposable. The secondary structure visualization was made using PDBsum [21], and amino acid sequence alignments are generated with SAS software [22] (Figure 1). The visualization of models was performed on UCF Chimera software [23] and PyMOL [24] loaded on a personal computer machine that has an Intel Quad core processor and four gigabytes of random accessed memory. Figures and electrostatic potential calculations were generated with PyMOL0.99rc6. The final model was submitted to the PMDB database [25] to obtain protein model databank (PMDB) identifier PM0076556.

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