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

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.

Figure 1

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.

Figure 2

The two-dimensional structure annotation showing sequential arrangements of helices and sheets in Cry1Ab15 toxin molecule using the PDB Sum (http://www.ebi.ac.uk/pdbsum/). The structure is as the spiral shape are helix labeled as H1 and H2; and the arrows as strands are labeled by their sheets A and B while motifs β are beta turn and γ are gamma turn while the bend tube shape is a beta hairpin.

Figure 3

The comparative three-dimensional, three-domain structure of the Cry1Ab15 ((b), (d), (f)) and Cry1Aa ((a), (c), (e)) molecules.

Figure 4

The comparative figures separately showing details among three structural domains of Cry1Ab15 and Cry1Aa molecules.

Figure 5

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/).

Figure 6

Evaluation of Cry1Ab15 using ProSA server (https://prosa.services.came.sbg.ac.at/). The plot indicating nearness of constructed structure with the native structures. The Z-score of evaluated model was −6.56, shown as a large black dot.

Figure 7

Ramachandran plot analysis of the Cry1Ab15 toxin oligomer showing placement of residues in deduced model. General plot statistics are: 94.0% (568/604) of all residues were in favored (98%) regions residues in additional allowed regions 99.0% (598/604) of all residues were in allowed (>99.8%) regions. The figure was generated using RAMPAGE web server (http://mordred.bioc.cam.ac.uk/).