Computational Modeling Deduced Three Dimensional Structure of Cry1Ab16 Toxin from Bacillus thuringiensis AC11

Abstract

The first theoretical structural model of newly reported Cry1Ab16 δ-endotoxin produced by Bacillus thuringiensis AC11 was predicted using homology modeling technique. Cry1Ab16 resembles the Cry1Aa protein structure by sharing a common three domains structure responsible in pore forming and specificity determination along with few structural deviations. The main differences between the two is in the length of loops, absence of α7b, α9a, α10b, α11a and presence of additional β12b, α13 components while α10a is spatially located at downstream position in Cry1Ab16. A better understanding of the 3D structure shall be helpful in the design of domain swapping and mutagenesis experiments aimed at improving toxicity.

Keywords: Cry toxins; Insecticidal crystal protein; Receptor insertion; Third-party annotation; α-Helical bundle.

Fig. 1

Amino acid sequence alignment of the Cry1Ab16 including those of genuine δ endotoxins. The sequence displayed are from Cry1Aa (1ciy:A); Cry3Aa (1dlc:A); Cry8ea1 (2qkg:A); Cry3bb1 (1ji6:A). All sequences were obtained from PDB database. The sequential number above represents the number of amino acids. The residues highlighted in red color represent helix; those in blue represent strand; in green represent turn; and those in black represent coil and are generated using SAS software (http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/sas)

Fig. 2

The two-dimensional structure annotation showing sequential arrangements of helices and sheets in Cry1Ab16 toxin molecule using the PDB sum (www.ebi.ac.uk/pdbsum/)

Fig. 3

Evaluation of Cry1Ab16 model a on ProSA server. The plot indicating nearness of developed model with the native structures. The Z-score of evaluated model is shown as large black dot. b Ramachandren plot analysis showing placement of its residues in deduced model. General plot statistics are: 551 (91.2%) residues in favored regions; 43 (7.2%) of residues were in allowed regions; the outlier residues totals to 10 (1.7%) only. The plot was generated using RAMPAGE web server (http://mordred.bioc.cam.ac.uk/)

Fig. 4

Complete protomer structure of the Cry1Ab16 toxin. a Superposition C^α backbone of Cry1Aa1 (blue) and Cry1Ab16 (pink) molecules. Images are generated using UCF chimera (http://www.cgl.ucsf.edu/chimera). b Ribbon diagram showing three-dimensional three domain oligomer structure. c Surface electrostatic potential representation of Cry1Ab16 toxin