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We report the computational structural simulation of the Cry1Ab19 toxin molecule from B. thuringiensis BtX-2 based on the structure of Cry1Aa1 deduced by x-ray diffraction. Validation results showed that 93.5% of modeled residues are folded in a favorable orientation with a total energy Z-score of -8.32, and the constructed model has an RMSD of only 1.13. The major differences in the presented model are longer loop lengths and shortened sheet components. The overall result supports the hierarchical three-domain structural hypothesis of Cry toxins and will help in better understanding the structural variation within the Cry toxin family along with facilitating the design of domain-swapping experiments aimed at improving the toxicity of native toxins.

As part of an effort to obtain a fungal 1-aminocyclopropane-1-carboxylate deaminase encoding gene from Phytophthora sojae expressed sequence Tag database, we identify and characterize the ACCD from P. sojae using bioinformatics data mining tools and techniques. Computed structural model of P. sojae ACCD was found to consist of mixed α/β motifs and probable loops. The predicted model resembles the structure of Pseudomonas ACCD (RMSD-0.44 Å). The main differences observed between them are the presence of partial length of domain one, and longer helix α4. Ramachandran plot analysis revealed that portion of all residues falling into the most favorable regions was 95.0%. The substrate - and geometrical- docking of developed structure postulated functional capability of ACCD to carry out ACC cleavage reaction. The catalytic site in homo-tetrameric structure open to opposite directions separated by ∼37.97 Å distance arranged around central axis. This study provides a comprehensive identification and characterization of the ACCD in P. sojae and it may be helpful in the transcriptional and expression based study of P. sojae pathogenesis.

The theoretical homology based structural model of Cry1Ab15δ-endotoxin produced byBacillus thuringiensisBtB-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 ofβ0 andα3, and the absence ofα7b,β1a,α10a,α10b,β12, andα11a whileα9 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 energyZ-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.