Evaluation of the Bacillus thuringiensis Cry4Ba Structure by Simulated Annealing

Abstract

ABSTRACT

The evaluation of the Cry4Ba toxin in aqueous solution was investigated using the molecular dynamics simulation method (MD). The purpose of this research is compare the quality of Cry4Ba structures obtained from homology modelling, sequences of in vacuo simulated annealing and snap-shot of MD in water.The original atomic coordinates were subsequently treated by 20 cycles of in vacuo simulated annealing simulations based on GROMOS96 force field. Each cycle consists of (i) heating phase from 0 to 500 K for 10 ps, (ii) constant-temperature dynamics at 500 K for 10 ps, (iii) cooling phase from 500 to 0 K for 10 ps, and (iv) steepest descent energy minimization. The snap-shot of MD sample from 20 configurations which minimized each structure by a steepest descent algorithm. Each resulting structure was evaluated by WHATCHECKⁱ and PROCHECKⁱⁱ programs.