Improvement of turn structure prediction by molecular dynamics: a case study of alpha 1-purothionin

Because of the problems in predicting a correct conformation for loop regions in homology-based prediction, disagreements are often found between the predicted models and the refined X-ray structures of the same protein in loop regions. Such a situation has been encountered for alpha 1-purothionin (alpha 1-PT). Hence, attempts have been made to improve the predicted model of alpha 1-PT by limited molecular dynamics using both AMBER and XPLOR. With molecular dynamics, the previously predicted incorrect turn region reverts to the correct conformation as seen in the X-ray refined structure. In contrast to the model which is not subjected to molecular dynamics, the improved model refines with the X-ray data of alpha 1-PT in fewer cycles, without any manual rebuilding and with comparable or better refinement statistics. Also, the improved model serves as a better starting model in the determination of the structure with the molecular replacement methods.