Improvement of turn structure prediction by molecular dynamics: a case study of {alpha}1-purothionin |
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Authors: | Rao, Usha Teeter, Martha M. |
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Affiliation: | Department of Chemistry, Boston College Chestnut Hill, MA 02167, USA |
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Abstract: | Because of the problems in predicting a correct conformationfor loop regions in homology-based prediction, disagreementsare often found between the predicted models and the refinedX-ray structures of the same protein in loop regions. Such asituation has been encountered for 1-purothionin (1-PT). Hence,attempts have been made to improve the predicted model of 1PTby limited molecular dynamics using both AMBER and XPLOR. Withmolecular dynamics, the previously predicted incorrect turnregion reverts to the correct conformation as seen in the X-rayrefined structure. In contrast to the model which is not subjectedto molecular dynamics, the improved model refines with the X-raydata of 1PT in fewer cycles, without any manual rebuilding andwith comparable or better refinement statistics. Also, the improvedmodel serves as a better starting model in the determinationof the structure with the molecular replacement methods. |
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Keywords: | /math/alpha.gif" ALT=" {alpha}" BORDER=" 0" >1-PT/ energy minimization/ molecular dynamics/ simulated anncaling/ turn prediction |
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