Simulation of the interaction between ScyTx and small conductance calcium-activated potassium channel by docking and MM-PBSA.

ABSTRACT: Computational methods are employed to simulate interaction of scorpion toxin ScyTx in complex with the small conductance calcium-activated potassium channel rsk2. All of available 25 structures of ScyTx in the Protein Data Bank determined by NMR were considered for improving performance of rigid protein docking of ZDOCK. Four main binding modes were found among a large number of predicted complexes by using clustering analysis, screening with expert knowledge, energy minimization, and molecular dynamics simulations. The quality and validity of the resulting complexes were further evaluated by molecular dynamics simulations with the generalized Born solvation model and by calculation of relative binding free energies with the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) in t

SUBMITTER: Wu Y 

PROVIDER: S-EPMC1304333 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature