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

Biophysical Journal
Yingliang WuWen-Xin Li

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 the AMBER 7 suit of programs. The complex formed by the 22nd structure of the ScyTx and rsk2 channel was identified as the most favorable complex by using a combination of computational methods, which contain further introduction of flexibility without restraining residue side chain. From the resulted spatial structure of the ScyTx and rsk2 channel, ScyTx associates the mouth of the rsk2 channel with alpha-helix rather than beta-sheet. Structur...Continue Reading

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Citations

Dec 5, 2006·The Journal of Biological Chemistry·Andreas NoltingMartin Stocker
Aug 7, 2007·Journal of Biomolecular Structure & Dynamics·Wu YingliangLi Wenxin
Jan 14, 2009·Journal of Molecular Recognition : JMR·Monia TarantaSalvatore Cannistraro
Nov 1, 2011·Journal of Molecular Recognition : JMR·Simona SantiniSalvatore Cannistraro
Jan 3, 2006·Biophysical Journal·Qing Zhang, Tamar Schlick
Apr 8, 2014·Biochemical and Biophysical Research Communications·Zongyun ChenYingliang Wu
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·Benoît Roux
May 24, 2016·Journal of Biomolecular Structure & Dynamics·Masomeh MehrabiMohsen Shahlaei
Sep 19, 2016·Journal of Neuroimmune Pharmacology : the Official Journal of the Society on NeuroImmune Pharmacology·O V NekrasovaA V Feofanov
Aug 19, 2007·Journal of Molecular Recognition : JMR·Valentina De GrandisSalvatore Cannistraro
Jun 16, 2007·The Journal of Biological Chemistry·Alexandre FontayneHans Deckmyn
Mar 8, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Evelyne Deplazes
Apr 22, 2010·Journal of Proteome Research·Song HanWenxin Li

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