Aggregation of the microtubule associated protein tau (MAPT) within neurons of the brain is the leading cause of tauopathies such as Alzheimer's disease. MAPT is a phospho-protein that is selectively phosphorylated by a number of kinases in vivo to perform its biological function. However it may become pathogenically hyperphosphorylated, causing aggregation into paired helical filaments (PHFs) and neurofibrillary tangles (NFTs). The phosphorylation induced conformational change on a peptide of MAPT (htau225-250 ) was investigated by performing molecular dynamics (MD) simulations with different phosphorylation patterns of the peptide (pThr231 and/or pSer235) in different simulation conditions to determine the effect of ionic strength and phosphate charge. All phosphorylation patterns were found to disrupt a nascent terminal β-sheet pattern ((226) VAVVR(230) and (244) QTAPVP(249) ), replacing it with a range of structures. The double pThr231/ pSer235 phosphorylation pattern at experimental ionic strength resulted in the best agreement with NMR structural characterisation, with the observation of a transient α-helix ((239) AKSRLQT(245) ). PPII helical conformations were only found sporadically throughout the simulations. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.