Intrinsically disordered proteins and regions play important roles in the regulation of protein dynamics and protein-protein interactions. In this thesis two IDPs, both of which have been implicated in neurodegenerative diseases, are explored using fully atomistic molecular dynamics simulations. The first is the N-terminal fragment of the huntingtin protein, which controls the protein’s localisation and function in vivo. The second is the disordered pro domain of the proNGF dimer, which antagonises NGF in the brain. Huntingtin is the causative agent of Huntington’s disease, which is a progres- sive neurodegenerative disease, characterised by CAG repeats in the first exon of Huntingtin, which are translated into a polyglutamine (polyQ) tract, responsible for protein aggregation and subsequent neuron death. Huntingtins poly-Q tract is preceded by a 17-residue regulatory fragment (Htt1-17), which is intrinsically dis- ordered in aqueous environments but forms an amphipathic helix in the presence of TFE or DPC micelles. Htt1-17 regulates localisation and function of the full-length protein and is subject to multiple post-translational modifications in the cell. I used molecular dynamics simulations with a novel enhanced sampling method, to study the effect of phosphorylation, phosphomimetic substitutions and acetylation on the secondary structure of Htt1-19. ProNGF is the precursor to the neurotrophin NGF, and is involved in apoptotic signalling in the brain. A disturbed proNGF:NGF was shown to lead to Alzheimer’s disease. A high-resolution structure of the pro domain has been missing so far. I modelled the proNGF dimer by combining experimental data with long MD simu- lations.