Computational Studies of Intrinsically Disordered Proteins

Frequently elusive to experimental characterizations, intrinsically disordered proteins (IDPs) can be probed using molecular dynamics to provide detailed insight into their complex structure, dynamics, and function. However, previous computational studies were often found to disagree with experiment due to either force field biases or insufficient sampling. In this study, nine unstructured short peptides and the HIV-1 Rev protein were simulated and extended to microseconds to assess these limitations in IDP simulations. In short peptide simulations, a tested IDP-specific force field ff14IDPSFF outperforms its generic counterpart ff14SB as agreement of simulated NMR observables with experiment improves, though its advantages are not clear-cut in apo Rev simulations. It is worth noting that sampling is probably still not sufficient in the ff14SB simulations of apo Rev even if 10 ms have been collected. This indicates that enhanced sampling techniques would greatly benefit IDP simulations. Finally, detailed structural analyses of apo Rev conformations demonstrate different secondary structural preferences between ff14SB (helical) and ff14IDPSFF (random coil). A natural next step is to ask a more quantitative question: whether ff14SB is too ordered or ff14IDPSFF is too disordered in simulations of more complex IDPs such as Rev. This requires further quantitative analyses both experimentally and computationally.