MOLECULAR DYNAMICS SIMULATIONS OF NATIVELY UNFOLDED PROTEINS

这个子项目是众多研究子项目之一

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The FG-nucleoporins (FG-nups) are natively-unfolded domains with phenylalanine-glycine motifs that play key roles in nucleocytoplasmic transport. We are using classical molecular dynamics simulations using Amber to analyze the dynamical properties of a number of FG-nups and FG-nup mutants. Specifically we are running multiple replicate simulations of the FG-Nups starting from an extended conformation and then analyzing the trajectories using both established metrics for characterizing polymers and newly developed metrics for quantifying the rates of structural change and internal structural correlation. The goal of this development application is to continue the preliminary simulations begun with an AAP allocation, with a specific goal of determining the behavior of these nucleoporins for multiple 10's of nanoseconds using both implicit and explicit solvent models.