Conformational Sampling of FG-Nucleoporins using Extended Molecular Dynamics Simulations

Abstract

FG nucleoporins (FG-nups) are intrinsically-disordered proteins that fill the central channel of the Nuclear Pore Complex (NPC) and are believed to mediate the selective gating of cargo molecules through the NPC. Previous molecular dynamics (MD) simulations of FG-nup fragments approximately 100 amino acids (AAs) in length have shown that different FG-nups adopt different average shapes, ranging from compact premolten globules to extended coils, which are the basis for a new model for NPC gating. For MD studies of disordered proteins there are still open questions about the appropriate simulation times and protocols needed to sufficiently search conformation space, and how different force fields and ionic conditions affect the resulting structural ensembles. For this reason we have performed MD simulations on smaller, 25 and 50 AA fragments of key FG-nups for microsecond timescales, using both implicit and explicit solvent, as well as different ionic conditions. Our goal is to see if their dynamical properties exhibit previously-documented behavior for the larger fragments and to evaluate the thoroughness of conformational sampling for the FG-nups. We will represent the results of multiple replicate simulations on different FG- nups, analyzed using a variety of methods that range from conventional measures of protein size and structure, to new tools based on contact maps, clustering, and dimensionality- reduction techniques.