Structural Ensembles of Intrinsically Disordered FG-Nucleoporins Depend on Force Field

Abstract

Intrinsically disordered proteins (IDPs) fulfill important biological roles including cell signaling, cell cycle regulation, and rubber-like elasticity. IDPs pose a tremendous challenge both to traditional structural determination methods as well as their theoretical description via molecular dynamics (MD) simulations: it is difficult to obtain sufficient data to determine the ensembles of structurally heterogeneous systems. Furthermore, because established MD force fields have been developed primarily to study folded proteins, it is not clear how accurately these force fields are able to describe disordered states.Here, we performed microsecond-timescale MD simulations using four recently-developed force fields: Amber ff99SB∗-ILDN, Amber ff03w, CHARMM22∗, and CHARMM36. We studied a set of FG-nucleoporin peptides with sequences derived from yeast Nsp1p. FG-nucleoporins are IDPs responsible for the high selectivity of the nuclear pore complex (NPC). They form a mesh-like structure in the central region of the NPC that controls the passage of macromolecules into and out of the nucleus. FG-nucleoporins are a prototypic example of the biological role of protein disorder, and beyond their particular function are key model systems for disordered proteins.Overall trends, such as temperature-induced unfolding and differences in compactness between cohesive and extended coil domains of Nsp1p, are described reasonably well by all force fields. However, we find marked differences in the extent of hydrogen bonding and secondary structure preferences. The average chain dimensions with the CHARMM force fields are more than 20% larger than the Amber force fields. Taken together, our results strongly suggest that disordered states are particularly sensitive to force field choice. As a next step, we will therefore compare to experimental measurements of both chain dimensions and secondary structure to determine which force field provides the most accurate description.