Paper Citing NAMD - Abstract
Miao, Lingling; Schulten, Klaus
Transport-Related Structures and Processes of the Nuclear Pore Complex Studied through Molecular Dynamics
STRUCTURE, 17:449-459, MAR 11 2009
Nuclear pore complexes (NPCs) are selectively gated pathways between nucleoplasm and cytoplasm. Whereas small molecules can diffuse freely through NPCs, large molecules (>40 kD) can pass only when bound to transport receptors. The NPC central channel is filled with disordered proteins, rich in phenylalanine-glycine (FG) repeats, referred to as FG-nups. Our simulations, carried out at coarse-grained and all-atom levels, show that arrays of FG-nups tethered to a planar surface, at an FG-repeat density found in the NPC, form dynamic brush-like structures of multiprotein bundles, whereas individual FG-nups form dynamic globular structures. More than half of the FG-repeats are found on the surface of the bundles, offering a favorable environment for transport receptors. Binding to FG-repeats and a sliding motion of NTF2 induced by binding and unbinding to phenylalanines were observed when adding this transport receptor into one of the brush-like structures.
