A jumbo problem: mapping the structure and functions of the nuclear pore complex

Abstract

Macromolecular assemblies can be intrinsically refractive to classical structural analysis, due to their size, complexity, plasticity and dynamic nature. One such assembly is the nuclear pore complex (NPC). The NPC is formed from ∼450 copies of 30 different proteins, called nucleoporins, and is the sole mediator of exchange between the nucleus and the cytoplasm in eukaryotic cells. Despite significant progress, it has become increasingly clear that new approaches, integrating different sources of structural and functional data, will be needed to understand the functional biology of the NPC. Here, we discuss the latest approaches trying to address this challenge.

Figure 1

The NPC, and the traffic through it, has been visualized by many different techniques, representatives of which are shown here: fluorescence microscopy including single molecule techniques, atomic force microscopy, scanning electron microscopy, transmission electron microscopy, molecular modeling, and crystallography and NMR.

Figure 2

Determining the architecture of the NPC by integrating various types of data. Data from various experiments are translated into ‘spatial restraints’, encoding the information each experiment reveals about the relative position of each component in the NPC. An ensemble of structural solutions that satisfy the data is then obtained by minimizing the violations of the spatial restraints, starting from many different random configurations. This ensemble is analyzed in terms of protein positions, contacts, and configuration [32,36].