From Protein Structure to Function with Bioinformatics.pdf

9 Protein Dynamics: From Structure to Function 221open to the closed state. CAS/Cse1p is a nuclear transport receptor consisting of960 amino acids that binds importin-α and RanGTP in the nucleus. The heterotrimericcomplex (Fig. 9.1) can cross nuclear pores and dissociates by catalyzedGTP hydrolysis in the cytoplasm and, thus, represents an important part of thenucleocytoplasmic transport cycle in cells.For the function of the importin-α/CAS system it is essential that, after dissociationof the complex in the cytoplasm, CAS/Cse1p undergoes a large conformationalchange that prevents reassociation of the complex. X-ray structures ofCse1p show that the cargo bound conformation adopts a superhelical structurewith curls around the bound RanGTP (Fig. 9.2 left), whereas the cytoplasmicform exhibits a closed ring conformation that leads to occlusion of the RanGTPbinding site (Fig. 9.2 right). In order to understand the mechanism of this conformationalswitch, Zachariae and Grubmüller carried out MD simulations of Cse1pstarting from the cargo bound conformation. They found that, mainly driven byelectrostatic interactions, the structure of Cse1p spontaneously collapses andadopts a conformation close to the experimentally determined cytoplasmic formwithin a relatively short timescale of 10 ns. Simulations of mutants with differentelectrostatic surface potentials did not reveal a significant conformational changebut remained in an open conformation which is in good agreement with experimentalfindings (Cook et al. 2005). This example shows that functionally relevantconformational changes that occur on short time scales can be studied by MDsimulations. However, in this particular case the simulation has – due to the removalof importin-α and RanGTP – not been started from an equilibrium conformationFig. 9.1 Heterotrimeric complex of Cse1p (blue), RanGTP (yellow) and importin-α (red). Cse1padopts a superhelical structure and binds RanGTP and importin−α. The complex can cross nuclearpores and dissociates by catalyzed GTP hydrolysis in the cytoplasm