The Mode Less Traveled By

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Science  18 Sep 2009:
Vol. 325, Issue 5947, pp. 1475
DOI: 10.1126/science.325_1475a
CREDIT: LEZON ET AL., PLOS COMP. BIOL. 5, E1000496 (2009).

One popular theme pervading recent chatter about enzyme catalysis is the linking of intrinsic macro-molecular dynamics to function. The abundance of high-resolution protein structures has facilitated these studies, and Lezon et al. show just how much can be done even when only moderate-resolution structure models are available.

The nuclear pore complex (NPC) spans the nuclear envelope and supports passive transport between the cytoplasm and the inside of the nucleus. Modeling the NPC as a simple torus (86 nm in diameter, with a central hole 34 nm in diameter) revealed two low-frequency motions; these have the lowest energy and hence are the most populated. The first involved bending above and below the toroidal plane, whereas the second was an in-plane stretching and contraction of the torus into an ellipse. Refining the model by incorporating specifics, such as the eight spokes pointing inward from the toroidal rim and the greater mass on the cytoplasmic face of the NPC, did not change which two modes dominated. Some parts of the torus exhibited greater mobility (red) and some less (blue), and the eight-fold symmetry enhanced cooperative motions across the NPC. Finally, a comparison of these findings to the snapshots of Dictyostelium NPCs taken by cryoelectron tomography suggests that the bending mode underlies the reorganization of spokes observed during nuclear transport.

PLoS Comp. Biol. 5, e1000496 (2009).

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