Our DNA lives inside the nucleus, separated by a membrane from the rest of the cell, the cytoplasm. Proteins that help read and regulate our genes have to get in through narrow channels called “nuclear pores,” and many of them cannot make the trip alone. This shuttling between the cytoplasm and the nucleus is essential for cellular function and is assisted by specialized escort proteins. TNPO3, short for “Transportin-3,” is one such escort, carrying its cargo, the serine/arginine-rich (SR) proteins, from the cytoplasm into the nucleus. Inside the nucleus, TNPO3 releases the SR proteins when it meets another partner called “Ran-GTP.” Ran-guanosine triphosphate (GTP) is escorted back to the cytoplasm by the same TNPO3. The cover of the November 3 issue of Biophysical Journal shows what this escort TNPO3 looks like along this pathway.
The colored surface is a free-energy landscape, a map of the different shapes that TNPO3 can take. Think of it as hilly terrain: each point is one possible shape of the protein, and its height shows how much energy that shape costs. Like a ball rolling downhill, the protein tends to settle into the shapes that it prefers, the low-energy valleys shown in yellow-green. High-energy regions, in purple, correspond to shapes that it rarely adopts. Circular insets show snapshots from our simulations, linked by dotted lines to the regions of the landscape to which they belong. In the insets, TNPO3 is salmon, SR cargo is light blue, and Ran-GTP is yellow. The orange arrows trace the route as its partners change, and the white wavy arrows between the blue and yellow ligands mark ligand exchange.
On its own, the receptor is an open, flexible solenoid. SR cargo holds it in a partly extended shape, and Ran-GTP pulls it into a compact form at the deepest valley. Between them lies an intermediate that both partners can fit, and it may help one hand off to the other. Our study quantifies these energetic differences, which a single static structure cannot capture. Understanding how receptors like TNPO3 change shape could help explain how nuclear import is regulated and how it goes wrong.
The structures were rendered in PyMOL from representative structures taken from the trajectories. The landscape was plotted in Matplotlib from our umbrella sampling data and features from the equilibrium simulations.
More work from our lab is available at http://www.csb.iitkgp.ac.in/.
— Sonali Chatterjee, Atanu Maity, and Ranjit Prasad Bahadur