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made with VMD
Nanoengineers building nanodevices achieve technological solutions at scales of 100 nanometers or 0.0001 mm. Nanoengineering is a brand new human technology, just a few decades old. In living cells, nanoengineering solutions are actually a few billion years old and therefore much more intricate. An impressive example is the nuclear pore, hundreds to thousands of which dot the nuclear membrane that separates in eukaryotic cells the genome and its molecular control factors from the cytoplasm of the cell. Only since very recently could cell biologists begin to resolve the molecular architecture of the nuclear pore. Given the pore's many-fold functions, like letting small molecules pass easily, but larger ones only as cargoes of special proteins, the transport factors, or adapting the pore size when large cargoes need to pass, the architecture of the nuclear pore is complex, involving an assembly of hundreds of proteins. The interior of the pore is filled with 600 amino acid-long "finger" proteins tethered at the periphery. The finger proteins are largely disordered such that experimental methods lack resolving power and computational modeling is needed to figure out their dynamic arrangement and traffic control function, but such modeling was largely unfeasible; only a small fraction of the nuclear pore volume could be covered computationally. The advent of petascale computing increased the size-scale of biomolecular simulations hundred-fold and a recent report employing the programs NAMD and VMD took advantage of the new generation of computers, simulating the dynamic, disordered arrangement of nuclear pore proteins. The simulations, still at an early stage, suggest a detailed, atomic level picture of the nuclear pore interior together with an explanation of molecular traffic control. More on our nuclear pore website.