made with VMD
RNA molecules are continuously synthesized in living cells as carriers of biological information written in the sequence of basic RNA units, called nucleotides. To keep cells healthy, RNA molecules not longer needed or with errors have to be removed. A large barrel-like protein complex, the RNA exosome, is a molecular machine that degrades unneeded RNA molecules, pulling them inside its long internal channel and cutting them sequentially into single nucleotides. A new molecular dynamics study, employing NAMD, shows that a special active protein subunit of the exosome, called Rrp44, grips tightly the RNA molecule throughout its extended channel. Rrp44 grips RNA molecules with five or more nucleotides in length while their ending nucleotides get sequentially cut, whereas shorter RNAs are only weakly bound and unlikely to be cut. The simulations reveal how the exosome can act both as a molecular motor that pulls RNA, without energy input other than the one released in nucleotide cleavage, as well as an enzyme that cuts RNA. More information is available on our RNA exosome website.
A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee. Read more
Starting with a discovery at Harvard in 1971 of a hidden state, Klaus Schulten spent a large portion of his career demystifying the polyenes, versatile molecules central to vision and photosynthesis. By Lisa Pollack. Read more
- Elucidation of lipid binding sites on lung surfactant protein A using X-ray crystallography, mutagenesis and molecular dynamics simulations. Biochemistry, 2016. In Press.
- Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms. International Workshop on OpenPOWER for HPC (IWOPH'16), 2016. In Press.
- The water permeability and pore entrance structure of aquaporin-4 channels depend on lipid bilayer thickness. Biophysical Journal, 2016. In Press.