According to news out of TACC recently, Harvard Medical School researchers recently published results from computational studies they’ve been doing of a protein that is crucial to the hearing process
Cadherin-23 is also one of the proteins that malfunctions in individuals with hereditary deafness. Scientists believe one in 1,000 individuals in the U.S. are affected by this kind of disease, and 7.5 percent of hereditary deafness cases are caused by mutations in cadherin-23.
…The Harvard research team, including Sotomayor and Wilhelm Weihofen, and led by Rachelle Gaudet and David P. Corey, used the Ranger supercomputer at the Texas Advanced Computing Center (TACC) to simulate the 3D structure of cadherin-23 obtained from x-ray data. Then, they set the protein in motion, simulating the behavior of each atom as it reacted to forces that mimicked the effect of sound waves.
In simulations that involved up to 355,000 atoms, the team found that these particular proteins aren’t springy, but stiff. And they found a clue about what goes wrong in certain types of hearing loss
The simulations also showed that some deafness-related mutations to the protein do not alter the fold and strength of cadherin-23 directly. Rather, they change the way the protein binds calcium, which ends up weakening its structure.
Nifty application of HPC, and some very common codes (NAMD and VMD).