Monster Tinker-Toys

Those wooden balls and rods from chem class won’t cut it in the science of DNA. It takes supercomputers to model the diabolical complexity of proteins.

Anyone who took high-school chemistry can remember the little tinker-toy models of molecules, with their rods representing chemical bonds and their colored balls representing atoms. The models were (and are) useful because they’re three-dimensional, serving as reminders of how organic structures fill space. And for small molecules – those under 100 atoms – models work quite well as visualization aids.
But they hardly work at all for the gigantic molecules called proteins, monster agglomerations of tens of thousands of atoms which control most of the processes of living things. Proteins perform intricately choreographed dances within the cell, and the shapes they assume in these dances are of critical importance,
helping to mold and assemble molecules, split them and put them together again in rapid-fire sequence.
Theoretically, if the composition of a protein is known, it should be possible to predict its shape and interaction from basic principles of physics and chemistry. But in practice, modeling a protein is diabolically difficult: it requires enormous computing power and depends on methods and insights only beginning to be developed. The study of the interaction of proteins both with one another and with the genetic materials DNA and RNA is called “proteinomics.”
This discipline is at the center of the next generation of biology and medical knowledge. Scientists like Ian Haworth of the USC School of Pharmacy play crucial roles in making proteins and other large molecules visible in computer simulations. Haworth’s work with molecular biologist Norman Arnheim is helping explain how and why DNA carrying certain kinds of messages is prone to a particular mutation – called “triplet repeats” – that causes genetic conditions like Huntington’s disease.
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