Raising the Bar for Biomolecular Modeling

Researchers in the University of Calgary found that amino acid residues form a type of barrier to help in the method of electron transfer between proteins.

“This raises the bar for biomolecular modeling,” says Dennis Salahub, U of C co author of a paper published today in the prestigious journal Proceedings of the National Academy of Sciences (PNAS). “At a fundamental level, it’s by far the most detailed insight that’s been obtained for the dynamic function of water in this type of electron transfer, or for that matter any biochemical reaction.”

Electron transfer between proteins is the cornerstone of biological energy transfer. Every life form uses this procedure to convert sun or food into chemical energy.

The interdisciplinary team of researchers found the electron goes over a bridge made of a water molecule, while deposits on among the proteins form a kind of ‘molecular breakwater’ while the electron travels around the bridge, to keep other water molecules away.

“You do not want too many (water molecules around the bridge) because it gets too crowded and they are all bumping into each other and you can’t get one to fit at just the correct location and the right angle (for the bridge) for any duration of time,” says PhD scholar and co author Nathan Babcock. “It is like being on a busy subway at which you can not get comfy.”

The speed of electron transfer is markedly reduced as well as in manufactured mutations with a breakwater that is flawed, the water bridge is disrupted, he says.

The research team examined a 40 nanosecond amount of electronic coupling of the proteins methylamine dehydrogenase and amicyanin.

“This is fundamental research however, you can imagine how studies such as this could be applied to various genetically modified organisms, and in case you are able to gain control over some, you may put it to use to either speed up or slow down a special reaction,” says Salahub.

He says the work was made possible with the collaboration of two of the U of C’s interdisciplinary research institutes; the Institute for Biocomplexity and Informatics (IBI) and the Institute for Quantum Information Science (IQIS).