Computer models explain the ‘why’ of the molecular machinery of sight

Feb 4, 2016

Every significant breakthrough – from a baby’s curiosity to a scientist etching his or her name in the history books – begins with one question, one syllable, one word: Why?

Massimo Olivucci
Massimo Olivucci, Ph.D., director of the Laboratory of Computational Photochemistry and Photobiology in the Center for Photochemical Sciences at Bowling Green State University

One of the more concentrated “whys” biologists often seek to answer relates to why our eyes select specific molecules in their formation as opposed to other more stable ones. According to recent research by Massimo Olivucci, Ph.D. – director of the Laboratory of Computational Photochemistry and Photobiology in the Center for Photochemical Sciences at Bowling Green State University – it ties back to natural selection.

The key to understanding this lies in rhodopsins, or retinal proteins, which are a family of membrane proteins present in all life domains; and chromophores, the parts of a molecule responsible for its color. Microbial and animal rhodopsins bind a retinal chromophore that performs functions such as light sensing, light-powered ion-pumping or light-gated ion-channeling.

There are literally hundreds of rhodopsins in the animal and microbial worlds, and they share many structural features, according to Olivucci.

Where the need for understanding arises is in one key difference between the animal and microbial worlds, and Olivucci’s team is working to unravel this “why.”

Olivucci’s research provides a molecular understanding of how animal rhodopsins use the 11-cis chromophore to achieve better light sensitivity than that of microbial rhodopsins, which uses a more stable all-trans chromophore.


“Maybe nature has some reason to select this certain chromophore?” said Hoi Ling Luk, who performed the research for the paper “Molecular bases for the selection of Chromophore of Animal Rhodopsins,” under the direction of Olivucci. “What we are doing is trying to use a computing model to understand the photochemistry of that.”

By using powerful Ohio Supercomputer Center systems to run sophisticated computations that model the light-responsiveness of chromophores, Olivucci’s research group has shown it is possible to identify, “a distinctive electronic character of the 11-cis chromophore that could have become an effective target for natural selection.”

Hoi Ling Luk
Hoi Ling Luk

According to Luk, this fundamental understanding of how these biological photoreceptors work has great potential. These photo-switchable proteins can have a variety of applications in biological research, including optogenetics. The end result of Olivucci’s research may even be to create evolutionary advantages for improving light sensitivity.

“These are very difficult calculations,” Luk said. “We have a belief that the faster you go, the faster you will get to the photoproduct. We want to run hundreds and hundreds of these because if you run that amount of trajectories you’ll really see what happens.

“That’s why OSC is very important to us, because otherwise we can’t function.”

Olivucci’s group is supported by the National Science Foundation and, as an international funding agency, the Human Frontier Science Program.