UC San Francisco (UCSF) scientists have broken a long-standing impasse in our understanding of the sense of smell and created the first molecular-level 3D image showing how an odor molecule activates a human olfactory receptor, a crucial step in decoding the sense of smell.
The results will appear online on March 15, 2023 in Nature, are poised to rekindle interest in the science of smell with implications for fragrances, food science and beyond. Olfactory receptors — proteins that bind odor molecules on the surface of olfactory cells — make up half of the largest and most diverse family of receptors in our body; A deeper understanding of them paves the way for new insights into a range of biological processes.
“This has been a big goal in this field for some time,” said Aashish Manglik, MD, PhD, associate professor of pharmaceutical chemistry and senior author of the study. The dream, he said, is to map the interactions of thousands of scent molecules with hundreds of olfactory receptors so a chemist could design a molecule and predict how it would smell.
“But we couldn’t create this map because without an image, we don’t know how odorant molecules react with their corresponding olfactory receptors,” Manglik said.
A picture paints the scent of cheese
Smell includes about 400 unique receptors. Each of the hundreds of thousands of scents we can recognize is made up of a mixture of different odor molecules. Any type of molecule can be recognized by a number of receptors, which requires the brain to solve a puzzle every time the nose catches a whiff of something new.
“It’s like hitting keys on a piano to create a chord,” said Hiroaki Matsunami, PhD, professor of molecular genetics and microbiology at Duke University and a close associate of Manglik. Matsunami’s work over the past two decades has focused on decoding the sense of smell. “Seeing how an olfactory receptor binds an odorant explains how this works at a fundamental level.”
To create this image, Manglik’s lab used a type of imaging called cryo-electron microscopy (cryo-EM), which allows researchers to see the atomic structure and study the molecular shapes of proteins. But before Manglik’s team could visualize the olfactory receptor that binds an odor molecule, a sufficient amount of the receptor protein first had to be purified.
Olfactory receptors are notoriously difficult, some say impossible, to make in the laboratory for such purposes.
Manglik and Matsunami’s teams looked for an olfactory receptor that was abundant in both the body and the nose, thinking it would be easier to create artificially, and one that could also detect water-soluble odorants. They settled on a receptor called OR51E2, which is known to respond to propionate – a molecule that contributes to the pungent smell of Swiss cheese.
But even OR51E2 proved difficult to produce in the lab. Typical cryo-EM experiments require a milligram of protein to generate atomic-level images, but co-first author Christian Billesbøelle, PhD, a senior scientist in the Manglik lab, developed approaches to use just 1/100 milligram of OR51E2 in the snapshot of the receptor and odor within reach.
“We achieved this by overcoming several technical impasses that have choked the field for a long time,” said Billesbøelle. “In this way, we were able to get the first glimpse of an odorant connecting to a human olfactory receptor at the moment an odor is recognized.”
This molecular snapshot showed that propionate adheres tightly to OR51E2 thanks to a very specific fit between odorant and receptor. The finding is consistent with one of the roles of the olfactory system as a guardian of danger.
While propionate contributes to the rich, nutty flavor of Swiss cheese, its smell alone is far less appetizing.
“This receptor is laser-focused on trying to detect propionate and may have evolved to detect when food is spoiled,” Manglik said. Instead, receptors for pleasant smells like menthol or caraway might interact more loosely with odorants, he speculated.
Just a touch
In addition to using a large number of receptors simultaneously, another interesting property of the sense of smell is our ability to detect tiny amounts of smells that come and go. To study how propionate activates this receptor, the collaboration hired City of Hope quantitative biologist Nagarajan Vaidehi, PhD, to use physical methods to simulate and film how OR51E2 is activated by propionate.
“We ran computer simulations to understand how propionate causes a shape change in the receptor at the atomic level,” Vaidehi said. “These shape changes play a critical role in how the olfactory receptor initiates the cell’s signaling process that leads to our sense of smell.”
The team is now developing more efficient techniques to study other odorant-receptor pairs and to understand the non-olfactory biology associated with the receptors that have been linked to prostate cancer and serotonin release in the gut.
Manglik envisions a future where novel smells can be designed based on understanding how a chemical’s shape leads to a perceptual experience, much like pharmaceutical chemists today design drugs based on the atomic shapes of disease-causing proteins.
“We’ve dreamed of tackling this problem for years,” he said. “We now have our first approach, the first look at how the olfactory molecules bind to our olfactory receptors. For us, this is just the beginning.”
Financing: This work was supported by NIH grants R01DC020353, K99DC018333 and the UCSF Pioneering Biomedical Research Program funded in part by the Sandler Foundation. Cryo-EM equipment at UCSF is supported in part by NIH grants S10OD020054 and S10OD021741. Please refer to the paper for further funding.