How proteins orchestrate the biology of the cell

Even the simplest of organisms must be attuned to conditions in an ever-changing environment to thrive. Intersecting networks of molecules keep cells on track, sensing and responding to both internal and external factors.

A deep analysis of a protein central to cellular function by scientists at UCSF’s Quantitative Biosciences Institute (QBI), in collaboration with colleagues at the University at Massachusetts, highlights just how elaborately interconnected these cellular networks can be.

A team led by QBI investigator and UCSF School of Pharmacy faculty member Tanja Kortemme, PhD, uncovered dozens of sites on that protein, a molecular switch called Gsp1, where small changes dramatically disrupt the protein’s activity inside cells. Many of those sites lie far away from the part of Gsp1 that carries out its work, exerting their effects through a phenomenon known as allostery. The research was published on February 17 in Cell Systems.

Allostery occurs when perturbation to a protein, such as a mutation or an interaction with a cellular regulator, changes the way a distant part of the protein functions. A single molecule can be subject to many layers of allosteric regulation, creating opportunities for cells to integrate information and coordinate their activities.

“Allostery is a powerful tool that organisms use to become better at what they need to do to survive in complex environments,” explained Christopher Mathy, PhD, a former graduate student in Kortemme’s lab.

Allosteric regulation is of particular interest to drug developers, because manipulating an allosteric site can be an effective way of controlling a protein’s activity to treat disease.

But the sites where this type of regulation occurs have been elusive. Biologists proposed the idea of allostery more than 60 years ago, but “you didn’t know where the allosteric sites were because you didn’t know where to look,” said Kortemme. With the tools of modern biology, Kortemme and Mathy didn’t have to know where to look: they looked everywhere.

The focus of their analysis, Gsp1, belongs to a family of proteins called GTPases, which regulate a variety of cellular processes and play important roles in human health. Gsp1 is best known for its role in transporting cellular materials, but also serves as a critical node in a vast cellular network, likely interacting directly or indirectly with hundreds of other molecules to modulate cellular activities.

Kortemme’s team had already found a few spots in the Gsp1 protein that are subject to allosteric regulation in 2021, and suspected there might be more. But they were surprised when a systematic analysis turned up twenty such sites, most of which had never been examined before.

To create their map, the research team generated thousands of mutated Gsp1 proteins, swapping out a single amino acid in each one. Then they watched what happened to yeast cells when the mutated proteins replaced intact Gsp1. Nearly a third of these proteins sickened the cells and dramatically slowed their growth. When the team mapped those influential mutations onto the structure of the protein, they were clustered in patches all over, and many of the mutations exerted allosteric effects.

With so many allosteric sites, there are lots of opportunities for other cellular players to modulate Gsp1’s activity.

“We think that this paradigm of being so sensitive to regulation is likely going to be the case for other biological switches as well,” Kortemme said. “Mapping additional proteins in this way could make it easier to predict the behavior of dynamic biological systems, as well as give drug developers new leads.”

Additional authors on the paper were Parul Mishra, PhD; Julia Flynn, PhD; Tina Perica, PhD; David Mavor, PhD; and Daniel Bolon, PhD.