Novel Technique Reveals Potential Pathways that Control Protein Function

A new method developed by researchers at the Centre for Genomic Regulation (CRG) in Barcelona has revealed the number of potential therapeutic targets on the surfaces of human proteins is much greater than previously thought.

The findings of a new study in the journal Nature, in a paper titled, “Mapping the energetic and allosteric landscapes of protein-binding domains.”

“Allosteric communication between distant sites in proteins is central to biological regulation but still poorly characterized, limiting understanding, engineering, and drug development,” the researchers wrote. “An important reason for this is the lack of methods to comprehensively quantify allostery in diverse proteins. Here we address this shortcoming and present a method that uses deep mutational scanning to globally map allostery.”

The method, in which tens of thousands of experiments are performed at the same time, has been used to chart the first ever map of these elusive targets, also known as allosteric sites, in two of the most common human proteins, revealing they are abundant and identifiable.

“Not only are these potential therapeutic sites abundant, there is evidence they can be manipulated in many different ways. Rather than simply switching them on or off, we could modulate their activity like a thermostat. From an engineering perspective, that’s striking gold because it gives us plenty of space to design ‘smart drugs’ that target the bad and spare the good,” explained André Faure, PhD, postdoctoral researcher at the CRG and co-first author of the paper.

The technique is called double deep PCA (ddPCA), which the researchers describe as a “brute force experiment.” ICREA research professor Ben Lehner, PhD, coordinator of the systems biology program at the CRG and author of the study explained: “We purposefully break things in thousands of different ways to build a complete picture of how something works. It’s like suspecting a faulty spark plug, but instead of only checking that, the mechanic dismantles the entire car and checks it piece by piece. By testing ten thousand things in one go we identify all the pieces that really matter.”

The method works by changing the amino acids that make up a protein, resulting in thousands of different versions of the protein with just one or two differences in the sequence. The effects of the mutations are then tested all at the same time in living cells in the laboratory.

“Each cell is a tiny factory making a different version of the protein. In a single test tube, we have millions of different factories and so we can very rapidly test how well all the different versions of a protein work,” added Lehner.

“While some tools can predict a protein’s structure by reading its sequence, our method goes one step further by telling us how a protein works. This is part of a bigger vision to make biology as engineerable as airplanes, bridges, or computers. We have faced the same challenges for over 70 years, but it turns out they are more tractable than we previously thought. If we succeed it will open a new field with unprecedented possibilities,” concluded Lehner.