Distribution of rescuing mutations diagram from figure 2B
Researchers' Findings Indicate Plasticity in Allosteric Signaling

Biochemistry Assistant Professor Vatsan Raman and IPiB graduate student Megan Leander have published findings in the Proceedings of the National Academy of Sciences (PNAS) on how proteins work. The findings are key to allostery, a property of proteins which is central to biology. Allosteric proteins play critical roles in cellular function, including signal transduction, metabolism, and gene regulation. Understanding how allostery works is a fundamental question in protein biophysics, and has high relevance to disease.

For instance, cancer genomes contain mutations in allosteric proteins that disrupt communication. And together, G-protein coupled receptors, nuclear receptors, ion channels and kinases – all allosteric proteins – account for 44% of all human protein drug targets.

Photo of Prof Vatsan Raman
Prof. Vatsan Raman

But what is allostery?

“Perhaps a good analogy for allostery that most people can relate to is a Rube Goldberg machine,” said Raman. “Most of us have seen a Rube Goldberg machine in real life or on TV. If you move a lever at one end, the lever rolls a ball, the ball falls into a balance, the balance tilts over, so on and so forth until some action happens at the other end far from the origin.”

Photo of Megan Leander
Megan Leander

Imagine instead of a Rube Goldberg machine, a protein. When a protein is perturbed at one end, say by binding to another molecule, that perturbation is communicated through a network of amino acids within the protein resulting in a response at the other end. Depending on the protein, the response could be binding to DNA, binding to a different protein, catalysis and so on. The long-distance coupling between perturbation at one end and response at another end is allostery.

In the PNAS publication, Raman, Leander and their collaborators at Boston University show two things: first, that allostery is “plastic.” This means that when allosteric communication is broken by a mutation, function can be restored easily by a compensatory mutation far away from the mutation that breaks function.

“It turns out there are many, many compensatory mutations for every breaking mutation,” said Raman. Our results suggest that evolution has figured out multiple solutions to allostery, which is in contrast to the traditional notion that allostery is a brittle and finely-tuned network.”

They also show that residues critical for these allosteric communications are poorly conserved, which also seems counterintuitive given that allostery is essential for function. Instead, residues required for structural integrity are highly conserved, suggesting evolutionary pressure to preserve fold over function.

“Once nature gets the fold right,” said Raman, “there are many ways to create and preserve function.”

These unexpected findings offer a better biophysical understanding of allostery and has important implications for how natural proteins evolve.

“Our longer term goal is two-fold: First, to more broadly understand how mutations affect disease-relevant proteins. Can we predict what a mutation does without having to do laborious experiments? We think we can by learning from large datasets. Second, we want to identify allosteric sites for drug targeting,” said Raman.

“In fact,” said Raman, “a major focus in pharmaceutical sciences is targeting drugs to the allosteric site instead of the active site to enhance target selectivity and reduce side effects. Our approach in the PNAS paper shows that allosteric sites in a protein can be systematically identified.”