In fact, just over a decade ago scientists had discovered that similar droplets are naturally present inside cells. These fascinating constructs are liquid-like assemblies of proteins alone, or proteins with RNA or DNA; they form something like oil drops in water, through phase separation between two liquids. Inside the droplets, proteins may reach concentrations that are hundreds of times higher than they are outside. In 2018, Science magazine nominated droplets for the Breakthrough of the Year, referring to the study of such droplets as “one of the hottest topics in cell biology.” Yet much is still unknown about the mechanisms by which these droplets form and what purposes they serve in cells – for example, might they be used for storage or for performing regulatory functions.
That’s where the two biological mysteries converge. Tawfik, of Weizmann’s Biomolecular Sciences Department, undertook the study of peptide-RNA droplets to see whether they might have played a role in the origin of proteins, but it was clear that this research could also shed new light on the roles that similar droplets play today in the human body.
The dimer hunt
Tawfik and colleagues hypothesized that in the prelife world, the peptide-RNA droplets formed in the primordial soup may have served as protocells, forerunners of modern living cells. The droplets would have created a kind of compartment, bringing peptides close together from their isolation in the vast, dilute soup, thereby enabling them to self-assemble into dual structures called dimers: pairs of peptide molecules drawn to one another by molecular forces. A dimer might later fuse into a single molecule, creating an ancestral two-word protein akin to the one reconstructed by the scientists.
Finding evidence for the existence of such dimers, however, was problematic because they could not be detected by standard structure-solving methods that apply to solutions: The resolution provided by these methods is too low for this task. To overcome this hurdle, Tawfik and colleagues teamed up with Prof. Daniella Goldfarb of Weizmann’s Chemical and Biological Physics Department, who studies the structure and dynamics of proteins by means of electron paramagnetic resonance. “This collaboration grew out of my friendship with Danny,” Goldfarb recalls. “He told me that he had a hypothesis about the evolution of complex proteins from primordial peptides, and I suggested testing this idea experimentally, using the expertise of my lab.”