Unraveling the “Dark Energy” Found in the Structural Protein Universe

Astronomers use the term dark energy to refer to energy in the universe that is unaccounted for by ordinary matter but necessary to explain cosmology. Astronomy, however, isn't the only field with missing energy. Rice University professor Peter Wolynes and postdoctoral researcher Carlos Bueno, along with Universidad de Buenos Aires collaborators Ezequiel Gaplern, Ignacio Sánchez and Diego Ferreiro, recently published a paper describing the "dark energy" found in the structural protein universe. This missing energy comes from the tension between the form of a protein and its function.

Proteins are made up of long strings of amino acids, folded into an almost endless array of complex shapes. Since amino acids have many different chemistries, they can repel or attract each other like magnets. Most parts of a protein will, therefore, fold into a low-energy state, minimizing conflict between differing forces. The changes in energy as a protein folds into its lowest-energy state, called its physical energy, guide it into its native structure in which it would be found in in the wild.

Shape, however, is not everything. The functions of proteins are even more varied than their shapes, ranging from binding partners to catalyzing reactions. Each function relies on sites within the protein that have been folded into shapes necessary for their tasks but would not guide the protein's folding. A protein whose job is to bind an ion, for example, could require two conflicting amino acids placed near each other to make the binding possible. This would give the binding site the shape necessary to complete its task but impede the protein as it tries to fold into its lowest energy state, resulting in energetic frustration. 

Wolynes's team was interested in these energetically frustrated regions, which they thought could hold insight into the evolution of protein function. By looking at the amino acid sequences of related proteins with corresponding tasks in different organisms, the researchers could calculate what they called "evolutionary energy." While physical energy is based on the structure of the folded protein, evolutionary energy is calculated from the distribution of amino acid sequences evolved to fulfill a particular function. 

When we calculated the difference between physical energy and evolutionary energy, we found there is missing energy in the functional protein universe, unaccounted for by folding physics. We called this 'dark energy,' borrowing from the similar missing energy concept found in astronomy." 

Peter Wolynes, the D.R. Bullard-Welch Foundation Professor of Science and corresponding author on the paper

If a protein site was responsible for a function like binding, Wolynes' team found that its evolutionary energy was high, differing from its physical energy. This indicates the energy cost of keeping the function of that particular site is high. But if a site was not responsible for an active function, its evolutionary energy was low, more closely matching its physical energy. By mapping out dark energy over a protein, the researchers could see how it varied from site to site, much like how a traffic map can show congestion in different areas of a city. 

"Dark energy not only expands our understanding of the constraints on the protein universe, but it allows us to quantitatively describe how evolutionarily important a particular function, like binding, is to a protein," Wolynes said. "Dark energy can represent the cost of any given protein function: The higher the cost, the more important the function must be." 

Interestingly, Wolynes adds, protein folding itself is a result of evolutionary pressure. Proteins produced by cells fold naturally, but random strings of amino acids generated in labs do not. The protein fold is itself an evolved trait. Ultimately, dark energy provides insight into the competing evolutionary pressures shaping a protein's form and function.