Before revision:  At the same time, the sum of mutual entropies across all pairs of residues within the protease shows a significant increase over the years, indicating an increase in epistasis in response to treatment, a trend not seen within sequences from untreated subjects. Our findings suggest that information theory can be an important tool to study long-term trends in the evolution of macromolecules.
After revision:  At the same time, the sum of mutual entropies across all pairs of residues is a necessary (but not sufficient) condition for epistasis, allowing us to use information as a proxy for epistasis. We analyze the "fossils" of the evolutionary trajectories of a protein contained in the sequence data, and show that epistatic interactions continue to enrich in the HIV-1 protease as more potent drugs enter the market. While initially epistatic interactions are likely to constrain the evolvability of a protein, we find no evidence that the HIV-1 protease has reached its potential for adaptation after 9 years of adapting to a changing drug environment. The protein is able to encode information about novel and more potent drugs using epistatic interactions, while maintaining sufficient diversity and thermostability. We propose that this mechanism is central to protein evolution not just in HIV-1 protease, but for any protein adapting to rapidly changing conditions