New insight into long‐range nonadditivity within protein double‐mutant cycles

Additivity principles in chemistry, biochemistry, and biophysics have been used extensively for decades. Nevertheless, it is well known that additivity frequently breaks down in complex biomacromolecules. Nonadditivity within protein double mutant free energy cycles of spatially close residue pairs is a generally well‐understood phenomenon, whereas a robust description of nonadditivity extending over large distances remains to be developed. Here, we test the hypothesis that the mutational effects tend to be nonadditive if two structurally well‐separated mutated residues belong to the same rigid cluster within the wild type protein, and additive if they are located within different clusters. We find the hypothesis to be statistically significant with P‐values that range from 10−5 to 10−6. To the best of our knowledge, this result represents the first demonstration of a statistically significant preponderance for nonadditivity over long distances. These findings provide new insight into the origins of long‐range nonadditivity in double mutant cycles, which complements the conventional wisdom that nonadditivity arises in double mutations involving contacting residues. Consequently, these results should have far‐reaching implications for a proper understanding of protein stability, structure/function analyses, and protein design. Proteins 2008. © 2007 Wiley‐Liss, Inc.