Nonneutral evolution of volume fluctuations in lysozymes revealed by normal-mode analysis of compressibility

The evolution of structural fluctuations of proteins was examined by calculating the isothermal compressibility (βT) values of chicken lysozyme and its six evolutionary mutants at Thr40, Ile55, and Ser91 (a ternary mutant corresponding to bobwhite lysozyme) from their X-ray structures by normal-mode analysis at 300 K. The βT values of the two extant lysozymes from chicken and bobwhite were 1.61 and 1.59 Mbar− 1, respectively, but five other evolutionary mutants showed larger βT values of up to 2.17 Mbar− 1. These results suggest that ancestral lysozymes exhibit larger volume fluctuations than extant ones, and hence that the molecular evolution of lysozymes has followed a nonneutral evolutionary pathway. The evolutionary mutants contained large amount of cavities, although no change was visible in the X-ray structures. There was a linear correlation between βT and total cavity volume, predicting that the cavity volume or atomic packing is an important factor regulating volume fluctuations during the molecular evolution of this protein.

Highlights► Compressibility of evolutionary lysozymes are calculated by normal mode analysis. ► Volume fluctuation of lysozymes follows a nonneutral evolutionary pathway. ► Internal cavity is an important factor regulating volume fluctuation of lysozymes.