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

Mimura Shigefumi

Yamato Takahisa

Kamiyama Tadashi

Gekko Kunihiko

Biophysical Chemistry

The evolution of structural fluctuations of proteins was examined by calculating the isothermal compressibility (beta(T)) 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 Or 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 beta(T) 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 beta(T) 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. (C) 2011 Elsevier B.V. All rights reserved.

Isothermal compressibility

Lysozyme

Molecular evolution

Nonneutral pathway

Normal-mode analysis

Volume fluctuation

Biology [ 460 ]

eng

Elsevier Science BV

(c) 2012 Elsevier B.V. All rights reserved.

[ISSN] 0301-4622

[DOI] 10.1016/j.bpc.2011.11.005

[NCID] AA00566073

[DOI] http://dx.doi.org/10.1016/j.bpc.2011.11.005