Tuesday, June 9, 2009
Paper by Yang, Bahar, and Widom featured on the cover of Biophysical Journal
Satellite tobacco mosaic virus (STMV) is one of the smallest viruses known. Its capsid contains 60 icosahedrally arranged identical protein subunits. Normal modes of capsid vibration resemble vector spherical harmonic functions and can be classified according to the icosahedral symmetry group. The layout and color scheme of this figure follow the artwork “Che Guevara” by Andy Warhol. See the article by Yang, Bahar, and Widom on page 4438.
Coarse-grained elastic network models elucidate the fluctuation dynamics of proteins around their native conformations. Low-frequency collective motions derived by simplified normal mode analysis are usually involved in biological function, and these motions often possess noteworthy symmetries related to the overall shape of the molecule. Here, insights into these motions and their frequencies are sought by considering continuum models with appropriate symmetry and boundary conditions to approximately represent the true atomistic molecular structure. We solve the elastic wave equations analytically for the case of spherical symmetry, yielding a symmetry-based classification of molecular motions together with explicit predictions for their vibrational frequencies. We address the case of icosahedral symmetry as a perturbation to the spherical case. Applications to lumazine synthase, satellite tobacco mosaic virus, and brome mosaic virus show that the spherical elastic model efficiently provides insights on collective motions that are otherwise obtained by detailed elastic network models. A major utility of the continuum models is the possibility of estimating macroscopic material properties such as the Young's modulus or Poisson's ratio for different types of viruses.