Normal modes analyses of macromolecules

Normal modes analysis (NMA) has been a valuable tool for the study of the flexibility and the slow range of motion of proteins, and it nicely complements Molecular Dynamics techniques, where simulations are possible for only limited time spans. We demonstrate the usefulness of NMA by the example of a large globular protein, G-actin, and the filaments it forms: F-actin. We also discuss some less known aspects of NMA: (a) The density of modes of globular proteins departs from Debye’s prediction for solids, and is anomalous. (b) The use of dihedral angles, rather than Cartesian degrees of freedom, gives rise to interesting nonlinear effects, such as oscillations of certain subsets at twice the natural frequency of the mode. (c) For slow modes of macromolecules it is sufficient to use very simple-minded potentials, without the rich level of details habitual in NMA and Molecular Dynamics.