Normal Mode Analysis of Trp RNA Binding Attenuation Protein: Structure and Collective Motions

The Trp RNA-binding protein (TRAP) has a toroidal topology and a perfect 11-fold symmetry, which makes it an excellent candidate for a vibrational study of elastic properties. Normal mode analysis in combination with correlation matrix calculations was used to detect collective low-frequency motions in TRAP. The results reveal the presence of highly correlated modes at the lower end of the spectrum, which directly reflect the annular and toroidal topology. The integral of the correlations over the low-frequency torsional part of the vibrational spectrum further demonstrates the relative rigidity of the 11 monomer building blocks of TRAP. The internal flexibility of each monomer and the effects of Trp-binding were also examined. The study clearly shows the determining influence of symmetry and topology on the elastic properties and also offers a detailed view on the Trp affinity of TRAP.