Journal of Chemical Information and Modeling vol:51 issue:9 pages:2361-2371
The trp RNA-binding protein (TRAP) has a toroidal topology and a perfect 11-fold symmetry, which make it an excellent candidate for a vibrational study of elastic properties. Normal mode analysis in combination with correlation matrix calculations were used to detect collective low-frequency motions in TRAP. The results reveal the presence of highly-correlated modes at the spectral origin which directly reflect the annular and toroidal topology. Integral correlations over the low-frequency part of the vibrational spectrum further demonstrate the relative rigidity of the 11 monomer building blocks of TRAP. The internal flexibility of each monomer and the effects of tryptophan-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.