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. Author manuscript; available in PMC: 2017 Jul 21.
Published in final edited form as: J Am Chem Soc. 2014 Oct 27;136(44):15631–15637. doi: 10.1021/ja507812v

Figure 4.

Figure 4

Selected properties from the TAR50a MD simulation. (A) ΩISB values plotted vs. simulation time (grey line). The black line is obtained by applying a Fast Fourier Transform filter in order to reduce the noise in the data. The right panel reports the distribution of the calculated ΩISB angle values (black line). The Gaussian curves used to fit the ΩISB distribution are in orange, while the sum of the fitting Gaussians is in red. (B) Calculated RMSFs values of each nucleotide atoms (grey), of the C4’ atoms of each nucleotide (red) and of C5 atoms of each nucleotide (green). RMSF values of U23, U25, and U38 are highlighted by dots in each curve. (C) Time evolution (upper panels) and distribution (bottom panels) of the χ torsional angle of U23, U25 and U38, as observed in the MD simulation TAR50a. Correspondent plots for the TAR50b, TAR10a, and TAR10b simulations are reported in the SI.