RNA Thermodynamic Structural Entropy - Fig 6

(A) Relative frequency of the difference in entropy values for 960 transfer RNAs from the RF00005 family of the Rfam 11.0 database. (1) DP-FTD with average entropy difference 0.2512 ± 0.4935 with maximum of 3.1622 and minimum of 0. (2) DP-FTD* with average entropy difference 0.2502 ± 0.4934 with maximum of 3.1602 and minimum of -0.0020. (3) DP-ViennaRNA with average entropy difference 0.2475 ± 0.4975 with maximum of 3.1520 and minimum of -0.1743. (4) DP-ViennaRNA* with average entropy difference 0.2494 ± 0.4946 with maximum of 3.1572 and minimum of -0.0777. It is noteworthy that FTD is always less than DP, FTD* exceeds DP by a tiny margin only rarely, while ViennaRNA and ViennaRNA* more often exceed DP. Recall that the average deviation DP-FTD increases with increasing sequence length, as shown in the right panel of Fig 1. The same is true for DP-FTD*, DP-ViennaRNA, DP-ViennaRNA* (data not shown). (B) Free energy of arginyl-transfer RNA from Aeropyrum pernix with tRNAdb accession code tdbR00000589 [37] for temperatures ranging from 37°C to 38°C in increments of 0.01. The blue piecewise linear curve was created using RNAeval -T from the Vienna RNA Package [10]. The red linear curve was created by (1) calculating the entropy S_t = G(37) − G(38) of the tRNA cloverleaf structure by subtracting the free energy at 38°C from the free energy at 37°C, as determined using RNAeval -T, (2) computing the enthalpy H_t = G(37) + (273.15 + 37) · S_t, and then (3) computing the free energy at temperature T by G(T) = H_t − T · S_t. The jagged free energy curve is due to the fact that Vienna RNA Package represents energies as integers (multiples of 0.01 kcal/mol), so that loop energies jump at particular temperatures.