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. 2019 Dec 27;18:137–152. doi: 10.1016/j.csbj.2019.12.003

Fig. 2.

Fig. 2

Per-nucleotide interaction of single-stranded RNA (ssRNA) within the tunnel of PNPase. A) Interaction free energy between each individual RNA nucleotide and PNPase residues. The position indices correspond to those shown in Fig. 1C. B) Interaction free energy between PNPase residues and either guanosine (G) or 8-oxo-7,8-dihydroguanosine (8-oxoG) (base + sugar + phosphate groups) individually introduced at the indicated position of the ssRNA. C) Interaction free energy of the isolated nucleobase, either guanine (Gua) or 8-oxo-7,8-dihydroguanine (8-oxoGua). The average and standard deviation interaction free energy values in panel A – C are calculated over triplicate 50 ns explicit solvent MD simulations of the RNA-protein complex. Error bars plotted as ± one standard deviation. Statistical analysis conducted using one-tailed homoscedastic t-test, * refers to p-value < 0.05, and ** refers to p-value < 0.001.