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. 2015 Jul 21;43(16):7731–7743. doi: 10.1093/nar/gkv729

Figure 4.

Figure 4.

Summary of interactions, contributions to the effective binding energy, and RMSF as well as proposed signaling pathways from the mutation sites to the binding site. (A) Scheme summarizing non-covalent interactions (Tables 1 and 2), contributions to the effective binding energy (Figure 2), and RMSF (Figure 2) of nucleotides forming the first (white ellipses) and second (light gray ellipses) shell of the PTC binding site and the two mutation sites (dark gray ellipses). Non-covalent interactions are displayed in green for linezolid-H50Swt and in orange for linezolid-H50Smut. Information on contributions to the effective binding energy and RMSF of each nucleotide are depicted on the left side for linezolid-H50Swt and on the right side for linezolid-H50Smut, respectively. See the legend for further details. (B) Routes by which the information of the double mutation is transmitted via second shell nucleotides to U2504 (red arrows) and C2452 (blue arrows), respectively, as well as synergistic effects between these two routes (yellow arrows). The gray arrow depicts a blocking effect of U2504 by U2572 in H50Swt described in (9), but not observed on the time scale of our simulations.