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. 2010 Apr 7;38(14):4844–4855. doi: 10.1093/nar/gkq213

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© The Author(s) 2010. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 6. — Effects of modulating the A2450–C2063 pair on the PTC architecture. (A) In the surface representation of the structure obtained at the end of the MD simulation of the wt PTC, a continuous ‘interaction ring’ is formed involving the A2450–C2063 pair, A2062, a constrained monovalent ion (magenta), the phenylalanine side chain (asterisk) of A-site bound Phe-tRNA^Phe and A76 of deacylated tRNA in the P-site. (B) Removal of the adenine N6-amino group by introducing purine at residue 2450 resulted in the loss of base pairing with C2063 and a complete disconnection of A2062 and the A-site tRNA. (C) Removal of the entire nucleobase at 2450 severely affected the PTC architecture also resulting in the loss of interactions of A2062 with the aa-tRNA in the A-site. Instead the amino acid side chain of Phe-tRNA^Phe seems to interact with the nucleobase at C2063. (D) Removal of the base at 2063 showed less dramatic effects since A2062 was still able to reach the aa-tRNA in the A-site. However, the A2450–C2063 base pair is destroyed as well as A76 of P-tRNA is positioned significantly different in respect to A2450 as compared to the wt situation in (A).