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. 2011 Apr 12;39(14):6201–6212. doi: 10.1093/nar/gkr165

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© The Author(s) 2011. 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 3. — Tertiary structure analysis by DMD simulations indicates that the unfolding energy barrier is lower for ¹⁶⁶T allele, thus enhancing its conformational flexibility to explore higher energy states. (a and b) Structures of variants as predicted using DMD. Leftmost structures represent the native tertiary structure for each allelic variant. The middle structures are the secondary structural elements as predicted by DMD. The rightmost structures are represented in sausage format where thicker backbones represent larger root mean squared fluctuations within the native ensemble (see ‘Materials and Methods’ section). Regions of the RNA are color-coded to correspond to different motifs: Loop I (blue), Stem I (green) and Stem II (red). (a) Structures of ¹⁶⁶C-allelic variant. (B) Structures of ¹⁶⁶T-allelic variant. (c) The folding transition temperature for ¹⁶⁶T is lower than ¹⁶⁶C, as denoted by the peak in specific heat of folding. Specific heats were determined using weighted histogram analysis method. The vertical droplines represent the standard deviation for each plot point. (d) Histogram of free energies derived from replica-exchange simulations. The native ensembles that correspond to the structural motifs as predicted by Mfold are denoted on the plot. (e and f) Maps illustrating frequency of contacts at a temperature of 0.10 ε/k_B. (e) Frequency of contacts for ¹⁶⁶C-allelic variant. The most frequent contacts shown are representative of the native state alone, where the first lower left diagonal line is representative of Stem I (nucleotides 5 through 32 of the simulation correspond to nucleotides 124 through 151 on the transcript). The second smaller diagonal line on the upper right of the plot represents the contacts formed from the Stem II (nucleotides 34 through 51). (f) Frequency of contacts for ¹⁶⁶T-allelic variant. Even at the lowest simulation temperature, the ¹⁶⁶T SNP creates an ensemble of states where many different enthalpic contacts are made throughout its folding simulation but are entropically unfavorable.