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Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin.

Zhuang Z, Jaeger L, Shea JE - Nucleic Acids Res. (2007)

Bottom Line: On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle.This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction.Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.

ABSTRACT
The T-loop motif is an important recurrent RNA structural building block consisting of a U-turn sub-motif and a UA trans Watson-Crick/Hoogsteen base pair. In the presence of a hairpin stem, the UA non-canonical base pair becomes part of the UA-handle motif. To probe the hierarchical organization and energy landscape of the T-loop, we performed replica exchange molecular dynamics (REMD) simulations of the T-loop in isolation and as part of a hairpin. Our simulations reveal that the isolated T-loop adopts coil conformers stabilized by base stacking. The T-loop hairpin shows a highly rugged energy landscape featuring multiple local minima with a transition state for folding consisting of partially zipped states. The U-turn displays a high conformational flexibility both when the T-loop is in isolation and as part of a hairpin. On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle. This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction. Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context.

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Related in: MedlinePlus

Temperature dependence of the hairpin energy landscape. The PMF of the hairpin is plotted as a function of hairpin RMSD (compared of crystal conformer) versus the number of non-native hydrogen bonds (NN) at 275, 300, 347 and 400 K. Local minima are considered to be significant when they contains more than 2% of the population and are separated by a barrier of at least 1.5 kcal/mol. All RMSD values are in Angstroms units (Å). PMF is plotted in units of kcal/mol, where 1 kcal roughly equals to 0.6 KT at 300 K.
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Figure 4: Temperature dependence of the hairpin energy landscape. The PMF of the hairpin is plotted as a function of hairpin RMSD (compared of crystal conformer) versus the number of non-native hydrogen bonds (NN) at 275, 300, 347 and 400 K. Local minima are considered to be significant when they contains more than 2% of the population and are separated by a barrier of at least 1.5 kcal/mol. All RMSD values are in Angstroms units (Å). PMF is plotted in units of kcal/mol, where 1 kcal roughly equals to 0.6 KT at 300 K.

Mentions: To assess the ruggedness of the energy landscape, we also investigate the temperature dependence of the RNA hairpin PMF. Here, we consider a minimum to be significant when it is separated by a barrier larger than 1.5 kcal/mol and contains at least 2% of the total population. At both low temperature (275 K) and room temperature (300 K), we observed local minima corresponding to state N, I and U, as defined above (Figure 4). Interestingly, we found that the U state from 275 K corresponds to a specific coil-like structure, while the U state at 300 K corresponds to a more heterogeneous population of coil structures. We speculate that the particular coil conformer observed at 275 K is only marginally stable at extremely low temperatures. When the temperature is raised slightly to 300 K, this particular coil conformer quickly overcomes energy barriers and inter-convert with other coil conformers or converts to more stable N and I state. As temperature is raised further to 347 K (Figure 4), N and I are no longer viewed as separate minima. At the same time, a newly emerged extended conformer E becomes more populated (where <0.7% of the structures belongs to E at 275 K, while 8% of the structures belongs to E at 347 K). At 400 K (Figure 4), state N is no longer significantly populated, signaling the final loss of native population. E is populated, but it ceases to be a separated minimum due to low barrier height at 400 K. The most populated structures at 400 K are coil-like unfolded structures (U), which are entropically favored due to their great structural heterogeneity. These structures seem to be flexible and rapidly inter-convert with each other due to the low barrier heights.Figure 4.


Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin.

Zhuang Z, Jaeger L, Shea JE - Nucleic Acids Res. (2007)

Temperature dependence of the hairpin energy landscape. The PMF of the hairpin is plotted as a function of hairpin RMSD (compared of crystal conformer) versus the number of non-native hydrogen bonds (NN) at 275, 300, 347 and 400 K. Local minima are considered to be significant when they contains more than 2% of the population and are separated by a barrier of at least 1.5 kcal/mol. All RMSD values are in Angstroms units (Å). PMF is plotted in units of kcal/mol, where 1 kcal roughly equals to 0.6 KT at 300 K.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2175325&req=5

Figure 4: Temperature dependence of the hairpin energy landscape. The PMF of the hairpin is plotted as a function of hairpin RMSD (compared of crystal conformer) versus the number of non-native hydrogen bonds (NN) at 275, 300, 347 and 400 K. Local minima are considered to be significant when they contains more than 2% of the population and are separated by a barrier of at least 1.5 kcal/mol. All RMSD values are in Angstroms units (Å). PMF is plotted in units of kcal/mol, where 1 kcal roughly equals to 0.6 KT at 300 K.
Mentions: To assess the ruggedness of the energy landscape, we also investigate the temperature dependence of the RNA hairpin PMF. Here, we consider a minimum to be significant when it is separated by a barrier larger than 1.5 kcal/mol and contains at least 2% of the total population. At both low temperature (275 K) and room temperature (300 K), we observed local minima corresponding to state N, I and U, as defined above (Figure 4). Interestingly, we found that the U state from 275 K corresponds to a specific coil-like structure, while the U state at 300 K corresponds to a more heterogeneous population of coil structures. We speculate that the particular coil conformer observed at 275 K is only marginally stable at extremely low temperatures. When the temperature is raised slightly to 300 K, this particular coil conformer quickly overcomes energy barriers and inter-convert with other coil conformers or converts to more stable N and I state. As temperature is raised further to 347 K (Figure 4), N and I are no longer viewed as separate minima. At the same time, a newly emerged extended conformer E becomes more populated (where <0.7% of the structures belongs to E at 275 K, while 8% of the structures belongs to E at 347 K). At 400 K (Figure 4), state N is no longer significantly populated, signaling the final loss of native population. E is populated, but it ceases to be a separated minimum due to low barrier height at 400 K. The most populated structures at 400 K are coil-like unfolded structures (U), which are entropically favored due to their great structural heterogeneity. These structures seem to be flexible and rapidly inter-convert with each other due to the low barrier heights.Figure 4.

Bottom Line: On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle.This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction.Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.

ABSTRACT
The T-loop motif is an important recurrent RNA structural building block consisting of a U-turn sub-motif and a UA trans Watson-Crick/Hoogsteen base pair. In the presence of a hairpin stem, the UA non-canonical base pair becomes part of the UA-handle motif. To probe the hierarchical organization and energy landscape of the T-loop, we performed replica exchange molecular dynamics (REMD) simulations of the T-loop in isolation and as part of a hairpin. Our simulations reveal that the isolated T-loop adopts coil conformers stabilized by base stacking. The T-loop hairpin shows a highly rugged energy landscape featuring multiple local minima with a transition state for folding consisting of partially zipped states. The U-turn displays a high conformational flexibility both when the T-loop is in isolation and as part of a hairpin. On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle. This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction. Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context.

Show MeSH
Related in: MedlinePlus