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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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(A) The PMF of T-loop in isolation plotted as a function of T-loop Rg versus RMSD at 300 K. T-loop in isolation shows a single minimum in the PMF. A representative structure is shown at the top left of the plot. The native state is not populated and it is not shown as a minimum on the plot. The PMF is plotted such that the energy of the global minimum is at 0 kcal/mol. (B) The PMF of the T-loop in the context of a hairpin at 300 K is plotted as a function of the T-loop RMSD versus Rg. For clarity, stems are not shown in the images. The PMF shows multiple distinct minima. All sample structures shown in the plot exhibit characteristic features (discussed in text) shared by the ensemble of structures found in the clusters. The energy of the global minimum (native) is 0 kcal/mol. The energy of the second minimum (expanded) is 0.4 kcal/mol. The energy of the third minimum (coil) is 0.6 kcal/mol. Each contour line represents an increase of 0.2 kcal/mol or a reduction in probability by ∼28%. A local minimum is considered to be significant when it contains more than 2% of the population and is separated by a barrier of at least 1.5 kcal/mol. All RMSD and Rg values are in units of Angstroms (Å). The 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 2: (A) The PMF of T-loop in isolation plotted as a function of T-loop Rg versus RMSD at 300 K. T-loop in isolation shows a single minimum in the PMF. A representative structure is shown at the top left of the plot. The native state is not populated and it is not shown as a minimum on the plot. The PMF is plotted such that the energy of the global minimum is at 0 kcal/mol. (B) The PMF of the T-loop in the context of a hairpin at 300 K is plotted as a function of the T-loop RMSD versus Rg. For clarity, stems are not shown in the images. The PMF shows multiple distinct minima. All sample structures shown in the plot exhibit characteristic features (discussed in text) shared by the ensemble of structures found in the clusters. The energy of the global minimum (native) is 0 kcal/mol. The energy of the second minimum (expanded) is 0.4 kcal/mol. The energy of the third minimum (coil) is 0.6 kcal/mol. Each contour line represents an increase of 0.2 kcal/mol or a reduction in probability by ∼28%. A local minimum is considered to be significant when it contains more than 2% of the population and is separated by a barrier of at least 1.5 kcal/mol. All RMSD and Rg values are in units of Angstroms (Å). The PMF is plotted in units of kcal/mol, where 1 kcal roughly equals to 0.6 KT at 300 K.

Mentions: In order to compare the folding of the T-loop sub-motif in the presence and absence of a local context (the stem), we determined potentials of mean force (PMF) of both the T-loop in isolation and as part of a hairpin as a function of the all-atom RMSD of the T-loop (with respect to the crystal conformer) and Radius of gyration (Rg). The T-loop in isolation shows a PMF at 300 K with one major basin centered around Rg values of 7.4 Å and all-atom RMSD ranking between 5.5 and 6 Å (Figure 2A). Visual analysis of the structures within the cluster reveals that the T-loop in isolation tends to be in a coil conformation such that base stacking interactions are optimized. The presence of U-turn sub-motif does not seem to have any effects on the conformation of the T-loop in isolation. Kinks found in the backbone of T-loop are often necessary to fulfill optimal base stacking interactions. Overall, the coil structures deviate significantly from the T-loop crystal conformation and contain none of the signature hydrogen bonds belonging to this particular motif. These results indicate that the T-loop in isolation has no tendency to fold into its well-recognized crystal conformers (18). Neither of its structural components (U-turn or U:A trans W/H bp) is capable of directing the folding of the T-loop motif in this context. A suitable local environment appears critical for the formation of a U-shaped loop.Figure 2.


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

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

(A) The PMF of T-loop in isolation plotted as a function of T-loop Rg versus RMSD at 300 K. T-loop in isolation shows a single minimum in the PMF. A representative structure is shown at the top left of the plot. The native state is not populated and it is not shown as a minimum on the plot. The PMF is plotted such that the energy of the global minimum is at 0 kcal/mol. (B) The PMF of the T-loop in the context of a hairpin at 300 K is plotted as a function of the T-loop RMSD versus Rg. For clarity, stems are not shown in the images. The PMF shows multiple distinct minima. All sample structures shown in the plot exhibit characteristic features (discussed in text) shared by the ensemble of structures found in the clusters. The energy of the global minimum (native) is 0 kcal/mol. The energy of the second minimum (expanded) is 0.4 kcal/mol. The energy of the third minimum (coil) is 0.6 kcal/mol. Each contour line represents an increase of 0.2 kcal/mol or a reduction in probability by ∼28%. A local minimum is considered to be significant when it contains more than 2% of the population and is separated by a barrier of at least 1.5 kcal/mol. All RMSD and Rg values are in units of Angstroms (Å). The 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

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Show All Figures
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Figure 2: (A) The PMF of T-loop in isolation plotted as a function of T-loop Rg versus RMSD at 300 K. T-loop in isolation shows a single minimum in the PMF. A representative structure is shown at the top left of the plot. The native state is not populated and it is not shown as a minimum on the plot. The PMF is plotted such that the energy of the global minimum is at 0 kcal/mol. (B) The PMF of the T-loop in the context of a hairpin at 300 K is plotted as a function of the T-loop RMSD versus Rg. For clarity, stems are not shown in the images. The PMF shows multiple distinct minima. All sample structures shown in the plot exhibit characteristic features (discussed in text) shared by the ensemble of structures found in the clusters. The energy of the global minimum (native) is 0 kcal/mol. The energy of the second minimum (expanded) is 0.4 kcal/mol. The energy of the third minimum (coil) is 0.6 kcal/mol. Each contour line represents an increase of 0.2 kcal/mol or a reduction in probability by ∼28%. A local minimum is considered to be significant when it contains more than 2% of the population and is separated by a barrier of at least 1.5 kcal/mol. All RMSD and Rg values are in units of Angstroms (Å). The PMF is plotted in units of kcal/mol, where 1 kcal roughly equals to 0.6 KT at 300 K.
Mentions: In order to compare the folding of the T-loop sub-motif in the presence and absence of a local context (the stem), we determined potentials of mean force (PMF) of both the T-loop in isolation and as part of a hairpin as a function of the all-atom RMSD of the T-loop (with respect to the crystal conformer) and Radius of gyration (Rg). The T-loop in isolation shows a PMF at 300 K with one major basin centered around Rg values of 7.4 Å and all-atom RMSD ranking between 5.5 and 6 Å (Figure 2A). Visual analysis of the structures within the cluster reveals that the T-loop in isolation tends to be in a coil conformation such that base stacking interactions are optimized. The presence of U-turn sub-motif does not seem to have any effects on the conformation of the T-loop in isolation. Kinks found in the backbone of T-loop are often necessary to fulfill optimal base stacking interactions. Overall, the coil structures deviate significantly from the T-loop crystal conformation and contain none of the signature hydrogen bonds belonging to this particular motif. These results indicate that the T-loop in isolation has no tendency to fold into its well-recognized crystal conformers (18). Neither of its structural components (U-turn or U:A trans W/H bp) is capable of directing the folding of the T-loop motif in this context. A suitable local environment appears critical for the formation of a U-shaped loop.Figure 2.

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