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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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The PMFs of the RNA hairpin at 300 K are shown as a function of a number of order parameters. NH is the number of native hydrogen bonds and NN the number of non-native hydrogen bonds. Rg is the radius of gyration of the hairpin and RMSD is the root mean square deviation from the hairpin crystal conformation in the ribosome. The crystal structure has 12 native hydrogen bonds: 3 belong to the U-turn sub-motif, 2 belong to the U-A trans WC/H bp and 7 belong to the helical stem. Local minima are indicated in red. The transition state is defined as the barrier region between the native and non-native basins. The energy of the native and non-native basin is similar, and the energy of the transition state is at least 1.5 kcal/mol higher than the two basins. Sample transition state structures, which contain 1–3 native hydrogen bonds in the helical stem, are shown here. All RMSD and Rg 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 3: The PMFs of the RNA hairpin at 300 K are shown as a function of a number of order parameters. NH is the number of native hydrogen bonds and NN the number of non-native hydrogen bonds. Rg is the radius of gyration of the hairpin and RMSD is the root mean square deviation from the hairpin crystal conformation in the ribosome. The crystal structure has 12 native hydrogen bonds: 3 belong to the U-turn sub-motif, 2 belong to the U-A trans WC/H bp and 7 belong to the helical stem. Local minima are indicated in red. The transition state is defined as the barrier region between the native and non-native basins. The energy of the native and non-native basin is similar, and the energy of the transition state is at least 1.5 kcal/mol higher than the two basins. Sample transition state structures, which contain 1–3 native hydrogen bonds in the helical stem, are shown here. All RMSD and Rg 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 gain insight into the energy landscape and folding mechanism of the T-loop hairpin, we determined the PMF using a larger range of structural parameters. At 300 K, at least two major basins are found when plotting the PMF as a function of the following parameters: Rg, RMSD of hairpin (compared to crystal conformer), number of native hydrogen bond (NH) and number of non-native hydrogen bonds (NN) (Figure 3). The basin with low RMSD (low NN or high NH), corresponds to the native basin, while the non-native basin is characterized by high RMSD (high NN or low NH). It is worth mentioning that when the PMF is plotted over a limited set of parameters, each local minimum shown on the PMF may correspond to an ensemble of structures that are quite different from each other, highlighting the difficulty in representing the entire spectrum of structural heterogeneity using a limited set of structural parameters. Nevertheless, we found the use of Rg versus RMSD as a good coordinate sets to distinguish native from non-native structures. When the PMF is plotted as a function of the RMSD versus Rg at 300 K (Figure 3), we found in addition to the deep native state minimum (N), a non-native basin containing several sub-basins corresponds to different trapped states. The relative energies of both the native and non-native basin are similar, which indicates that both minima are populated at this temperature and that additional interactions with the environment might be necessary to further stabilize one conformer over another.Figure 3.


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

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

The PMFs of the RNA hairpin at 300 K are shown as a function of a number of order parameters. NH is the number of native hydrogen bonds and NN the number of non-native hydrogen bonds. Rg is the radius of gyration of the hairpin and RMSD is the root mean square deviation from the hairpin crystal conformation in the ribosome. The crystal structure has 12 native hydrogen bonds: 3 belong to the U-turn sub-motif, 2 belong to the U-A trans WC/H bp and 7 belong to the helical stem. Local minima are indicated in red. The transition state is defined as the barrier region between the native and non-native basins. The energy of the native and non-native basin is similar, and the energy of the transition state is at least 1.5 kcal/mol higher than the two basins. Sample transition state structures, which contain 1–3 native hydrogen bonds in the helical stem, are shown here. All RMSD and Rg 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

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Figure 3: The PMFs of the RNA hairpin at 300 K are shown as a function of a number of order parameters. NH is the number of native hydrogen bonds and NN the number of non-native hydrogen bonds. Rg is the radius of gyration of the hairpin and RMSD is the root mean square deviation from the hairpin crystal conformation in the ribosome. The crystal structure has 12 native hydrogen bonds: 3 belong to the U-turn sub-motif, 2 belong to the U-A trans WC/H bp and 7 belong to the helical stem. Local minima are indicated in red. The transition state is defined as the barrier region between the native and non-native basins. The energy of the native and non-native basin is similar, and the energy of the transition state is at least 1.5 kcal/mol higher than the two basins. Sample transition state structures, which contain 1–3 native hydrogen bonds in the helical stem, are shown here. All RMSD and Rg 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 gain insight into the energy landscape and folding mechanism of the T-loop hairpin, we determined the PMF using a larger range of structural parameters. At 300 K, at least two major basins are found when plotting the PMF as a function of the following parameters: Rg, RMSD of hairpin (compared to crystal conformer), number of native hydrogen bond (NH) and number of non-native hydrogen bonds (NN) (Figure 3). The basin with low RMSD (low NN or high NH), corresponds to the native basin, while the non-native basin is characterized by high RMSD (high NN or low NH). It is worth mentioning that when the PMF is plotted over a limited set of parameters, each local minimum shown on the PMF may correspond to an ensemble of structures that are quite different from each other, highlighting the difficulty in representing the entire spectrum of structural heterogeneity using a limited set of structural parameters. Nevertheless, we found the use of Rg versus RMSD as a good coordinate sets to distinguish native from non-native structures. When the PMF is plotted as a function of the RMSD versus Rg at 300 K (Figure 3), we found in addition to the deep native state minimum (N), a non-native basin containing several sub-basins corresponds to different trapped states. The relative energies of both the native and non-native basin are similar, which indicates that both minima are populated at this temperature and that additional interactions with the environment might be necessary to further stabilize one conformer over another.Figure 3.

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