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Predicting RNA folding thermodynamics with a reduced chain representation model
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| Zeitschriftentitel: | RNA |
|---|---|
| Personen und Körperschaften: | , |
| In: | RNA, 11, 2005, 12, S. 1884-1897 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Cold Spring Harbor Laboratory
|
| Schlagwörter: |
| author_facet |
CAO, SONG CHEN, SHI-JIE CAO, SONG CHEN, SHI-JIE |
|---|---|
| author |
CAO, SONG CHEN, SHI-JIE |
| spellingShingle |
CAO, SONG CHEN, SHI-JIE RNA Predicting RNA folding thermodynamics with a reduced chain representation model Molecular Biology |
| author_sort |
cao, song |
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CAO, SONG CHEN, SHI-JIE 1355-8382 1469-9001 Cold Spring Harbor Laboratory Molecular Biology http://dx.doi.org/10.1261/rna.2109105 <jats:p>Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of <jats:italic>Tetrahymena</jats:italic> group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule.</jats:p> Predicting RNA folding thermodynamics with a reduced chain representation model RNA |
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Cold Spring Harbor Laboratory, 2005 |
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| title |
Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_unstemmed |
Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_full |
Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_fullStr |
Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_full_unstemmed |
Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_short |
Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_sort |
predicting rna folding thermodynamics with a reduced chain representation model |
| topic |
Molecular Biology |
| url |
http://dx.doi.org/10.1261/rna.2109105 |
| publishDate |
2005 |
| physical |
1884-1897 |
| description |
<jats:p>Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of <jats:italic>Tetrahymena</jats:italic> group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule.</jats:p> |
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| description | <jats:p>Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of <jats:italic>Tetrahymena</jats:italic> group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule.</jats:p> |
| doi_str_mv | 10.1261/rna.2109105 |
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| institution | DE-D275, DE-Bn3, DE-Brt1, DE-D161, DE-Zwi2, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229 |
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| spelling | CAO, SONG CHEN, SHI-JIE 1355-8382 1469-9001 Cold Spring Harbor Laboratory Molecular Biology http://dx.doi.org/10.1261/rna.2109105 <jats:p>Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of <jats:italic>Tetrahymena</jats:italic> group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule.</jats:p> Predicting RNA folding thermodynamics with a reduced chain representation model RNA |
| spellingShingle | CAO, SONG, CHEN, SHI-JIE, RNA, Predicting RNA folding thermodynamics with a reduced chain representation model, Molecular Biology |
| title | Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_full | Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_fullStr | Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_full_unstemmed | Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_short | Predicting RNA folding thermodynamics with a reduced chain representation model |
| title_sort | predicting rna folding thermodynamics with a reduced chain representation model |
| title_unstemmed | Predicting RNA folding thermodynamics with a reduced chain representation model |
| topic | Molecular Biology |
| url | http://dx.doi.org/10.1261/rna.2109105 |