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Conformations of t-RNA: base pairing and stacking
B Lustig1, D G Covell, R L Jernigan
1Laboratory of Mathematical Biology, Washington Science Center, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.
Journal of Biomolecular Structure & Dynamics
|August 1, 1994
Summary
This study models transfer RNA (tRNA) folding using lattice models, revealing millions of possible 3D structures. Restricting conformational freedom, like through secondary structures, is key to exploring complex RNA folding.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Transfer RNA (tRNA) plays a crucial role in protein synthesis.
- Understanding tRNA's three-dimensional (3D) structure is vital for deciphering its function.
- Accurate modeling of RNA folding is computationally challenging due to the vast number of possible conformations.
Purpose of the Study:
- To develop and apply lattice models for predicting tRNA structure.
- To explore the conformational space of RNA folding, including secondary and tertiary structures.
- To investigate the feasibility of comprehensively analyzing 3D RNA structures.
Main Methods:
- Fitting the transfer RNA (tRNA) structure to a face-centered cubic lattice model.
- Generating low-energy secondary structures from proximal bases.
- Enumerating all possible tertiary pairs and conformational variations, including slip pairing.
- Calculating lattice folds for RNA internal loops with rigid stems and excluded volume considerations.
Main Results:
- Achieved a root-mean-square (RMS) deviation of 1.76 Å for the tRNA fit to a lattice model.
- Identified 32 possible chain folds for tRNA on the lattice.
- Generated over 2.3 million allowed conformers by combining secondary structures with possible tertiary pairs.
- Reduced over 36 million lattice folds to 258,979 configurations for a sixteen-base internal loop by incorporating rigid stems and excluded volume.
Conclusions:
- Lattice models provide a feasible approach for exploring the vast conformational space of RNA.
- Secondary structures significantly constrain the possible tertiary interactions and overall 3D structure.
- Thorough exploration of 3D RNA structures necessitates prior specification of conformational restrictions.