Three-dimensional structures of small RNA molecules
Principal Investigator
Peter Schuster
Co-Investigator:
Peter F. Stadler
Co-workers:
Alexander Renner, Stefan Kopp
Support:
Fonds zur Förderung der Wissenschaftlichen Forschung
Project No. P-11065-CHE:
Begin: July 1995
End: December 1998
Abstract
The three-dimensional structures of RNA molecules are investigated using both theoretical methods such as Molecular Modeling, Molecular Mechanics or Molecular Dynamics, and NMR spectroscopy. Secondary structure prediction, either in terms of the ground state or in terms of the partition function of the Boltzmann ensembles of all structures, serve as starting points for the 3D structure prediction. The double helical stacks are introduced into the computations with constant geometries as determined by the base pairing patterns of the secondary structures. In the case of small RNA molecules with up to 30 nucleotides that lack extremely flexible structural elements (such as large loops, joints, or long free ends) we are considering to calculate the minimum free energy structures by means of direct energy minimization.
Preliminary tests with small hairpin molecules with three- or four-base loops and chain lengths of 11 and 12 bases, respectively, showed two major outcomes:
- the structures are in good agreement with existing
experimental data for the same three- and four-base loops, and
- the geometries of all optimized structures follow a common
principle of minimizing the contact surface between the
heterocyclic bases and the solvent.
NMR spectroscopy experiments (L.R. Brown, IMB Jena K. Wuethrich, ETH Zuerich) will be carried out on the same small molecules and permit a direct comparison with the computed geometries. If there is basic agreement we plan to iteratively refine the structure predictions by means of mutual corrections of the structures obtained by NMR spectroscopy and Molecular Mechanics. In the case of RNA molecules with extremely flexible structural parts we want to supplement the structure prediction with Molecular Dynamics computations. Since we expect major problems it will be necessary to incorporate NMR data as structural constraints in the modeling. We plan to choose a sample of small flexible RNAs as models and study them extensively to gain experience with the flexible parts of molecules. The results of the investigations of small RNA molecules together with known structure data for the constant geometries of partial structures (A-RNA double helix, rigid geometries of small loops, etc.) and NMR data shall be used to predict the structures of larger RNAs with sequence lengths up to 100 bases. The preliminary final aim of this project is the development of a software package that is capable of predicting the 3D structure of an RNA molecule (using NMR data as input) without user-interventions.
Peter Schuster <pks@tbi.univie.ac.at>
Last modified: Wed May 9 10:04:01 CEST 2001