RNA, ribonucleic acid, folds into three-dimensional structures and thus achieves specificity in molecular recognition and enzymatic activity. Toward the long-term goal of RNA structure prediction, the Schroeder lab explores the structure of encapsidated satellite tobacco mosaic virus (STMV) RNA, the structures and energetics of prohead RNA (pRNA), and the thermodynamic stabilities of noncanonical pairs at RNA helix ends. None of these RNA structures are currently predicted well. Thus discovering the details of these RNA structures and energetics will provide new insight into the fundamental physical forces that direct RNA folding and function. Additional experimental data about RNA conformations, such as chemical modification, phylogenetic covariation, improved thermodynamic parameters, the magnesium dependence of RNA tertiary interactions, and global features such as the minimum number and length of helices, can further define the RNA conformational landscape and improve RNA structure predictions.
We finished the genome map,
now we cannot figure out how to fold it!
Genome sequencing projects and the rapid advances in nucleic acid sequencing technology provide abundant sequence (primary structure) information. The challenge remains how to use this information to understand the structure and function of RNA and protein molecules encoded within the genome sequence. Both RNA and proteins are biological polymers with non-random sequences of nucleotides and amino acids. The sequence of nucleotides or amino acids determines the structure of the molecule and thus also the function of the molecule. A folding funnel, like the one shown below, describes the folding of biological polymers to the lowest free energy conformation.
RNA Folding Problem
Figure from Dill &Chan (1997) Nat. Struct. Biol. Vol. 4, pp. 10-19
The diagram below shows how constraints from chemical probing experiments, crystallography, cryoelectron microscopy, or phylogenetic analysis can identify one region of the RNA folding funnel. Sometimes the functional structure may not be the lowest free energy structure. Sometimes an RNA may change its conformation. Viral RNA genomes must fold and unfold and refold many times during their life cycle. This makes viral RNA structure prediction especially challenging.
Figure from Schroeder et al. 2011 Biophysical Journal v. 101 p. 167
The figure below shows a model of the satellite tobacco mosaic virus icosahedral particle with the RNA helices shown as yellow tubes. The identity of the bases in the helices has been obscured by the icosahedral averaging done to solve the crystal structure; and the nonhelical RNA is also icosahedrally disordered. Thus, STMV presents a novel RNA folding problem. The minimum number of helices, the minimum length of the helices, the relative orientation of the helices to each other and to the protein shell, the total volume and overall shape of the RNA, and the icosahedral symmetry provide powerful restraints for RNA structure prediction. The RNA sequence itself shows no repetitive patterns but holds the secret to the RNA structure. The Schroeder lab is exploring the structure of STMV RNA through computational, chemical and mutagenesis techniques.
STMV Figure reproduced from VIPER website: http://viperdb.scripps.edu