Mesoscopic Modeling of RNA Structure and Dynamics

1. Mesoscopic Modeling of RNA Structure and Dynamics • Hin Hark Gan • A. Fundamentals of RNA structure • Hierarchical folding • Folding timescales • B. Issues in RNA modeling • Mesoscopic models of RNA structure • RNA energy function • Ribosome modeling

2. NSF Goal: Transformative Research Research that has the capacity to: (1) revolutionize existing fields, (2) create new subfields, (3) cause paradigm shifts, (4) support discovery, and (5) lead to radically new technologies. National Science Board

3. A1. Hierarchical folding 2D structure folds independently of the 3D structure Explains most of RNA fold’s free energy Brion & Westhof 1997

4. A2. Folding timescales 2D and 3D structures have distinct folding timescales. 10s (2D) Goal: Predict 3D structure and dynamics from input 2D fold. 1-10ms 50ms-100s Thirumalai et al 2001

5. ? B1. Mesoscopic Models: RNA Stems Perfect stems Similar to DNA modeling beads Imperfect stems ? Small bulge in stems • Unpaired bases are important for tertiary interactions • How to effectively model unpaired bases in helices?

6. Can DNA elastic models be applied to RNA? • Elastic constants: stretching (h), bending (g), twisting (C) • Applicable to long perfect helices (typically, <10 basepairs) • Imperfect helices require special considerations (e.g., varying elastic potentials and interactions) • Not applicable to single strand regions (h,g,C) E (h’,g’,C’) E’ - Varying constants and interactions

7. Mesoscopic Models: Single strands • Use existing coarse-grained models • Baker group: 1-bead model (considers only base, neglect sugar and phosphate, base centroid as the bead origin) • Amaral group: bead-pin model Overall mesoscopic RNA model is a mixture of elastic chain for helical segments and bead-pin model for unpaired bases.

8. B2. RNA Energy Function S – single strand region H – helical region Total energy = (H-H) + (H-S) + (S-S) = (coaxial) + (A-minor) + (ribose zipper) + (pseudoknots) + … + (Excluded volume) + (Van der Waals) + (Electrostatics) + … Tertiary motif terms usual terms • Tertiary motif interactions (similar to -, -, etc. • interactions for proteins) • Special importance of tertiary motifs for structure and dynamics? • - Parameters: , , ,…

9. S/H S/S H/H Coaxial helices Junction, “pseudo-stem” A (in helix bridge) Kim et al. 1974 Cate et al. 1996 A-minor motif Clustering of A G-C preferred Nissen et al. 2001 Tetraloop receptor Pseudoknots 2 intertwining regions Comp. bps Shen & Tinoco 1995 Van Batenburg et al. 2001 Tetraloop/internal loop 5′- GAAA -3′ 5′-CC-UAAG-3′ Pley et al. 1994 Cate et al. 1996 Butcher et al. 1997 Kissing hairpin 2 hairpins Self-comp., often 6 nt Chang & Tinoco 1994, Ennifar et al. 2001 Ribose zipper Antip. stem/loop interaction 5′-CC-3′ (Stem) 3′-AA-5′ (Loop) Cate et al. 1996 Tamura & Holbrook 2002 tRNA D-loop:T-loop D/T loop interaction Holbrook et al. 1978 Holbrook and Kim 1979 Tertiary Interaction NetworksRecurrent Structural Motifs are Key to 3D folds H: helix (ds) S: single strand (ss) By Laing, Xin

10. Derivation and Optimization of Energy Function • Structure data -> statistical potential, Eik ~ln(Pik ) • Thermodynamic data – denaturation curves from temperature and pH changes • Other RNA data sources (e.g., decoy structures) Brion & Westhof, 1997

11. B3. Modeling the Ribosome (NDPA proposal) RNA components proteins Goal: Model ribosome structure and dynamics using mesoscopic models for all RNA and protein components and their interactions. Steitz group, Science 2000

12. Impact on RNA Folding and Design LikelihoodTransformative of successResearch? Challenges • Folding of larger RNAs (100-500 nt) • Millisecond folding times • RNA design aided by predicted 3D folds • Ribosome dynamics and antibiotic action Likely Yes/No Probable Yes/No Likely Yes May be Yes