Mesoscopic Modeling of RNA Structure and Dynamics

Hin Hark Gan

A. Fundamentals of RNA structure1. Hierarchical folding2. Folding timescales

B. Issues in RNA modeling1. Mesoscopic models of RNA structure2. RNA energy function3. Ribosome modeling

NSF Goal: Transformative Research

Research that has the capacity to:Research that has the capacity to:

(1) revolutionize existing fields, (1) revolutionize existing fields,

(2) create new subfields, (2) create new subfields,

(3) cause paradigm shifts, (3) cause paradigm shifts,

(4) support discovery, and (4) support discovery, and

(5) lead to radically new technologies.(5) lead to radically new technologies.

National Science BoardNational Science Board

A1. Hierarchical folding2D structure folds independently of the 3D structure

Explains mostof RNA fold’s free energy

Brion & Westhof1997

A2. Folding timescales

Thirumalai et al 2001

10s (2D)

1-10ms

50ms-100s

2D and 3D structures have distinct folding timescales.

Goal:Predict 3D structure and dynamics frominput 2D fold.

B1. Mesoscopic Models: RNA Stems

?

beads

Perfect stems

Imperfect stems

Small bulge in stems ?

- Unpaired bases are important for tertiary interactions- How to effectively model unpaired bases in helices?

Similar to DNA modeling

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) (h,g,C) EE

(h’,g’,C’)(h’,g’,C’) E’ E’

- Varying constants and interactions

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.

B2. RNA Energy Function

Total energy

= (H-H) + (H-S) + (S-S)

= (coaxial) + (A-minor) + (ribose zipper) + (pseudoknots) + …

+ (Excluded volume) + (Van der Waals)

+ (Electrostatics) + …

- Tertiary motif interactions (similar to -, -, etc. interactions for proteins)- Special importance of tertiary motifs for structure and dynamics?- Parameters: , , , , ,… ,…

S – single strand regionH – helical region

Tertiary motifterms

usual terms

Tertiary Interaction NetworksRecurrent Structural Motifs are Key to 3D folds

H: helix (ds)S: single strand (ss)

By Laing, XinS/S

tRNA D-loop:T-loop

Kissing hairpin

Pseudoknots

Chang & Tinoco 1994, Ennifar et al. 2001

Shen & Tinoco 1995 Van Batenburg et al.

2001

2 hairpinsSelf-comp., often 6 nt

2 intertwining regions Comp. bps

D/T loop interaction

Holbrook et al. 1978 Holbrook and Kim 1979

H/H

Coaxial helices

Junction, “pseudo-stem”A (in helix bridge)

Kim et al. 1974Cate et al. 1996

S/H

Ribose zipper

Antip. stem/loop interaction5′-CC-3′ (Stem)3′-AA-5′ (Loop) Cate et al. 1996Tamura & Holbrook 2002

A-minor motif

Clustering of A G-C preferred

Nissen et al. 2001

Tetraloop receptor

Tetraloop/internal loop5′- GAAA -3′5′-CC-UAAG-3′

Pley et al. 1994Cate et al. 1996

Butcher et al. 1997

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

B3. Modeling the Ribosome (NDPA proposal)

Goal: Model ribosome structure and dynamics usingmesoscopic models for all RNA and protein components and their interactions.

Steitz group, Science 2000

RNA components

proteins

Impact on RNA Folding and Design

• 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

Likelihood Transformativeof success Research?Challenges