Organization of RNA structural motifs: Lessons from SCOR

1. Organization of RNA structural motifs:Lessons from SCOR Donna K. Hendrix Department of Plant and Microbial Biology University of California, Berkeley and Physical Biosciences Division Lawrence Berkeley National Laboratory dkhendrix@lbl.gov

2. Structural classification of RNAhttp://scor.lbl.gov • Search by • PDB or NDB id • primary sequence • key word • Directed Acyclic Graph Architecture

3. Classification principles • Backbone interactions • backbone-backbone • backbone-base • Base pairing • Watson Crick • non-canonical Base stacking Backbone conformation Sequence

4. SCOR 2.0 classification Structural classification • Hairpin loops • Internal loops Tertiary interactions • Ribose zippers • Coaxial helices, Tetraloop-receptor, A-minor motif, Kissing hairpin, Pseudoknots Functional classification • Molecular function • Motif function • Structural models

5. RNA structural classification • Conserved patterns and relationships • sequence • structure • Organize data for non-specialist • Classification for RNA model-building, engineering

6. How to give yourself eye strain SCOR 2.0.3 update: • 102 new structures • 20 structures removed from SCOR 2.0.2 • 85 structures previously in SCOR but not functionally annotated Moved server from LBL; cleaned up the code a little bit; upgraded OS/tomcat; Eric added apache services.

7. What defines an RNA structural motif? Conserved, repeated structural features • sequence • fold (backbone, stacking) • interactions (hydrogen bonds, stacking)

8. Primary structure • Identify by • conservation of sequence • binding or stability • Specify by sequence: • GUAUGA (Box C of C/D Box snoRNA) • CUCAGUACGAGAGGAAC (sarcin-ricin loop) M. Tamura and S.R Holbrook JMB 320:455 (2002)

9. Secondary structure motifs • Specify by Watson Crick base pairing • internal loops • hairpin loops • junction loops • some tertiary interactions (pseudoknots) 1euy, Sherlin, et. Al. JMB 299:431 (2000)

10. Structural, or 3-d motifs • Distinguished from secondary structural motifs by three-dimensional features and interactions • bases: pairing, stacking, base-backbone • backbone: backbone-backbone, torsion angles (including chi), pseudotorsion • Described by sequence, secondary structure features as well 1euy, Sherlin, et. Al. JMB 299:431 (2000)

11. Organization of structural motifs: hierarchical classification from SCOR 1.1 and 1.2 Internal Loops Non-Watson Crick paired stacked duplexes Several looped-out bases One Looped out base Base triple, no dinucleotide platform Unpaired, unstacked looped in bases Trans- glycosidic bond(s) Loops with unpaired stacked bases, no triples or dinucleotide platforms One looped-out base with stacked non-Watson Crick base pairs Loops with Dinucleotide platform

12. Limitations of the hierarchical classification (SCOR 1.1, 1.2) Internal Loops Non-Watson Crick paired stacked duplexes Several looped-out bases One Looped out base Base triple, no dinucleotide platform Unpaired, unstacked looped in bases Trans- glycosidic bond(s) Loops with unpaired stacked bases, no triples or dinucleotide platforms One looped-out base with stacked non-Watson Crick base pairs Loops with Dinucleotide platform 1exy:a:9,20,22 (G,C,A) Jiang, et al. Structure 7:1461 (1999) 1i6u: c:10-11, c:28 (A-U)A Tishchenko, et al., JMB 311:311 (2001)

13. Organization of structural motifs:SCOR 2.0 and the DAG classification • Use a directed acyclic graph (DAG) to represent the relationships among motifs • Increase searching options: by sequence, strand, PDB or NDB identifier, residue number and key words

14. Limitations of the hierarchical classification(SCOR 1.1, 1.2) Internal Loops Non-Watson Crick paired stacked duplexes Several looped-out bases One Looped out base Base triple, no dinucleotide platform Unpaired, unstacked looped in bases Trans- glycosidic bond(s) Loops with unpaired stacked bases, no triples or dinucleotide platforms One looped-out base with stacked non-Watson Crick base pairs Loops with Dinucleotide platform 1exy:a:9,20,22 (G,C,A) Jiang, et al. Structure 7:1461 (1999) 1i6u: c:10-11, c:28 (A-U)A Tishchenko, et al., JMB 311:311 (2001)

15. SCOR 2.0 DAG: internal loop base triples Internal Loops Loops with dinucleotide platforms Loops with base triples Loops with base triples, no dinucleotide platform Loops with simple dinucleotide platform Loops with a dinucleotide platform in a triple

16. Limitations of the DAG • No clean way to present orthogonal attributes • “hairball” • Multiple DAGs • Not easily searchable • Inherent awkwardness to browsing

17. Organization of structural motifs:hierarchically organized queryable attributes • PDB ID: 1dul • Location: chain b, res 146-150; chain b, res 161-165 • Sequence 146-UCAGG-150 165-GACGA-161 • Base pairings 146-165; U∙G; cis WC-WC 147-164; C∙A; trans WC/Hoogsteen 148-163; A∙C; trans WC/sugar edge 149-162; G∙G; trans bifurcated/Hoogsteen 150-161; G∙A; cis WC-WC • Base stacking Adjacent: 145-146, 146-147, 148-149, 149-150… Non-adjacent: 147-162, 148-164 (stack swap) • Pseudotorsions Residueηθχ 146.B 169.3 195.0 203.9 147.B 160.9 144.3 217.6 148.B 110.7 155.2 228.2 • RNA “Rotamers” … • Identify motifs that consist of these more atomic attributes. 1dul:146-150.b, 161-165.b E. coli SRP/RNA Batey, et al., Science 287:1232 (2000)

18. Feature-based structural classification • *Sequence • *Loop length • Base pairings • Pseudotorsion angles • Hydrogen bonds • Stacking • adjacent and non-adjacent Classification of structural elements by features Feature-based searching and characterization of motifs

19. RNA Structural Elements

22. Annotation issues: What is a motif? Recurrent structure Conserved structure Conserved function? I know it when I see it. Definition (glossary)

23. Annotation issues: Assessment Canonical Variations (-like, pseudo-, reverse-, inverse-) eVal

24. Annotation issues: Who is it for? Student. Naïve in knowledge of structural motifs, but expert in biology. Expert. Computer-readable, human-interpretable? But what about my favorite structure (sequence, motif)? BLAST?