RNA Helical Structures Prediction and Comparison Faculty of Life Sciences, Computer Science Department Bar-Ilan University Nussinov-Wolfson Structural Bioinformatics Group, Faculty of Exact Sciences Tel Aviv University RNA Helical Structures Prediction and Comparison Liron Barzilay and Tom Susel Project Advisor: Prof. Ruth Nussinov

Background: ncRNAs DNA mRNA Protein 3% ~30K ? DNA ncRNA 97% >60K

Bacteriophage MS2 Capsid Hepatitis delta virus Ribozyme E. Coli Initiator tRNA receptor 3 ectodomain complex with double-stranded RNA Haloarcula marismortui 50s ribosomal unit

Structure Importance 1: Function

Structure Importance 2: Drugs Anti-Biotic Targeting: RNA Helixes: Shallow groove Deep groove Mixture of RNA Helixes and phosphate groups:

Background: Structuring Main Idea  2D 3D ?

Background: Reduction to Helixes WHY Helixes?  >50% of all ncRNA nucleotides  Most conserved (even more than loops)  Usually Small (<15 BP, Common 2 BP)  1D≈2D

Idea: RCSB PDB  ~800 ncRNAs.  ~14500 Helixes. ~125000 2-BP Helixes (Window 2). 1D 3D 1D 3D

Modified Residues (Nucleosides): Intra-Chain Direction Reverse: Analysis: Complexity Modified Residues (Nucleosides):  mRNAs: 4-Letter Language.  ncRNAs: ~110-Letter Language. Intra-Chain Direction Reverse:  mRNAs: Standard 3’-5’/5’-3’.  ncRNAs: ~3% Reversed 3’-5’/3’-5’.

 Analysis: Complexity Broken Linkage:  mRNAs: Complete Phosphate Skeleton.  ncRNAs: ~80% Have One or More Phosphate Missing. Non-wc BPs   mRNAs: Non-WC BPs Are Rare.  ncRNAs: ~40% Non-WC BPs.

Analysis 1: Find Helixes Manual selection of ncRNA find_pairs 2D Only Valid Helixes 1D 2D BP Manager Strand A Strand B Positions A Positions B Initial DB 3D

Analysis 2: Clustering Distance Matrix Engine All Against All RMSD Strand A Strand B Positions A Positions B All Against All RMSD Distance Matrix Engine Window 2 Window 3 Window 6       9240X9240 6848X6848 2273X2273 CLUTO

Output: Helix and Cluster Information Analyzing Results Input: _Strand A_ Clusters DB _Strand b_ Finding The Best Fitted Cluster: Levenshtein Distance (Edit Distance) Finding The Representing Helix: Inner Cluster RMSD (for closest members) Output: Helix and Cluster Information

DEMO!

Some Statistics Code: Running Time: Requirements: C++: ~2200 lines. Perl: ~1200 lines. Html/Java script: ~200 lines. Memory and Multi-Processing Optimized. Include Wrap for 3 external tools. Running Time: Started with 1.2gb of ncRNA PDBs BP Manager: 2 hours .  500mb of Helix-Only PDBs DM Engine: 8h x 5 = 40 hours. Perl Scripts: 30m x 5 = 2.5 hours. 305mb of small PDBs + 2.2gb of Matrices Requirements: C++ code is for Ubuntu (Multi- Processing). Perl is OS-Independent. DM Engine and the associated Perl scripts are very demanding. For window 2 we needed Quad Core @ 3.0 GHz with 4gb of Memory to complete the run before memory overload.