RNA Structure Prediction: Understanding the Role of RNA in Genetics - Prof. Drena Leigh Do, Lab Reports of Bioinformatics

Download RNA Structure Prediction: Understanding the Role of RNA in Genetics - Prof. Drena Leigh Do and more Lab Reports Bioinformatics in PDF only on Docsity! #25 - More RNA Structure & BCB 544 Projects 10/19/07 BCB 444/544 Fall 07 Dobbs 1 1BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 BCB 444/544 Lecture 25  More RNA Structure  BCB 544 Projects #25_Oct19 2BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Mon Oct 15 - Lecture 23 Protein Tertiary Structure Prediction • Chp 15 - pp 214 - 230 Wed Oct 17 & Thurs Oct 18 - Lecture 24 & Lab 8 (Terribilini) RNA Structure/Function & RNA Structure Prediction • Chp 16 - pp 231 - 242 Fri Oct 18 - Lecture 25 (& Mon Oct 22) Gene Prediction • Chp 8 - pp 97 - 112 Required Reading (before lecture) 3BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Homework Assignment ALL: HomeWork #4 (emailed & posted online Sat AM) Due: Mon Oct 22 by 5 PM (not Fri Oct 19) Read: Ginalski et al.(2005) Practical Lessons from Protein Structure Prediction, Nucleic Acids Res. 33:1874-91. http://nar.oxfordjournals.org/cgi/content/full/33/6/1874 (PDF posted on website) • Although somewhat dated, this paper provides a nice overview of protein structure prediction methods and evaluation of predicted structures. • Your assignment is to write a summary of this paper - for details see HW#4 posted online & sent by email on Sat Oct 13 4BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 BCB 544 Only: New Homework Assignment 544 Extra#2 (posted online Thurs?) Due: Fri Nov 2 by 5 PM HW#2 is next step in Team Projects Will end lecture a few minutes early today - to allow time to meet & discuss 544 Teams & Projects 5BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Seminars this Week BCB List of URLs for Seminars related to Bioinformatics: http://www.bcb.iastate.edu/seminars/index.html • Oct 18 Thur - BBMB Seminar 4:10 in 1414 MBB • Sachdeve Sidhu (Genentech) Phage peptide and antibody libraries in protein engineering and ligand selection • Was great talk! • Oct 19 Fri - BCB Faculty Seminar 2:10 in 102 ScI • Lyric Bartholomay (Ent, ISU) Computational Biology and vector-borne disease: from the field to the bench 6BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Another local example: Combining Structure Prediction, Machine Learning & "Real" (wet-lab) Experiments to Investigate the Lentiviral Rev Protein: A Step Toward New HIV Therapies Susan Carpenter (Washington State Univ) Wendy Sparks Yvonne Wannemuehler Drena Dobbs, GDCB Jae-Hyung Lee Michael Terribilini Kai-Ming Ho, Physics Yungok Ihm Haibo Cao Cai-zhuang Wang Gloria Culver, BBMB Laura Dutca #25 - More RNA Structure & BCB 544 Projects 10/19/07 BCB 444/544 Fall 07 Dobbs 2 7BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Chp 16 - RNA Structure Prediction SECTION V STRUCTURAL BIOINFORMATICS Xiong: Chp 16 RNA Structure Prediction (Terribilini) • RNA Function • Types of RNA Structures • RNA Secondary Structure Prediction Methods • Ab Initio Approach • Comparative Approach • Performance Evaluation 8BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 RNA Function • Storage/transfer of genetic information • Newly discovered regulatory functions • miRNA & si RNA pathways, especially • Catalytic This slide has been changed 9BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 RNA types & functions regulation of transcription and translation, other?? regulatory RNAs (siRNA, miRNA, etc.) mRNA processing, polyA addition <catalytic> rRNA processing/maturation/methylation snRNA - small nuclear snoRNA - small nucleolar signal recognition particle (SRP) tRNA processing <catalytic> scRNA - small cytoplasmic precursors & intermediates of mature mRNAs & other RNAs hnRNA - heterogeneous nuclear translation (protein synthesis)tRNA - transfer translation (protein synthesis) <catalytic>rRNA - ribosomal translation (protein synthesis) regulatory mRNA - messenger Primary Function(s)Types of RNAs 10BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 RNA Structures • RNA forms complex 3D structures • Mainly "single-stranded" - but: • Single RNA strandscan self-hybridize to form Base-paired regions 11BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Levels of RNA Structure Like proteins, RNA has primary, secondary, and tertiary structure (& quaternary structure, too) 1. Primary structure = Ribonucleotide sequence 2. Secondary structure = Helix vs turn (base-paired vs single-stranded) Note: in RNA, helices often involve long-range interactions 3. Tertiary structure = 3D structure (also due to long-range interactions) 4. Quaternary structure = complex of 2 or more RNA strands Rob Knight Univ Colorado This slide has been changed 12BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Common structural motifs in RNA • Helices • Loops • Hairpin • Interior • Bulge • Multibranch • Pseudoknots • Tetraloops Fig 6.2 Baxevanis & Ouellette 2005 #25 - More RNA Structure & BCB 544 Projects 10/19/07 BCB 444/544 Fall 07 Dobbs 5 25BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 A U A U A=U A=U Basepair ΔG = -1.2 kcal/mole A U U A A=U U=A ΔG = -1.6 kcal/mole Basepair What gives here? C Staben 2005 Energy minimization: What are the rules? This is a new slide 26BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Energy minimization calculations: Base-stacking is critical AA UU -1 .2 CG GC -3 .0 AU or UA UA AU -1 .6 GC CG -4 .3 AG, AC, CA, GA UC, UG, GU, CU -2 .1 GU UG -0 .3 CC GG -4 .8 XG, GX YU, UY 0 - Tinocco et al. C Staben 2005 This is a new slide 27BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Ab initio RNA Structure Prediction: Uses Nearest-neighbor parameters • Most methods for ab initio prediction (free energy minimization) use nearest-neighbor energy parameters (derived from experiment) for predicting stability of an RNA secondary structure (in terms of ΔG at 37°C) & most available software packages use same set of parameters - Mathews, Sabina, Zuker This is a new slide 28BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Ab Initio Energy Calculation • Search for all possible base-pairing patterns • Calculate total energy of each structure based on all stabilizing and destabilizing forces Fig 6.3 Baxevanis & Ouellette 2005 Total free energy for a specific RNA conformation = Sum of incremental energy terms for: • helical stacking (sequence dependent) • loop initiation • unpaired stacking (favorable "increments" are < 0) This slide has been changed 29BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Dot Matrices • Can be used to find all possible base pair patterns • Compare input sequence to itself and put a dot where there is a complimentary base R Knight 2005 30BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Dynamic Programming • Finding optimal secondary structure is difficult - lots of possibilities • Compare RNA sequence with itself • Apply scoring scheme based on energy parameters for base stacking, cooperativity, and penalties for destabilizing forces • Find path that represents most energetically favorable secondary structure This slide has been changed #25 - More RNA Structure & BCB 544 Projects 10/19/07 BCB 444/544 Fall 07 Dobbs 6 31BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Problem with DP Approach • DP returns SINGLE lowest energy structure • There may be many structures with similar energies • Also, predicted secondary structure is only as good as energy parameters used • Solution: return multiple structures with near optimal energies 32BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Popular Ab Initio Prediction Programs • Mfold • Combines DP with thermodynamic calculations • Fairly accurate for short sequences, less accurate as sequence length increases • RNAfold • Returns multiple structures near predicted optimal structure • Computes larger number of potential secondary structures than Mfold, so uses a simplified energy function 33BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 2 - Comparative Prediction Approaches • Use multiple sequence alignment • Assume related sequences fold into same secondary structure 34BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Co-variation patterns in MSAs are critical • RNA functional motifs are conserved • To maintain RNA structure during evolution, a mutation in a base-paired residue must be compensated for by a mutation in residue with which it pairs • Comparative methods search for co-variation patterns in MSAs 35BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Consensus Structures • Predict secondary structure of each individual sequence in a MSA • Compare all structures and try to identify a consensus structure 36BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Popular Comparative Prediction Programs Two main types: 1. Require user to provide MSA • RNAalifold 2. No MSA required • Foldalign • Dynalign #25 - More RNA Structure & BCB 544 Projects 10/19/07 BCB 444/544 Fall 07 Dobbs 7 37BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 RNAalifold • Requires user to provide MSA • Creates a scoring matrix combining minimum free energy and co-variation information • DP used to identify minimum free energy structure 38BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Foldalign • User provides pair of unaligned RNA sequences • Constructs alignment & computes conserved structure • Suitable only for relatively short sequences 39BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Dynalign • User provides two unaligned input sequences • Calculates possible secondary structures using algorithm similar to Mfold • Compares multiple structures from both sequences to find a common structure 40BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 3 - Popular Programs that use Combined Computational Experimental Approaches • Mfold • Sfold • RNAStructure • RNAFold • RNAlifold 41BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 SL X SL Y SL Z SL Y SL Z SL X SL Y SL Z SL X SL Y SL Z SL X Mfold -54.84 kcal/mol RNAstructure -71.3 kcal/mol RNAfold -80.16 kcal/mol Sfold -51.14 kcal/mol Comparison of Predictions for Single RNA using Different Methods JH Lee 2007 42BCB 444/544 F07 ISU Dobbs #25 - More RNA Structure & BCB 544 Projects 10/19/07 Mfold plus constraints -54.84 kcal/mol Mfold -126.05 kcal/mol Comparison of Mfold Predictions: -/+ Constraints JH Lee 2007