1 / 103

Introduction to the RNA Folding Problems

Introduction to the RNA Folding Problems. C.-M. Chen thanks Shi-Jie Chen at University of Missouri-Columbia for providing the materials. What is RNA?. RNA Primary Structure. (- e). Structure of RNA backbone. 5'. (- e). (- e). (- e). 3'. RNA chain directionality: 5 ' 3 '

ross
Download Presentation

Introduction to the RNA Folding Problems

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Introduction to the RNA Folding Problems C.-M. Chen thanks Shi-Jie Chen at University of Missouri-Columbia for providing the materials

  2. What is RNA?

  3. RNA Primary Structure (-e) Structure of RNA backbone 5' (-e) (-e) (-e) 3' • RNA chain directionality: 5'3' • Backbone carries charge (-e) on each nucleotide • Formation of an RNA structure requires cations

  4. Four Types of Bases Adenine (A) Uracil (U) Guanine (G) Cytosine (C) Purines Pyrimidines

  5. Waston-Crick canonical base pair Bases Pairs A U C G

  6. RNA = Ribonucleic acid = Polynucleotide P O c c c O P each bond ~ 1.5 A nucleotide structure We need 7 torsional angles per nucleotide to specify the 3D structure of an RNA

  7. Torsion angles are like rotamers of protein side chain

  8. RNA Structure

  9. RNA secondary structure = base pairing U Base stacking provides stability

  10. RNA Helix A-form RNA helix; Grooves Binding sites

  11. RNA Secondary Structure Motif

  12. The Definition of RNA Secondary and Tertiary Structure A graphic representation of base pairing

  13. Secondary Structure Contact (Base Pair) Tertiary Structure Contact (Base Pair)

  14. An RNA Secondary Structure

  15. RNA Pseudoknot

  16. RNA Tertiary Structure tRNA 2° Structure tRNA 3° Structure

  17. Tertiary Interactions that Fold tRNA

  18. Tertiary Interactions are Critical to Functions TAR bound form free form • Base triplet is the key for TAR function • (to open up the major groove for protein binding)

  19. What does RNA do?

  20. The Central Dogma transcription splicing mRNA tRNA translation ribosome DNA pre mRNA mRNA protein

  21. RNAs are Critical to Cellular Functions • Messenger RNA (mRNA) • codes for protein • Small nuclear RNAs (snRNA) • splice mRNA in nucleus • Transfer RNA (tRNA) carries • amino acid to ribosome • Ribosomal RNA (rRNA) is the • integral part of the ribosome

  22. The RNA Folding Problem

  23. Goal:To predict structure stability folding kinetics function of an RNA from its sequence Ultimate goal:To predict RNA function from its sequence

  24. Why Study RNA Folding Stability? • mRNA has sufficient time to equilibrate before translation is initiated equilibrium stability Stability is tied to function Ribosome binds here mRNA

  25. Why Study RNA Folding Kinetics? B Aconversion is slow as compared with the translational process Conformation B is kinetically trapped. Kinetics is tied to Function

  26. RNA Folding Energetics

  27. Folding Free Energy of Secondary Structure Folding free energy: ΔG = G ( secondary structure) - G ( ) ΔG = ΔH – T ΔS

  28. Stabilizing Forces for RNA Secondary Structure • Restriction of rotor ΔS (strong)< 0 • Base stacking ΔH (strong)< 0 • Hydrophobic effectΔS (weak) > 0 • Hydrogen bondingΔH (weak)< 0 Stability =Stacking-Restriction of rotor

  29. ΔG for a Secondary Structure Nearest-Neighbor Model • stabilitystackinglocal interaction between adjacent base pairs • example( 1M Na+, 37°C) 3' 5' c G c G G c A A c G G c G c 5' 3' ΔGtot = -6.6 kcal/mol

  30. Experimental Thermodynamic Parameters ∆Hfor base stacks

  31. ∆Sfor base stacks

  32. ∆Sfor loops

  33. RNA Secondary Structure Prediction

  34. Phylogenetic Method • Structure is more conserved than sequence • Compare sequences of RNAs with the same function from different species • Find covariance bases that conserve base pairs (W-C pairs: G-C, A-U) c G UGGUGCACCA A U UAGUC GACUA G c G c UGGUG GACCA U A Known structure

  35. Free Energy minimization • Particularly useful if only one sequence is available • For all the possible secondary structures for a given sequence, find the structure with the min ΔG a. Algorithm: lowest ΔG for all 5-nt 6-nt full sequence b. Usually have multiple optimal structures http://www.bioinfo.rpi.edu/~zukerm/rna/mfold-3.1.html

  36. Ion-Dependence of RNA folding

  37. H2O and metal ions are integral parts of nucleic acid structure

  38. [Na+] stabilizes secondary structure From Tinoco & Bustamante,JMB (1999) 273,271 • [Na+] by 10 folds Tm by 3.8 C

  39. Multivalent Ions Stabilize Tertiary Fold Pseudoknot

  40. [Mg2+] Stabilization Na+ = 200mM + 50 From Tinoco & Bustamante,JMB (1999) 273,271

  41. RNA conformational changes are ion-dependent tRNA

  42. RNA folding kinetics strongly depends on ions Na+ Secondary structure Mg2+ Tertiary structure Metal ion binding sites can be formed before, during, or after the formation of the tertiary structure

  43. RNA Folding vs Protein Folding

  44. Part II. Basic Thermodynamics Thermodynamics is for systems in thermal equilibrium

  45. The population (concentration) of molecules in (macro)state A is determined by the free energy Low free energy = High population

  46. Relative population between U & N: • FU - FN= work required to convert U to N U/(U+N) N U

  47. U • Stability F G ΔG More stable N Larger ΔG

  48. Conformational fluctuation [A] A1 A A GA GA A1 A1 A2 t t

  49. Cooperativity (Two-State-ness) Two-State (U & N) Transition Corbett & Roche, Biochemistry 23, 1888 (1984)

More Related