1 Ref: Ch. 5 Mount: Bioinformatics i.Protein synthesis: ribosomal RNA transfer RNA messenger RNA...

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Ref: Ch. 5 Mount: Bioinformatics

i. Protein synthesis:

ribosomal RNA

transfer RNA

messenger RNA

ii. Catalysis

e.g. ribozymes

iii. Regulatory molecules

17.1 Roles of RNA Molecules

2iii. Regulatory molecules

Nucleic acid interactions - complementary base pairing

Protein interactions

- Shape

- Charge

- Hydrophobicity

17.2 Interactions of RNA Molecules

3- Hydrophobicity

Self-complementary regions undergo complementary base pairing

- depends on the formation of loops

- 5’ end of one part of the molecule aligned with 3’ end of other part

17.3 Shape of RNA Molecules

5’

3’

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17.4 Types of Structures

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17.4 Types of Structures

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17.4 Types of Structures

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17.4 Types of Structures

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17.4 Types of Structures

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17.4 Types of Structures

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17.5 Complex Interactions

Pseudoknot

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17.5 Complex Interactions

Kissing hairpins

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17.5 Complex Interactions

Hairpin-bulge contact

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1. The most likely structure is the most stable structure

2. Long regions of base pairing are more stable than short regions

3. GC base pairs are more stable than AU base pairs

4. Energies are estimated from experiments with synthetic RNA molecules

17.6 Principles for Predicting RNA Secondary Structure

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Energies are estimated from experiments with synthetic RNA molecules

5. The structure does not have knots

6. Loops need to contain at least 4 nucleotides

5’

3’

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Note:

• Many structures are possible• Formation of some loops prevents

formation of other loops• The stabilising effect of paired regions

is balanced against the destabilising effect of unpaired regions

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The stabilising effect of paired regions is balanced against the destabilising effect of unpaired regions

Sequence is drawn around circumference of circle

Arcs connect paired bases

Arcs don’t cross

(unless pseudoknots formed)

17.7 Circle Plot

17(unless pseudoknots formed)

Squiggle plotCircle plot

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WAG (Web Angis GCG)

RNA secondary structure

e.g. mfold

Input file: VapHGRNA

Output: VAPHGRNA MFOLD

Use Plotfold (from WAG) to display output

Save as GIF

17.8 ANGIS Programs

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Self-cleaving RNA molecules

Catalytic activity depends on 2o structure

17.9 Ribozymes

Lehninger Principles of Biochemistry 3rd Edition Nelson & Cox

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glmS gene produces enzyme GlmS

GlmS RNA is a ribozyme – can cleave itself

Ribozyme activity is greatly increased by the product of reaction catalysed by GlmS

Product of GlmS enzyme shuts off synthesis of GlmS enzyme

17.10 Regulatory RNA - glmS

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Cech (2004) Nature 428:263

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CsrA protein binds to specific mRNAs and prevents their translation

CsrB RNA is an antagonist of CsrA

- has 18 binding sites for CsrA protein

CsrA protein binds to CsrB and is not available to bind to the specific mRNAs

17.11 Regulatory RNAs – csrA, csrB

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Romeo 1998 Mol. Microbiol. 29:1321-1330

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RNA homologues maintain secondary structure

- covariation of paired bases

17.12 Evolutionary Relationships

5’

3’

A

U

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Analysis of sequences of homologues for covariation can be used to predict secondary structure

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Types of secondary structure

Principles for prediction of secondary structure

mfold program

Circle and squiggle plots

Secondary structure of regulatory RNA molecules

Covariation of paired bases in evolution

17.13 Summary