Protein-RNA interactions
As seen by structural biology


ecoli
Water
DNA
RNA
Protein
Lipids, sugars and
other small molecules
THE CELL
Molecular Art by David S. Goodsell

Structural biology techniques



DNA
RNA (rRNA,mRNA,tRNA)
Protein
Transcription
Translation
RNA Pol I
RNA Pol II
RNA Pol III
•RNA packaging, stability
•5’ capping, RNA editing
•splicing, alternative splicing
•3’ end processing
•(cleaveage and polyadenylation)
•export
RNA biogenesis
Gene expression program

•5’
•3’
Pre-mRNA
RNA binding proteins
RNA binding proteins control the fate of the pre-mRNA

RNA binding proteins
RBD
RNA Binding Domain
RRM/RBD/RNP
N
C
KH domain
N
C
dsRBM
N
C
Zinc binding
 proteins
cchc
cchc
ccch
N
C
N
C
N
C
RBD
protein-protein
Catalytic domain
SAM domain

RNA binding proteins of two types:
   - enzymes
polymerase, nuclease, modifying enzymes
   - binding proteins
protection, folding (chaperone), gene regulation

RNA binding proteins of two types:
- enzymes
polymerase, nuclease, modifying enzymes
- binding proteins
protection, folding (chaperone), gene regulation

Modular architecture of RNA-binding proteins
Taken from Lunde et al. Nat. Rev Mol. Cell Biol 2007


•Basic description
•Basic principles & Binding modes
•Thermodynamics
Protein-RNA interactions
As seen by structural biology

RNA-binding modules are often combined to perform
 multiple functional roles
Taken from Lunde et al. Nat. Rev Mol. Cell Biol 2007

Positive cooperativity in RNA-binding
Nrd1-Nab3.png


What information is recognized by proteins:
G
A
U
C
U
U
A
A
A
A
G
•5’
•3’
Recognition of RNA sequence
A-form duplex of RNA
•5’   3’
•A-U
•G-C
•C-G
•U-A
•A-U
•G-C
•C-G
•U-A
•A-U
•G-C
•3’   5’
Recognition of RNA shape

What recognition mode is used by proteins:
Rigid-body docking
+
Induced fit
+

0
Capping
7meGpppN=cap
Transcription
•5’UTR
•5’
•3’UTR
exon1
exon2
intron
•3’
Poly-A tail
•3’end processing
Splicing

Induced fit recognition
Examples


•5’cap binding protein, CBP20-CBP80
newrbdcap_04_0001
Mazza et al, EMBO J (2002)
CBP20-CBP80
Induced fit binding

Comparison with the struc- ture of uncomplexed CBC shows that cap binding induces co-operative
folding around the dinucleotide of some 50 residues from the N- and C-terminal extensions to the
central RNP domain of the small subunit CBP20.

CBP20-m7GpppG contacts
newrbdcap_05_0001 newrbdcap_05_0001
Induced fit binding

Rigid body docking
Examples


B2_3
Rigid-body docking
Viral B2 protein supresses RNAi by masking
dsRNA or siRNA.
Taken from Chao et al. Nat. Struct. Mol. Biol 2005

What recognition mode is used by proteins:
Rigid-body docking
+
Induced fit
+