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RNA DBP: modeling and
dynamics of RNA
Russ Altman
Vijay Pande
Outline
 Introduction to RNA
 Introduction to tetrahymena
intron
 Challenges in DBP
 Simulation of RNA
 Discussion
Central Dogma of Biology
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Growing
protein
chain
RNA Function
DNA
RNA polymerase
Messenger
RNA
20 Transfer RNA
(tRNA) charged with
amino acids
Messenger
RNA
Ribosome
(rRNA)
 0. Like DNA, RNA contains 4 subunits
(AUGC). It is less stable than DNA, so is not
a storage media.
 1. the DNA code a gene is copied into
messenger RNA (mRNA)
 2. mRNA is the version of the genetic code
translated at the ribosome.
 3. the ribosome is made up RNA (ribosomal
RNA or rRNA)
 4. The individual amino acids are brought to
the ribosome, as it reads the mRNA, by
molecules called transfer RNAs (tRNA)
RNA has 3D structure
Primary
Structure
AUUCGGCGACGAAU
AUUCG G G
UAAGC A
C
Secondary
Structure
Tertiary Structure
RNA folding is usually nested
1
76
Growing
protein
chain
RNA Function
DNA
RNA polymerase
Messenger
RNA
20 Transfer RNA
(tRNA) charged with
amino acids
Messenger
RNA
Ribosome
(rRNA)
RNA polymerase
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Growing
protein
chain
RNA Function
DNA
RNA polymerase
Messenger
RNA
20 Transfer RNA
(tRNA) charged with
amino acids
Messenger
RNA
Ribosome
(rRNA)
http://www.wadsworth.org/BMS/
http://www-smi.stanford.edu/projects/helix/ribo.html
QuickTime™
and a
QuickTime™
and a
TIFF (Uncompressed)
decompressor
TIFF (Uncompressed)
decompressor
are needed
see this to
picture.
aretoneeded
see this picture.
Genetic Code (T=U here)
(e.g. Tyrosine = UAU or UAC)
Growing
protein
chain
RNA Function
DNA
RNA polymerase
Messenger
RNA
20 Transfer RNA
(tRNA) charged with
amino acids
Messenger
RNA
Ribosome
(rRNA)
mRNA (yellow) interacting with
A and P site tRNA anticodons
Growing
protein
chain
RNA Function
DNA
RNA polymerase
Messenger
RNA
20 Transfer RNA
(tRNA) charged with
amino acids
Messenger
RNA
Ribosome
(rRNA)
Biological significance of RNA
folding?
 mRNA takes on 3D structure as it is
produced (cotranscriptional folding),
and this may affect:




stability within cell
speed of translation
frequency of translation
interactions with other molecules
(regulation of other mRNA, e.g.)
 The possibility that an RNA takes on a
3D structure that is recognized or used
by the cell constantly vexes biologists
who see unexpected phenomena.
Tetrahymena Intron
Dan Herschlag, Biochemistry
PI
Biological Aims
1. Determine mechanism of rapid
electrostatic collapse, structure of
collapsed particle, physical forces
2. Determine spectrum of intermediates
that are formed, and dynamic
properties.
3. Determine landscape for folding, and
features critical for driving down
native pathways.
Experimental Modalities
 Hydroxyl radical footprinting
(equilibrium and time-resolved)
 Small angle x-ray scattering
(equilibrium and time-resolved)
 Single molecule fluoresence energy
transfer (FRET)
 Single molecule force measurements
 Biochemical modifications to perturb
structure and folding (introduce point
mutations or entire extra pieces)
Coarse Grained L-21 and P4P6 Gnomad
L-21, 409 atoms
RMSD 1.2Å
132 secs CPU (Xportal1)
P4P6, 409 atoms
RMSD 15Å
45 secs CPU (Xportal1)
Hydroxyl Radical Footprinting
+ •OH
Lot’s of smaller RNA
molecules
32P
Run on a Gel
The more surface
exposed nucleotides
will be more reactive
A170
U169
G168
G167
A166
U165
A164
C163
A162
A161
G160
C159
U158
A157
C156
G155
U154
U153
C152
G151
C150
C149
C148
A147
C146
G145
C144
Site specific kinetics



k1
k2
k1
k2
U  I1  F


Small angle x-ray scattering
(SAXS)
Single molecule measurements
Biochemical modifications
Computational Challenges
 Moving to mesoscale for computability
 Optimization of models to be
consistent with data
 Constrained dynamics (drive trajectory
through milestone structures)
 Data visualization and ensemble
mapping (data is aggregate, models
are single)