Transcript exon f exon g

Human isoforms conformational dynamics
Conformations averaged over 2 replicates of 50-ns MD simulations
exon g
no f/g
d
f/g
e
i
I
j
1.0
0.5
0.0
10
210
215
220
5
Residue numbers
w. f
w. g
wt. f/g
0
RMSF (A)
n p
2.0
c
1.5
b
15
a
RMSF (A)
20
2.5
3.0
exon f
0
100
200
Residue numbers
300
225
Human isoforms conformational dynamics
exon f
exon g
F-helix
G-helix
no f/g
MAP kinase
insert
The removal of the helices F, G and the “MAP kinase insert” (helices α1L14 and
α2L14) allows for large amplitude motions of the A-loop.
Structural and functional role of exon f/g
exon f
Stabilizing F-helix
Exon f : D L W S V G C I M G E M V C H K I L F P G R D
Exon g : D I W S V G C I M G E M I K G G V L F P G T D
Anchor points for R- and C-spines
2.5
3.0
R228
K222
1.5
1.0
0.5
0.0
RMSF (A)
2.0
exon g
210
215
220
Residue numbers
225
Residues
predicted as
interacting
by JET2
Protein binding site prediction
exon f
exon g
no f/g
For questions
• X-ray structures?
 Yes more than 20, with interacting peptides or with inhibitors. 2 isoforms crystalized,
one with exon f, one with exon g; essentially no change between them
• What transcripts in Ensembl?
 Red or gold transcripts (protein coding). Gold transcripts and those with a CCDS
(Consensus Coding Sequence Set) have coding sequences that are well-supported
and are unlikely to change. Gold transcripts are identical between manual curation
from the VEGA/Havana set project and the Ensembl automatic annotation pipeline.
They are only available for human, mouse, and zebrafish.
http://www.ensembl.org/Help/View?id=143
For questions
•
Quality of the models
 Normalized DOPE score (Z-score): The DOPE score is an atomic distance-dependent statistical
potential based on a physical reference state that accounts for the finite size and spherical shape
of proteins by assuming a protein chain consists of noninteracting atoms in a uniform sphere of
radius equivalent to that of the corresponding protein. The normalized version (N-DOPE) was
used instead of the raw score; it is a standard score (Z-score) derived from the statistics of raw
DOPE scores. The mean and standard deviation of the DOPE score of a given protein is
estimated from its sequence. The mean score of a random protein conformation is estimated by
a weighted sum of protein composition over the 20 standard amino acid residue types, where
each weight corresponds to the expected change in the score by inserting a specific type of
amino acid residue. The weights are estimated from a separate training set of 1,686,320 models
generated by MODPIPE. Eramian et al Protein Sci. 2008 Nov;17(11):1881-93.
 G-factors from PROCHECK: The G-factor provides a measure of how "normal", or alternatively
how "unusual", a given stereochemical property is. In PROCHECK it is computed for properties
reflecting the torsion angles and the covalent geometry. The G-factor is essentially just a logodds score based on the observed distributions of these stereochemical parameters. When
applied to a given residue, a low G-factor indicates that the property corresponds to a lowprobability conformation. Engh RA and Huber R (1991). Accurate bond and angle parameters for
X-ray protein structure refinement. Acta Cryst., A47, 392-400.