What further experiments are needed to provide confidence that the structural data obtained from the SCAM analysis reflects the structure of a properly folded AlaE?
What further experiments are needed to provide confidence that the structural data obtained from the SCAM analysis reflects the structure of a properly folded AlaE?
Biochemistry
9th Edition
ISBN:9781319114671
Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Chapter1: Biochemistry: An Evolving Science
Section: Chapter Questions
Problem 1P
Related questions
Question
What further experiments are needed to provide confidence that the structural data obtained from the SCAM analysis reflects the structure of a properly folded AlaE?
Transcribed Image Text:Predicted topologies and predicted AG values:
- Inside -Outside
TM-helix (IN->OUT) TM-helix (OUT->IN) Signal peptide
TOPCONS
OCTOPUS
Philius
PolyPhobius
SCAMPI
SPOCTOPUS
PDB-homology
***No homologous TM proteins detected***
20
40
60
60
Consensus prediction (TOPCONS):
TOPCONS
Reliability
1
0.9
10
10
8
60
+
2
0
AG (kcal/mol)
80
100
120
140
High-resolution image
20
40
60
80
Position
100
120
140
High-resolution image.
Transcribed Image Text:kDa
55
Cysless
35
+P
20
10
+U
F16C
M18C
M36C
+P
+ MTSES
NEM
+++mPEG5K
+
E39C
K72C
V51C
+
+ MTSES
NEM
+++ MPEG5K
L860
Y96C
|D1066
+P
MTSES
NEM
+ + + MPEG5K
G125C
F139C
R143C
P
++
+
+ MTSES
NEM
+++ MPEG5K
Fig. 1 SCAM analysis of AlaE. Western blot analysis of whole cell
lysates from cells harbouring plasmids expressing cysteine-free
('Cysless') or single cysteine variants of alaE with and without treatment
with NEM, MTSES and mPEG5K. PEGylated (P) and unmodified protein
are indicated with arrows.
Outside
Membrane
DeepTMHMM - Most Likely Topology | Type: alpha TM
Probability
Inside
0
20
40
60
80
100
120
140
1.0
0.8
0.6
0.4
0.2
DeepTMHMM - Posterior Probabilities
0.0
20
40
60
80
Sequence
Membrane
Inside
G
100 120
Outside
140
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