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? Predicted topologies and predicted AG values:- Inside -OutsideTM-helix (IN->OUT) TM-helix (OUT->IN) Signal peptideTOPCONSOCTOPUSPhiliusPolyPhobiusSCAMPISPOCTOPUSPDB-homology***No homologous TM proteins detected***20406060Consensus prediction (TOPCONS):TOPCONSReliability10.91010860+20AG (kcal/mol)80100120140High-resolution image20406080Position100120140High-resolution image. kDa55Cysless35+P2010+UF16CM18CM36C+P+ MTSESNEM+++mPEG5K+E39CK72CV51C++ MTSESNEM+++ MPEG5KL860Y96C|D1066+PMTSESNEM+ + + MPEG5KG125CF139CR143CP++++ MTSESNEM+++ MPEG5KFig. 1 SCAM analysis of AlaE. Western blot analysis of whole celllysates from cells harbouring plasmids expressing cysteine-free('Cysless') or single cysteine variants of alaE with and without treatmentwith NEM, MTSES and mPEG5K. PEGylated (P) and unmodified proteinare indicated with arrows.OutsideMembraneDeepTMHMM - Most Likely Topology | Type: alpha TMProbabilityInside0204060801001201401.00.80.60.40.2DeepTMHMM - Posterior Probabilities0.020406080SequenceMembraneInsideG100 120Outside140

SCAM analysis predicts whether an amino acid in a transmembrane protein is within the membrane,…

Answered: What further experiments are needed to…

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

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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?

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.

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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