itc troubleshooting - atomika teknik · itc troubleshooting what can go wrong? gamze karakullukÇu,...
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ITC TroubleshootingWhat can go wrong?
Gamze KARAKULLUKÇU, MScApplication Engineer
gamze@atomikateknik.com | +90 549 745 30 04
ITC Troubleshooting
The Symptoms:
Baseline position
Baseline drift
Non sigmoidal binding isotherm
Stoichiometry far from 1 or integer value
Split (oscillating) peaks
Heat to Sample Cell = Negative Baseline Deflection
Heat to Reference Cell = Positive Baseline
Deflection
Cooling the Sample Cell = Positive Baseline
Deflection
Cooling the Reference Cell = Negative Baseline
Deflection
0
5
DP
DP
Temperature effects
Some instrumental factors
1. Lab conditions
2. Syringe
3. Stir speeds
4. Temperature setting
5. Plunger tip
0
5
DP
DP
Lab condition influence
0
5
DP
DP
Bent syringe
0
5
DP
MicroCal iTC200 - Syringe holding nut loose
DP
Syringe height
0
5
DP
Faster Stirring
Stir speeds
10 20 30 40 50 60 70
9.8
10.0
10.2
10.4
10.6
10.8
Ba
se
line
Po
sitio
n W
ith
Stirr
ing
(u
ca
l/se
c.)
Experimental Temperature (Deg. C)
Cell848
Cell849
Cell855
Cell857
Cell859
Cell860
Cell862
Cell864
Cell865
Cell866
Cell868
Cell869
###
###
Reference Power = 11 ucal/sec for all data shown below!
Baseline temperature dependence
Reference power=11 ucal/sec for all data shown
below!
Non instrumental factors
Baseline position is the first diagnostic for data
quality-information on:
Air bubbles
Cell cleanliness/“Sticky” proteins
Time between injections
0
5
DP
DP
Bubbles
0.00 20.00
9.6
9.8
10.0
Time (min)
µc
al/
se
c
De-gassing problem
0.00 20.008.28.38.48.58.68.78.88.99.09.19.29.39.49.59.69.79.89.9
Time (min)
µc
al/se
c
Before experiment:
De-gas, use proper filling technique (MicroCal iTC200)
During experiment:
Reload
Gently tap the bottom of the cell with the loading syringe
Re-insert injection syringe
The Cure
-8.33 0.00 8.33 16.67 25.00 33.33 41.67 50.00 58.33 66.67
2
4
6
8
10
12
14
16
Time (min)
µca
l/se
c
Not long enough between injections
Time (min)
mca
l/s
0.00 33.33 66.67 100.00 133.33 166.67
14
15
16
17
18
19
Time (min)
µca
l/se
c
Not long enough between injections
Time (min)
mca
l/s
Increase the time between the injections
This can be done ‘on the fly’ by going to the advanced
experimental tab and ‘update’ the change to injection
parameters > spacing (secs)
The Cure
“Sticky” proteins or cleanliness
0.00 8.33 16.67 25.00 33.33 41.67 50.00
-4
-2
0
2
4
6
Time (min)
µca
l/se
c
-16.67 0.00 16.67 33.33 50.00 66.67 83.33 100.00 116.67 133.33
14
16
Time (min)
µcal/sec
-33.33 0.00 33.33 66.67 100.00 133.33 166.67 200.00 233.33
10
12
14
16
Time (min)
µcal/sec
0.00 16.67
9.38
9.40
9.42
9.44
9.46
9.48
MESdegasb98RAW_CP
MESdegasb98BASE
MESdegasb113RAW_CP
MESdegasb113BASE
Time (min)
µcal/sec
Time (min)
mcal/
s
Dirty cell
Clean the cells with Contrad 70 (Decon 90) and repeat
If the problem persists after cleaning then may have to
“do biochemistry”
Change solution conditions e.g. pH, salt, co-solutes
Change protein construct
The cure
0.00 10.00 20.00 30.009.10
9.20
9.30
9.40
Data1RAW_cp
###
Time (min)
µcal/sec
Nice data but dirty cell
Examine effect on stoichiometry and if error is not
acceptable:
Reload
Clean cell
The cure
Non sigmoidal binding isotherm
No Binding
No Heat
Buffer mismatch
More than one binding event
Effect of DMSO mismatch
-5 0 5 10 15 20 25 30 35 40 45 50 55
0
1
2
3
4
5
6
7
C: 2 % mismatch in DMSO: syringe: 20 ml DMSO added to 1.0 ml buffer; cell: buffer only (no DMSO).
B: Slightly mismatched solution: syringe: 20 ml DMSO added to 1.0 ml buffer;
cell: 280 ml DMSO added to 14 ml buffer.
A: Matched solution: both cell & syringe have same solution (280 ml DMSO added to 14 ml buffer).
Time (min)
µcal/sec
2% DMSO into
2% DMSO-same stock
2% DMSO into
2% DMSO-separate stocks
2% DMSO into
0% DMSOm
ca
l/s
Buffer mismatch-no dialysis
0 20 40 60 80 100 120 140 160 180
-0.5
0.0
0.5
1.0
1.5
2.0
2.5
without dialysis
with dialysis
Time (min)
µca
l/se
c
The cure
Dialyze, or use desalting columns if possible
Check for additives that are in not in both cell and syringe. Also, ask what was sample purified from e.g. was protein lyophilized in buffer and not dialyzed?
Check pH of final solutions-should differ by less than 0.1 pH units. This issue is common when working with high concentrations of ligand-e.g. 500 mM and above-weak binding
-16.67 0.00 16.67 33.33 50.00 66.67 83.33 100.00 116.67 133.33 150.00
7.5
8.0
8.5
9.0
Experiment 2:
ligand into protein 2
Time (min)
µca
l/se
c
Control: ligand
into buffer
Experiment 1:
ligand into protein
1
No
saturation
or protein
not
matched
to ligand
Effect of buffer mismatch and/or low C
value
Time (min)
mca
l/s
Effect of buffer mismatch and/or low C
value
-16.67 0.00 16.67 33.33 50.00 66.67 83.33 100.00 116.67 133.33
29.0
29.5
30.0
30.5
31.0
31.5
Time (min)
µca
l/se
c
Time (min)
mca
l/s
See “mismatch” plus binding may be weaker than you
think
Increase sample concentrations
The cure
ITC: low heat
Heats for
experiment
same as control
0.00 16.67 33.33 50.00 66.67 83.33
4.26
4.28
4.30
4.32
4.34
4.36
4.38
4.40
4.42
4.44
4.46
4.48
4.50
4.52
Time (min)
µcal/sec
Control: ligand into buffer
ExperimentL ligand into protein
Change experimental temperature by at least 10ºC
and/or
Increase sample concentration
The cure
Unexpected stoichiometry
0.00 33.33 66.67 100.00 133.33 166.67
18.6
18.7
18.8
18.9
19.0
19.1
19.2
19.3
Time (min)
µca
l/se
c
Increase protein concentration or decrease ligand
concentration
Make sure protein is active
Also –c-value is high so we may want to change initial
[Lig]/[Prot] ratio
The cure
Split (oscillating) peaks
-8.33 0.00 8.33 16.67 25.00 33.33 41.67 50.00 58.33
-4
-2
0
2
Time (min)
µca
l/se
cOscillating
signal:
Power below 0
Time (min)
mcal/s
Instrument reference power too low
Clean sample and reference cell and increase ‘reference
power’ in advanced experimental tab
Note that ITC data can have exothermic and endothermic
peaks in same injection.
The cure
Insoluble Ligands
‘One site’ interactions are symmetrical and as such the
ligand can be put in the cell and the protein in the syringe
Reverse titration
-1.5
-1.0
-0.5
0.0
-10 0 10 20 30 40 50 60 70 80 90 100 110 120
Time (min)
µca
l/se
c
0.0 0.5 1.0 1.5 2.0 2.5
-12
-10
-8
-6
-4
-2
0
2
Molar Ratio
kca
l/m
ole
of in
jecta
nt
-0.8
-0.6
-0.4
-0.2
0.0
-10 0 10 20 30 40 50 60 70 80 90 100
Time (min)
µca
l/se
c
0.0 0.5 1.0 1.5 2.0 2.5
-14
-12
-10
-8
-6
-4
-2
0
2
Molar Ratio
kca
l/m
ole
of in
jecta
nt
Parameter Ligand in syringe Ligand in cell
N 0.99 0.97
KD 104 nM 105 nM
DG -9.4 kcal/mol -9.4 kcal/mol
DH -11.9 kcal/mol -12.4 kcal/mol
TDS -2.5 kcal/mol -3.0 kcal/mol
29.5µM Protein titrated with
1.1mM Compound
11.5µM Compound titrated with
179µM Protein
Cure-reverse the titration
Stoichiometry
“N” is the average number of binding sites per mole of
protein in your solution, assuming:
that all binding sites are identical and independent
that you have pure protein (and ligand)
that you have given the correct protein and ligand
concentrations
that all your protein is correctly folded and active
Stoichiometry not expected value
If stoichiometry less than expected value:
Protein concentration lower than you think
Ligand concentration higher than you think
Impure ligand and/or macromolecule
Misfolded protein (esp. for recombinants)
If 0.5, 1 ligand binding to 2 macromolecules (dimer?)
Binding does not fit simple independent model
Stoichiometry not expected value
If stoichiometry greater than expected value
Multiple binding sites on protein
Protein concentration higher than you think
Ligand concentration lower than you think
Binding does not fit simple independent model
ITC general conclusions!
Take care with sample preparation
Use appropriate run parameters
Check initial baseline position
Perform water-water titration to remove instrumental issues
De-gassing
Load carefully
Clean cell thoroughly, Clean cell thoroughly, Clean cell thoroughly
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