1. Study of the interaction between Abl
kinase domain and Gleevec inhibitor
Authors: Alec Elder, Sarah Moser, Molly Fields
CHM 33901 Biochemsitry Laboratory
Section: 1, Group: 2
January 13, 2015 – April 28, 2015
Abstract
Gleevec, an important cancer treatment drug, inhibits the Abelson kinase domain
to stop uncontrolled cell growth. In some patients the treatment has stopped
working or had no effect at all. Gleevec cannot bind to an Abelson kinase (Abl)
domain that has acquired mutations. This finding is very important for future
cancer treatment, specifically in chronic myelogenous leukemia (CML). To study
the effects of mutations in the Abelson kinase domain that effect Gleevec binding
we used; PCR to amplify the mutation of interest, protein purification techniques,
and Bradford/kinase assays to determine protein concentration and kinase activity
respectively. Our results did supportour hypothesis, but with small statistical
significance; Gleevec will have less inhibition on the mutant Abl- S417Y
compared with the wild type Abl, but due to impure protein samples of both WT
and mutant Abl the concentration of target protein was uncertain.
Introduction
Tyrosine kinases are associated with
signal transduction. One particular tyrosine
kinase, Abelson (depicted below) is tightly
regulated. It is auto-inhibited at its N-
terminus and the default activity setting is
off. Abl’s break cluster region (BCR), part
from chromosome 9 and part from
chromosome 22,
results in a mutant
gene called BCR-ABL.
The protein it encodes,
Bcr-Abl, includes the
kinase domain of c-Abl
but lacks the part
responsible for auto-
inhibition. The loss of
the residues
responsible for auto-inhibition, results in the
kinase being permanently on. This mutation
is responsible for uncontrolled cell
proliferation, which can lead to cancer.
Its inhibition has been a success in
the treatment of chronic myelogenous
leukemia. Abl Tyrosine kinase inhibitor
imatinib, also known as Gleevec, works by
inhibiting Bcr-ABL. It binds to the ATP-
binding site and in the nearby hydrophobic

2. pocket in the inactive conformation of the
Abl kinase domain (Taylor, 2010).
Eventually, some CML patients develop a
resistance to Gleevec and a few others do
not respond to Gleevec at all. The resistance
to Gleevec has been linked to mutations in
the ABL kinase domain. A mutation would
make the binding of Gleevec to the binding
sight unstable. Over fifty different
mutations, including single amino acid point
mutations have been identified
(Taylor,2010).
In this experiment we use Abl kinase
as a model for the full-length Bcr- Abl
protein. Abl kinase lacks the N-terminal Abl
regulation domains and is therefore
constitutively active. We expressed and
purified WT Abl kinase domain and used
site-directed mutagenesis to make a DNA
expression vector for S417Y mutants. This
mutant and H396P have been identified in
patients with Gleevec resistance.
We determined whether S417Y
mutation in the BCR-ABL gene confers
Gleevec resistance using an in vitro kinase
assay by observations in the kinase activity
in Wild type Abl and S417Y mutant Abl
domains, in the presence and absence of
Gleevec inhibitor. We evaluate crystal
structures to understand the mechanisms by
which Bcr-Abl mutations block drug
activity.
Methods
Primer design
We designed a primer for the Abl
kinase domain mutant S417Y for use in
polymerase chain reaction by making a
codon change in the middle of a 15-20
codon sequence. Our primer resides at the
674 bp to 698 bp of the wild type (WT) Abl
sequence. The primer melting temperature
was determined from the G-C base pair
percentage content and a GC clamp applied
to the 3’ end. The concentration of the
primers was determined by measuring the
optical density at 260 nm on the UV
spectrophotometer. Using the concentration
found a 25μM stock solution of the primers
was made to be used in the PCR reactions.
Polymerase Chain Reaction
The polymerase chain reaction
(PCR) to make the chimera DNA was
carried out in two reactions per mutant with
both reactions containing deionized water,
the pET28a-Abl plasmid and GoTaq Green
Master mix (2x). In reaction one, T7
promoter primer (25μM) and mutant S417Y
reverse primer (25μM) were added and in
reaction two T7 terminator primer (25μM)
and mutant S417Y forward primer (25μM)
were added. These samples were placed in a
thermocycler set to a 50OC annealing
temperature and went through 30 cycles.
After the cycles completed, the samples
were run on a 1% agarose gel for analysis.
Qiagen QIAquick PCR purification kit was
used to purify the samples and a final PCR
was run in a thermocycler at 45OC annealing
temperature containing the two purified
PCR reactions from above, deionized water,
GoTaq Green Master Mix, T7 promoter
primer (25μM) and T7 terminator primer
(25μM) to make the full length S417Y
mutant of 1114 bps. This final PCR reaction
was analyzed on a 1% agarose gel and
purified using the Qiagen QIAquick PCR
purification kit.
Xbaland xhol enzyme digest
An Xhol/Xbal double digest was
carried out by taking the final purified
S417Y mutant, deionized water, 1X
CutSmart Buffer and the Xhol/Xbal
enzymes and incubated in a 37OC water
bath. We applied the same digest to the
vector using miniprep DNA, deionized
water, 1X CutSmart Buffer and the
Xhol/Xbal enzymes. The digests were run
on a 1% agarose gel and the gel excised of

3. the insert S417Y mutant. The gel slices
containing the mutant were purified using
the Qiagen QIAquick Gel Extraction Kit.
Ligation and transformation
Ligation reaction included the
vector, insert, 2X Rapid Ligation buffer and
T4 DNA ligase. A negative control was also
ligated using vector, deionized water, 2X
Rapid Ligation buffer and T4 DNA ligase.
Transformation into E.coli DH5α plasmid
was performed by using the ligation
reactions and the pET28a-Abl WT plasmid.
The mixture was incubated on ice, a heat
shock applied and S.O.C (Super Optimal
broth with Catabolite repression) media
added to each tube. Using sterile technique
the transformed cells were spread onto agar
plates and incubated at 37OC overnight and
re-streaked. For transformation of the
S417Y mutant we combined the mutant and
YopH plasmid to BL21DE3 cells and
performed the same transformation
procedure as the WT from there.
Isolation of S417YAbl mutant
plasmid
Qiagen QIAquick Miniprep Kit used
to isolate the plasmid DNA of the S417Y
Abl mutants. Another PCR carried out to
confirm the mutation in S417Y Abl with a
forward reaction containing miniprep DNA,
T7 promoter primer (0.8 μM), Big Dye 3.1
Polymerase MIx and deionized water, and a
reverse reaction containing miniprep DNA,
T7 terminator primer (0.8 μM), Big Dye 3.1
Polymerase Mix and deionized water. The
thermocycler was set to a 45OC annealing
temperature for 99 cycles.
Expression of Abl kinase in presence
of Yop phosphatase
LB/kan/strep was inoculated with the
culture of Abl and Yop bacteria and placed
in a 37OC shaker, while the optical density
was checked periodically at 600 nm until it
reached 1.0 OD. A sample was collected for
our SDS-PAGE analysis. IPTG
(isopropylthio-β-galactosidase) was added to
induce the protein overnight.
Buffer Preparation
Ni-affinity purification column
buffers: Ni-NTA binding buffer (50 mM
Tris, 300 mM NaCl, pH 7.8); Ni-NTA
washing (50 mM Tris, 300 mM NaCl, 30
mM imidazole, pH 7.8); and Ni-NTA
elution buffer (50 mM Tris 300 mM NaCl,
30 mM imidazole, pH 7.8). Dialysis buffer
(10X Tris-buffered saline (TBS) dialysis
buffer (200 mM Tris, 1.37 M NaCl, pH 7.5).
SDS-PAGE buffers: 1.5 M Tris-HCl (pH
8.8); 0.5 M Tris-HCl (pH 6.8); 10X Tris-
Glycine-SDS electrophoresis buffer made
using 20% SDS; and 10X Tris-Glycine (TG)
transfer buffer. 5X reducing protein loading
buffer (SDS sample buffer), Coomassie
staining solution (0.25% Coomassie
Brilliant Blue, 50% methanol, and 10%
glacial acetic acid), Fast destain solution
(40% methanol and 10% glacial acetic acid),
Slow destain solution (5% methanol and
10% glacial acetic acid), 10% ammonium
persulfate (APS), 40%
acrylamide/bisacrylamide solution, 20%
SDS solution, and TEMED
(tetramethylethylenediamine).
Cell lysis and isolation using Ni-NTA
resin purification
The WT Abl cells were lysed using
B-PER detergent and protease inhibitor
cocktail solution until homogenous.
Purification of the WT Abl domain using
Ni-NTA resin by affinity chromatography
was carried out in three stages of Ni-NTA
binding buffer added and collected, washing
buffer added and collected, and lastly
elution buffer added and collected. The
remaining WT Abl protein from the
purification was loaded into a dialysis
cassette and left to dialyze in TBS at 4OC

4. overnight. This step was also performed for
the S417Y mutant Abl.
Bradford Assay
The dialyzed solution was placed
into a 10kDa MWCO centrifugal
concentrator and spun down to concentrated
WT Abl protein. We quantified the protein
using a Bradford Assay of the standard
Bovine Serum Albumin. Coomassie
Brilliant Blue reagent was added to view the
protein samples in the spectrophotometer.
This step was also performed for the S417Y
mutant Abl.
SDS-PAGE
Preparation of the purification
samples included adding 2X sample loading
buffer to the samples to be run on the SDS-
PAGE gel. We ran two SDS-PAGE gels for
the WT and S417Y mutant both made with a
10% separating gel using deionized water,
1.5 M Tris-HCl (pH 8.8), 40%
acrylamide/bisacrylamide solution and 10%
SDS. The stacking gel contained deionized
water, 0.5 M Tris-HCL (pH 6.8), 40 %
acrylamide/bisacrylamide solution and 10%
SDS. After running the gels, we stained
them using Coomassie Brilliant Blue
staining solution to aid in analysis.
Kinase assay with or without Gleevec
present
A standard curve for the serial
dilutions was made using 1X assay buffer
and 1mM stock phosphate in 8 tubes and
doubled. The samples were prepared by
making the solutions a 1 mM ATP stock
using 10 mM ATP and 1x assay buffer, 1
mM ADP stock using 10 mM ADP and 1x
assay buffer, 10 ng/μL Coupling
phosphatase 4 from 100 ng/μL CP4 and 1x
assay buffer,0.33 μg/μL WT/S417Y mutant
protein by adding the protein and 1X assay
buffer, 0.75mM of peptide and 25 μM of
Gleevec inhibitor. 2 tubes contained the
negative control with ATP (0.2 mM),
peptide substrate (0.2 mM), CP4 (0.2μg), 1x
assay buffer, and DMSO. 2 tubes contained
the positive control with ADP (0.2mM),
peptide substrate (0.2 mM), CP4 (0.2μg), 1x
assay buffer and DMSO. 2 tubes contained
the WT Abl kinase - inhibitor with ATP (0.2
mM), peptide substrate (0.2 mM), CP4
(0.2μg), WT Abl (0.1 μg/μL) and DMSO. 2
tubes contained the WT Abl kinase +
inhibitor with ATP (0.2 mM), peptide
substrate (0.2 mM), CP4 (0.2μg), WT Abl
(0.1 μg/μL) and Gleevec inhibitor (0.5μM).
2 tubes contained S417Y mutant Abl kinase
- inhibitor with ATP (0.2 mM), peptide
substrate (0.2 mM), CP4 (0.2μg), S417Y
Abl (0.1 μg/μL) and DMSO. 2 tubes
contained S417Y mutant Abl kinase +
inhibitor with ATP (0.2 mM), peptide
substrate (0.2 mM), CP4 (0.2μg), S417Y
Abl (0.1 μg/μL) and Gleevec inhibitor
(0.5μM). Malachite Green Reagents A and
B were added to the tubes and the OD
observed to make the standard curve for the
kinase assay.
Crystal structure viewing and
modeling
PyMol was used to view the crystal
structure of Abl- S417Y and Gleevec.

5. Results
Fig. 1:Analysis of PCR reactions 1 & 2 on 1% Agarose gel for S417Y Abl mutants
lane 4:GoTaq (not purified) PCR reaction 1: ~743 bp, lane 5: GoTaq (not purified) PCR reaction
2:~395 bp
Fig. 2 Final PCR reaction on 1% agarose gel
Fig. 3: Xhol and Xbal double digest of Abl-S417Y mutants
Fig. 4: Transformation examples using Abl-
H396P (example)
Plate 1: Vector only negative control
Plate 2: pET28a-ABL positive control
Plate 3: Abl-H396P
In figure one; we analyzed PCR
reactions to see if our primer designs were
successful. The band in lane four is
estimated to be around 743 bp and the band
in lane five to be about 395 bp.
Reaction 1 contained the T7 promoter and
mutant reverse primer whereas reaction 2
contained the T7 terminator and mutant
forward primer. We then ran a final PCR
reaction to analyze the full-length S417Y
Abl mutant DNA using gel electrophoresis.
In figure two you can see a bright band
estimated to be around 1114 bp.
We then ran another gel electrophoresis with
the S417Y mutant insert digest to excise the
mutant gene and purify it by determining
DNA concentration and purity. In figure 3 a
band around 974 bp is present, which we
then excised. The mutant inserts were then
transformed using E.Coli DH5α competent
cells for plasmid replication. In figure four
the picture is of an example negative,
positive and Abl-H396P were as expected.
Our Abl-S417 mutant turned results were
very similar.
Fig. 4
Fig. 3Fig. 2Fig. 1

6. Fig. 6 Bradford assay for purified and concentrated WT Abl protein: Average to yield final concentration:
0.89 mg/ml, BSA stock concentration used: 0.51 µg/µL
Fig. 7 Bradford assay for purified and concentrated mutant Abl protein S417Y: Average to yield final
concentration: 0.82 mg/ml
Fig. 7: Coomassie Stain of SDS-PAGE of WT Abl samples
Lane 1 & 2: 2x SDS, lane 3: Standard, lane 4: pre-induction sample, lane 5: post-induction sample, lane 6: binding
buffer sample, lane 7: wash buffer sample, lane 8: elution buffer sample, lane 9: pure sample, lane 10: 2x S
Fig. 8 Coomassie Stain of SDS-PAGE of Abl- S417Y samples
Lane 1 & 2: 2x SDS, lane 3: Standard, lane 4: pre-induction sample, lane 5: post-induction sample,
lane 6: binding buffer sample, lane 7: wash buffer sample, lane 8: elution buffer sample, lane 9: pure
sample, lane 10: 2x SDS
We then did a Bradford assay to
determine the final concentration of our
purified and concentrated WT Abl protein,
shown in figure 5. We then expressed the
Abl-S417Y mutant kinase domains using
IPTG induction. Figure 6 shows our
Bradford assay standard curve which we
used to find our Abl S417Y protein
concentration. We then prepared an SDS-
PAGE gel to check the purity of the WT Abl
mutant kinase domain. Figure 7 shows the
results of the SDS-PAGE. Lane 9 shows our
protein between 37-25 D. We also have a
band just above 37 D and between 75 and 50
D. Next we did another SDS-PAGE with
coomassie brilliant blue stain again, shown
in figure 8. Lane 9 is the pure sample. The
protein’s band is located between 25-37D,
another band around 37 D, one around 50
and some smaller bands and streaks.
We did a kinase assay and found the
standard curve which we then found the
percent inhibition from, figures 10 and 9
respectively. Finally we used PyMol to view
the crystal structure of Abl-S417Y mutant
(Figures 11 through 13.)
Fig. 5
Fig. 6
1 2 3 4 5 6 7 8 9 101 2 3 4 5 6 7 8 9 10
Fig. 8
Fig. 7

7. Fig. 11 Abl- S417Y crystal structure
Fig. 12 Stick structure
Abl-S417Y binding pocket: magenta, Gleevec: green, DFG motif: blue, Binding A loop: yellow
Fig. 13 Cartoon and stick structure
Abl-S417Y binding pocket: green, Gleevec: orange, DFG motif: Blue, Binding A loop: magenta
Discussion
In this experiment we investigated
how mutations in Abl kinase could impose
drug resistance to Gleevec, a common drug
for the treatment of CML. To do this we
used WT Abl kinase along with an S417Y
mutant Abl kinase. We first needed to make
this mutation using site-directed
mutagenesis which was done using two step
PCR. pET28a-Abl plasmid was used along
with mutant forward and reverse primers in
Fig. 13
Fig. 14
Fig. 13
Fig. 10
Fig. 9
Fig. 12
Fig. 11

8. separate reactions. Reaction 1 contained the
T7 promoter primer and Mutant Reverse
primer while reaction 2 contained the T7
terminator primer and mutant forward
primer. These reactions would amplify
certain sequences with predetermined length
in order to verify the reaction accuracy. The
expected results included a 743 base pair
(BP) segment from reaction 1 and a 395 BP
segment from reaction 2. An agarose gel
was run and results are posted in figure
1. This experiment was successful
according to the DNA ladder comparison.
The lengths of target DNA were between the
850 BP and 650 BP markers for reaction 1
and between the 400 BP and 300 BP
markers for reaction 2.
Next we needed to make a full length
S417Y mutant. To do this T7 terminator
and promoters were used along with the
purified DNA templates from reactions 1
and 2. Figure 2 depicts the agarose gel from
this experiment. The sample was not pure
but there was high fluorescence in the band
which was slightly higher than the 1000 BP
marker. The size of the full length S417Y
mutant is 1114 BP, making the Abl-S417Y
final PCR reaction a success. This band was
excised and the DNA extracted using a
Qiagen purification kit. Next restriction
endonuclease digests were completed using
Xbal and Xhol to create “sticky” ends on the
final PCR products, gel electrophoresis was
used to check the accuracy of the
digests. Figure 3 displays this gel and
confirms that the experiment was accurate
resulting in a band close to the 1000BP
marker which is close to the expected 974
BP.
This mutant insert was then ligated
into an antibiotic resistant vector using T4
DNA ligase. E. coli DH5 alpha cells were
used to replicate the plasmid. We used a
positive control (pET28a-Abl WT plasmid)
which is a complete plasmid (no ligation
reaction was performed) that has resistance
to Kanamycin. The negative control did not
have the insert so the vector was in
fragments, thus not having kanamycin
resistance. Because not all ligation reactions
were successful for the mutant, not as many
colonies were seen on the plate as compared
to the positive control. The colonies that did
grow on the treated plate therefore contained
the insert and were selected for further
growth as seen in figure 4.
Two colonies from the mutant
cultures were chosen and grown in starter
culture. Mutant bacterial cells were also
pelleted and the DNA was extracted from
both colonies. The concentration and purity
of the DNA was then checked using the
260/280 ratio before being sequenced by
unidirectional PCR with fluorescently
labeled ddNTPs to confirm the desired
mutation and the absence of any undesirable
mutations. Once the mutation was
confirmed the mutant was co-expressed with
YopH plasmid and was transformed into E.
coli BL21DE3 cells. YopH plasmid was
used because of its high specificity for
phosphotyrosine and its lack of
discrimination between substrate proteins
thereby preventing toxicity. IPTG was
introduced to induce Abl protein expression
in both WT and mutant cultures. A Bradford
assay was used to quantify the
concentrations of WT and mutant proteins
that were obtained through cell lysis, Ni-
NTA affinity chromatography, and dialysis;
Figures 5 and 6 show the WT and mutant
concentrations respectively. SDS-PAGE gel
was used to check the purity of both WT and
mutant Abl. Figure 7 depicts the pure WT
protein with attached hexahistidine tag in
lane 9 with a band between 37kDa and
25kDa which is where the Abl protein
should be with a size of 32kDa. There is also
a band between 75kDa and 50kDa. YopH
protein, according to the protein data base, is
just over 70kDa which if bound to

9. hexahistidine could have made it in to the
pure protein.
There were more impurities observed
in the SDS-PAGE of the mutant protein as
seen in figure 8. The three bands found in
the WT gel were also seen in the mutant gel
including the Abl protein along with two
others. These proteins could have bound to
the column and been eluted along with the
protein of interest. If there was error in any
of the buffers used during each step of the
purification process, other proteins could
have changed in a way that allowed them to
bind to the column.
A kinase assay was used to test the
WT and mutant Abl kinase domains in the
presence or absence of Gleevec and the
results can be seen in figure 9. In both the
WT and mutant samples the specific activity
was hindered when Gleevec was introduced
which was expected due to its competition
with ATP in the hinge region where the
binding pocket is located as seen in both
figures 12 and 13. In Gleevec, only the
pyridine and pyrimidine rings interfere
directly with the ATP binding site by
blocking the binding of the adenine base of
ATP. The rings are stabilized inside the
binding site by hydrogen binding, van der
Walls forces, and hydrophobic interactions.
There are hydrogen bonds at Met318,
Thr315, Phe311, Asn322. The S417Y
mutation in the inactive site of the kinase
increased the specific activity. It was
hypothesized that the mutation would
destabilize the inactive conformation
therefore allowing ATP to bind more
readily. In the inactive conformation the
DFG motif is flipped 180 degrees, Asp381
can no longer interact with Mg-ATP, and
Phenylalanine points into to binding site; all
opposing the binding of ATP. The mutation
opposes this confirmation, therefore
allowing a higher specific activity.
Although the results confirm our
hypothesis, it was with little significance
(9.3% increase in specific activity in mutant
compared to WT). To improve upon this
experiment, better purification should be
performed to make sure the protein of
interest is in high concentration. Because
the protein tested was not pure, the Bradford
assay was inaccurate (detects any protein) so
the concentration of our target protein could
not be accurately determined. This could
explain the low specific activity observed in
the mutant protein.
Conclusion
The purpose of this experiment was
to understand how CML patients can
become resistant to Gleevec treatment
through mutations of Abl kinase. This was
confirmed through experimentation,
specifically the S417Y mutation. Further
experiments should consider other mutations
common in CML patients that could
possibly affect the binding of Gleevec. From
these mutations new drugs could be
developed to fit the geometry and binding
properties required.

10. References
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Weisberg, E., et al., Second generation inhibitors of BCR-ABL for the treatment of imatinib-
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Wu, Z.L., et al., Phosphatase-coupled universal kinase assay and kinetics for first-order-rate
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