1. Using Engineered Conditional Stability to Optimize
Dimerization of a Synthetic Ligand Binding Protein
Colton McDavid2, Benjamin W. Jester1,2, Stanley Fields1,2,3
1Howard Hughes Medical Institute, University of Washington, Seattle, WA. 2Department of Genome Sciences, University of Washington, Seattle, WA. 3Department of Medicine, University of Washington, Seattle, WA.
PAIRING DIG AND PRO DIMERS
Several mutations to the ligand-binding domain of DIG 10.3 changed the ligand-
binding specificity from digoxigenin to progesterone (PRO). We paired five of
these progesterone variants with Dig 10.3 and with each other using luciferase
expression as a quantitative alternative to HIS3 expression.
CONCLUSION AND FUTURE DIRECTIONS
ACKNOWLEDGEMENTS
Utilizing directed evolution, we identified several converging mutations that appear
to have a stabilizing influence on DIG 10.3’s dimer interface. We are continuing to
test the effects of each mutation on DIG 10.3. Our goal is to identify mutations that
increase the affinity of DIG to form hetero-dimers over non functional homo-dimers
and apply these mutations to our DIG/PRO dimer. Such mutations provide a
modular system with a variety of potential downstream applications including
biosensors and orthogonal gene circuits.
Special thanks to Ben Jester and Stan Fields for the opportunity to engage in
undergraduate research and to Christine Tinberg and David Baker for DIG 10.3.
The UW Undergraduate Research Program for the experience of working in a lab
and HHMI for funding my work.
Of continuing importance in the field of synthetic biology is the development of
tools to aid in understanding protein-protein interfaces and inter-protein
interactions. To this end, we developed a method utilizing directed evolution to
optimize the dimerization of DIG 10.3 (DIG), a synthetic protein engineered to
bind the small molecule digoxigenin. We exploited the inherent instability of DIG
to isolate variants that are dependent on the presence of digoxigenin for stability
and are rapidly degraded in its absence. We then identified pairs of these
conditionally stable variants that preferentially form hetero-dimers over homo-
dimers and used them to identify mutations to the protein-protein interface that
optimize dimerization of DIG in the presence of ligand.
ABSTRACT
GENERAL METHOD
Our system consists of a DNA binding domain, Gal4, and a transcriptional activation
domain, VP16, which when brought into proximity recruit RNA polymerase to the
HIS3 reporter gene. One copy of Dig 10.3 is fused to Gal4 and one to VP16 such that
dimerization of DIG 10.3 in the presence of digoxigenin leads to transcription.
Because both Gal4 and VP16 are necessary for transactivation, DIG hetero-dimers
activate transcription but homo-dimers are nonfunctional.
IDENTIFYING THE BEST DIG 10.3 HETERODIMERS
We paired several dimer interface mutants of DIG 10.3 and assessed their dimer
stability by comparing growth in minimal media lacking histidine and containing
digoxigenin and 3AT, a competitive inhibitor of the HIS3 gene product. The ability of S.
cerevisiae to grow depends on the successful dimerization of DIG.
Fig 1. DIG 10.3 dimerizes in the presence of digoxigenin to activate transcription of the reporter gene.
Without digoxigenin, DIG 10.3 is rapidly degraded.
Fig 3. Relative luminescence data following the addition of D-Luciferin to DIG-containing yeast
allowed us to determine the best hetero-dimer pairs. A DMSO control was used at <1% total
concentration because both digoxigenin and progesterone were dissolved in DMSO.
Fig 5. Several converging mutations came out of our selection and the wild type sequence was
enriched by about 5-fold, which suggests that the selection successfully enriched for stable dimers.
1. Tinberg, C.E., et al. Nature 501, 212-216 (2013).
REFERENCES
Gal-DIG
Designation
DIG-VP16 Designation Mutation(s)
GDWT DVWT NONE
GD1 DV1 E83V
GD2 DV2 E83V, P127S
GD3 DV3 V104A
GD4 DV4 Y36H
GD5 DV5 I81F
p415cyc p416cyc EMPTY
Gal-PRO
Designation
PRO-VP16 Designation Mutation(s)
GPWT PVWT NONE
GP1 PV1 Y101F
GP2 PV2 Y34F, Y101F, Y99F (3F)
GP3 PV3 3F, K96M, L14Q, F19Y, V124E
GP4 PV4 3F, K96E, V104A
GP5 PV5 3F, H9R, E15G, I64F, A92T
p415cyc p416cyc EMPTY
Fig 4. DIG1 (shown on the right) contains the mutation E83V.Mutants of DIG 10.3 (shown on the left)
were selected to dimerize with DIG1. Both proteins are shown binding digoxigenin.
Fig 7. Mutations produced by our selection favor dimerization with DIG 1 over DIG 4. Expression of
luciferase increased further by combining our mutants with DIG 1b, which contains the mutation E83R.
0
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Luciferase Expression of Selection Mutants
DMSO
5 Dig
50 Dig
Fig 2. Our initial DIG variants (their specific mutations described on the left) were assayed for growth on
plates lacking histidine and containing 10 or 100µM digoxigenin and 1 µM 3AT.
1 mM 3AT x 100µM
digoxigenin 100 µM digoxigenin
1mM 3AT x 10 µM
digoxigenin 10 µM digoxigenin
GD5 x DV1
GD3 x DV1
GD2 x DV1
GD1 x DV1
GD x DV4
GD x DV1
P415cyc x DV1
0
2
4
6
8
Frequency
Convergent Mutations to Dig 10.3
P37S P37L P37Q P59L T43S L25M R123S I6T G95D
IDENTIFYING CONVERGENT MUTATIONS
Using the most stable DIG 10.3 heterodimer, GD/DV1, we mutagenized the DIG
domain of the Gal-Dig 10.3 fusion using error-prone PCR. We then plated our mutant
library on media lacking histidine and containing digoxigenin. Of 98 sequences
representing the largest colonies on the plates, we identified several recurring
mutations to the same subset of residues, suggesting that our selection succeeded in
enriching for stabilizing mutations.
DIG 10.3 domain fused to Gal4 DIG1 (E83V) fused to VP16
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GD/DV1 PG2/PV2 PG2/DV1
Luciferase Expression of Best Dimer Pairs
DMSO
100µM Dig
10µM Dig
10µM Pro
1µM Pro
100µM Dig/ 10µM Pro
100µM Dig/1µM Pro
10µM Dig/1µM Pro
TESTING SELECTION MUTANTS
We used site-directed mutagenesis to generate some of the mutants from the
selection clone them into plasmids. In order to assess the stabilizing effects of each
mutation, we gathered both quantitative and qualitative data using both the HIS3
and luciferase reporters.
Fig 6. Mutants produced by our selection grow as well as, if not better than GDWT when paired with
DV1, suggesting that the converging mutations that came out of the selection are stabilizing.
GD
P37S,P59L,G95D
P59L,G95D
P37S,P59L
R123S
G95D
T43S
P37L
P37Q
P37S
L25M
I6T
1 mM 3AT x 1 µM digoxigenin 1 mM 3AT x 10 µM digoxigenin