fret based hts assay kit for sumo1-ubc9 interaction
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FRET Based HTS Assay Kit for SUMO1-UBC9 Interaction. David Bui Richard Lauhead Randall Mello Michelle Tran Team E. Introduction. Why is it important to have this kit? - PowerPoint PPT PresentationTRANSCRIPT
FRET BASED HTS ASSAY KIT FOR SUMO1-UBC9 INTERACTION
David BuiRichard Lauhead
Randall MelloMichelle Tran
Team E
Introduction• Why is it important to have this kit?
Disregulation of the SUMO pathway has been linked to diseases including ovarian carcinoma, melanoma, and lung adenocarcinoma. (Mo and Moschos 2005)
http://www.biochem.mpg.de/jentsch/Mueller.html
• Forster Resonance Energy Transfer• Energy transfer
between donor and acceptor fluorophores at the distance of 2-10 nm(Dos Remedios and Moens 1995)
• Engineered CFP (Cypet) and YFP (Ypet) genetically engineered to proteins SUMO-1 and E2 Conjugating enzyme Ubc9 of the Sumoylation pathway
Goals• Develop a high throughput
screening kit based on FRET that allows for detection of protein-protein (SUMO1-UBC9) interactions• Allows for basic
screening of inhibitors that alter binding between target proteins
• Combine two target proteins at a specific concentration ratio• If proteins do not bind
FRET does not occur• If proteins do bind
energy transfer will occur
FRET picture adapted from www.nature.com/.../v4/n7/fig_tab/nrm1153_F2.html
• Develop a process to optimize a HTS kit
• Meet NIH standards
Project Flow ChartProtein Expression
Cypet-SUMO1, Ypet-Ubc9, Ubc9
2 weeks
Protein PurificationNi-NTA Column
Chromatography/Dialysis
2 weeks
Protein CharacterizationBradford assay, fluorescence characterization, SDS PAGE
Protein Gel etc..3 weeks
Protein Expression Optimization
IPTG, 7-16 hour growth/expression
2 weeks
Kit Design/ Quality Control Lyophilization, Oxidation, and Stability studies with
urea3 weeks
Z Factor Studies for HTS FRET Ratio optimization Cypet-SUMO1/Ypet-Ubc9
Concentration optimization 3 weeks
Ubc9 Mock Inhibitor Studies Ubc9+Ypet-Ubc9/
Ubc9+Cypet-SUMO1/Ypet-Ubc9+Cypet-SUMO1
concentration experiments 2 weeks
Inhibitor Kd Modeling Effects of Inhibitor Kd
on Bound Protein, Kdapp equations 2 weeks
Last Quarter Summary Determine sensitivity of the FlexStation II
RESULTS: As low as 25 ng, but useable around 500 ng of fluorescent protein
Determine method for characterizing Fluorescent protein concentration RESULTS: Bradford Assay and Fluorescent
Standard Curves Determine if purification affects the assay and an
optimal purification protocol RESULTS: Purity has no effect and Protocol 1 was
chosen Lyophilization Studies
RESULTS: Does not effect protein stability
Work Done Prior to Senior Design
CYpet and Ypet were engineered as FRET pairs
UBC9 was identified as a protein that binds to SUMO1 in the SUMO pathway.
Kd between SUMO1 and UBC9 was determined by BIACORE(SPR) as 0.75
FRET was determined to work between CYpet-SUMO1(CS1) and Ypet-UBC9(YU9)
450 470 490 510 530 550 570020000400006000080000
100000120000140000160000
Fluorophore Spectrums: CYpet and Ypet
FRET Spectrum RawYpet Spectrum ex: 414 nmBackgroundFRET Spectrum processedCypet SpectrumCypet without background
Wavelength (nm)
Fluo
resc
ence
(RFU
)
Expression OptimizationInnoculate 1:50
Protocol 1
Protocol 2
Protocol 3
Protocol 4
IPTG added when OD = .4
.5 mM .1 mM 1mM .5 mM
Time Incubated
3 hours 16 hours
3 hours 16 hours
Incubation Temp. oC
37 25 37 25
Protocol 1
Protocol 2
Protocol 3
Protocol 4
0
2000
4000
6000
8000
10000
12000
14000
Expression optimization
Cypet-SUMO1 Concen-tration producedYpet-UBC9 Concentra-tion Produced
Protocol
Fluo
resc
ent
Prot
ein
conc
entr
atio
n(ng
/uL)
Protocol 2 works the best
Introduction to Z’ Factor The Z’ Factor is a characteristic
parameter for the quality of the assay, without intervention of test compounds
sC+, mC+ :the mean and standard deviation of positive hits sC-, mC- :the mean and standard deviation of negative hits
Well #
Test
Val
ue
Plot of Positive hits and negative hits
Z < 0.0 ; Not usable Assay0.0 < Z < 0.5 ; A Doable Assay0.5 < Z < 1.0 ; An Excellent AssayZ= 1.0 ; Ideal Assay
Ji-Hu Zhang et. al.
Z’ Factor Ratio Ratio:
Use 10 wells for each test of positive and negative hits
Run the tests at different ratios of CS1 to YU9
1:1.2 1:2 1:2.8 1:3.6 1:4.4 1:5.2
-0.4-0.3-0.2-0.1
00.10.20.30.40.50.60.70.80.9
Z' Factor with Each Well hav-ing 0.21 uM Cypet-Sumo1 in
60 uL DB
[CyPet-SUMO1] : [YPet-Ubc9] ratio
Z' F
acto
r
Ratio of 1:2.8 is useable ratio of Cypet-SUMO1 to Ypet-UBC9
Z’ Factor Protein Amount Protein amount
Use ten wells for each run of positive and negative hits
Run the test with differing amount of CS1 and YU9 and a constant ratio of 1 : 2.8
0.15 0.2 0.25 0.3 0.35 0.4-0.1
00.10.20.30.40.50.60.70.8
Z' factor for determining a useable amount of protein
Z' Factor for Protein Amount
Amount of CYpet uM
Z' F
acto
r
Useable protein amount selected is 0.25 mM CS1 and 0.7 mM YU9
Z’ Factor Time Stability How long does the
assay need to incubate before it is measureable?
5 10 20 30 40 50 600
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Z' Factor Time Stability
Z' Factor with 0.25 uM CS1 and ratio 1:2.8
Time(min)
Z' F
acto
r
This shows that this assay is usable after incubating only 5 minutes
Modeling Equations for Kd
in presence of an Inhibitor:
]91[]9[*]1[
YUCSYUCSKdapp
)][1(inh
ddapp KInhibitorkK
)][1(
]9[*]1[]91[
inhd K
InhibitorK
YUCSYUCS
75.0500][
7.0]9[25.0]1[
dkMinhibitor
MYUMCS
mmm
Kd of inhibitor
[CS1
YU9]
mM
Effects of Inhibitor Kd on Bound Protein
max
Thanks to high [inhibitor] this assay will detect inhibitors with high Kd values
Design Conclusions Designed a set of experiments to
optimize the steps from protein expression to binding assays in a HTS format
Demonstrated that purity of proteins has no effect on the FRET ratio
Demonstrated that lyophilization is not necessary in kit design over non-lyophilized protein
Z’-Factor Conclusions FRET-based HTS binding assay meets Z’-Factor signal requirements of
>0.5 at a FRET Ratio of 1:2.8, at concentrations of 0.25 and 0.70 uM per well for Cypet-SUMO1 and Ypet-Ubc9, and over a 60 minute period
BRET Technology: Luciferase reporter enzyme used at 3 uM per well in one 384-well HTS study to reach a Z’-Factor over 0.5 (Molecular Biology in Medicinal Chemistry Volume 21,pg.20. Wiley-VCH 2004)
5 10 20 30 40 50 6000.10.20.30.40.50.60.70.8
Z'-factor Stability at FRET Ratio 1:2.8 and concentra-
tions of CYpet-SUMO1: Ypet-Ubc9 at 0.25:0.70 uM
Z'-Factor
Time(min)
Z'- f
acto
r
Kocan, Martina, Heng B. See, and Ruth M. Seeber. "Demonstration of Improvements to the Bioluminescence Resonance Energy Transfer (BRET) Technology for the Monitoring of G Protein–Coupled Receptors in Live Cells." Journal of Biomolecular Screening (2008). Society of Biomolcecular Sciences.
Future Work• Investigate mock inhibitor to incorporate with kit
• Allows for kit users to compare and analyze other positive hits
• Optimize protein expression• Engineer CYpet-SUMO1 and Ypet-Ubc9 to have an E. coli
secretion sequence
• Package materials and create an instructions manual to bring kit to a commercial level
Acknowledgements
Dr. Jiayu Liao
Vipul Madahar
Yang Song
Gokul Upadhyayula
Thank you!!!!
Jerome Schultz
Questions? www.engr.ucr.edu/~mitran
appendix
0 0.5 1 1.5 2 2.5 3 3.50.3
0.4
0.5
0.6
0.7
0.8
0.9f(x) = − 0.0928184628352445 ln(x) + 0.772608308994995R² = 0.990307680907584
Average FRET ratios with different concentrations of Urea
Average FRET ratios with dif -ferent concentrations of UreaLogarithmic (Average FRET ra-tios with different concentra-tions of Urea)
Urea Concentration M
FRET
Rat
io 5
30/4
75
Appendix-2
450 470 490 510 530 550 5700
20000
40000
60000
80000
100000
120000
140000
160000
180000
200000
Z Factor Run for 1: 2.8
Wavlength(nm)
Fluo
resc
enc(
RFU
)
Appendix 3