# CAII cell concentrations to evaluate
cell_concentrations = [
0.010 * ureg.millimolar, 0.020 * ureg.millimolar, 0.040 * ureg.millimolar
]
# Protocol for 'control' titrations (water-water, buffer-buffer,
# titrations into buffer, etc.)
control_protocol = ITCProtocol(
'control_protocol',
sample_prep_method='Plates Quick.setup', # thorough cleaning
itc_method='ChoderaWaterWater.inj',
analysis_method='Control',
experimental_conditions=dict(target_temperature=25,
equilibration_time=60,
stir_rate=1000,
reference_power=5),
injections=[
dict(volume_inj=0.2, duration_inj=0.4, spacing=60, filter_period=0.5)
] + 10 *
[dict(volume_inj=3.0, duration_inj=6, spacing=120, filter_period=0.5)],
)
# Protocol for 1:1 binding analysis
blank_protocol = ITCProtocol(
'1:1 binding protocol',
sample_prep_method='Chodera Load Cell Without Cleaning Cell After.setup',
itc_method='ChoderaHSABlank.inj',
analysis_method='Control',
experimental_conditions=dict(target_temperature=25,
equilibration_time=300,
naproxen_sodium_solution = SimpleSolution(compound=naproxen_sodium, compound_mass=25.245 * ureg.milligram, solvent=buffer, solvent_mass=10.0728 * ureg.gram, location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType,
3))
drugs = [indoxylsulfate, naproxen_sodium]
drug_solutions = [indoxylsulfate_solution, naproxen_sodium_solution]
drug_kas = [indoxylsulfate_ka, naproxen_ka]
# Define ITC protocol.
# Protocol for 'control' titrations (water-water, buffer-buffer,
# titrations into buffer, etc.)
control_protocol = ITCProtocol(
'control protocol',
sample_prep_method='Plates Quick.setup',
itc_method='ChoderaWaterWater.inj',
analysis_method='Control')
# Protocol for 1:1 binding analyis
blank_protocol = ITCProtocol(
'1:1 binding protocol',
sample_prep_method='Chodera Load Cell Without Cleaning Cell After.setup',
itc_method='ChoderaHSA.inj', # TODO Define new protocol with more injections?
analysis_method='Onesite') # TODO better default analysis present?
binding_protocol = ITCProtocol(
'1:1 binding protocol',
sample_prep_method='Plates Standard.setup',
itc_method='Chodera_HSA.inj', # TODO Define new protocol with more injections?
analysis_method='Onesite') # TODO better default analysis?
# Protocol for cleaning protocol
binding_cleaning_protocol = ITCProtocol(
drugs = [aspirin, naproxen_sodium]
drug_solutions = [aspirin_solution, naproxen_sodium_solution]
drug_kas = [aspirin_ka, naproxen_ka]
# Define ITC protocol.
# Protocol for 'control' titrations (water-water, buffer-buffer,
# titrations into buffer, etc.)
control_protocol = ITCProtocol(
'control_protocol',
sample_prep_method='Chodera Load Cell Without Cleaning Cell After.setup',
itc_method='ChoderaWaterWater5.inj',
analysis_method='Control',
experimental_conditions=dict(target_temperature=25,
equilibration_time=60,
stir_rate=1000,
reference_power=5),
injections=[
dict(volume_inj=0.1, duration_inj=0.4, spacing=60, filter_period=0.5)
] +
5 * [dict(volume_inj=1.5, duration_inj=6, spacing=120, filter_period=0.5)],
)
blank_protocol = ITCProtocol(
'1:1 binding protocol',
sample_prep_method='Chodera Load Cell Without Cleaning Cell After.setup',
itc_method='ChoderaHSA20.inj',
analysis_method='Onesite', # Protocol for 1:1 binding analysis
experimental_conditions=dict(target_temperature=25,
equilibration_time=300,
stir_rate=1000,
# Receptor cell concentrations to evaluate
#cell_concentrations = [0.010 * ureg.millimolar, 0.020 * ureg.millimolar, 0.030 * ureg.millimolar]
#cell_concentrations = [0.020 * ureg.millimolar]
cell_concentrations = [0.025 * ureg.millimolar]
#
# Protocol for 'control' titrations (water-water, buffer-buffer,
# titrations into buffer, etc.)
control_protocol = ITCProtocol(
'control_protocol',
sample_prep_method='Plates Quick.setup', # thorough cleaning
itc_method='ChoderaWaterWater.inj',
analysis_method='Control',
experimental_conditions=dict(target_temperature=25,
equilibration_time=60,
stir_rate=1000,
reference_power=5),
injections=[
dict(volume_inj=0.2, duration_inj=0.4, spacing=60, filter_period=0.5)
] + 10 *
[dict(volume_inj=3.0, duration_inj=6, spacing=120, filter_period=0.5)],
)
binding_protocol = ITCProtocol(
'1:1 binding protocol',
sample_prep_method='Plates Quick.setup',
itc_method='ChoderaHSA.inj',
analysis_method='Onesite',
experimental_conditions=dict(target_temperature=25,
equilibration_time=300,
stir_rate=1000,
source_plate.RackLabel,
source_plate.RackType, 3))
drugs = [indoxylsulfate, naproxen_sodium]
drug_solutions = [indoxylsulfate_solution, naproxen_sodium_solution]
drug_kas = [indoxylsulfate_ka, naproxen_ka]
# Define ITC protocol.
# Protocol for 'control' titrations (water-water, buffer-buffer,
# titrations into buffer, etc.)
control_protocol = ITCProtocol(
'control protocol',
sample_prep_method='Plates Quick.setup',
itc_method='ChoderaWaterWater.inj',
analysis_method='Control',
num_inj=5,
v_inj=Quantity('10 microliter'),
v_cell=Quantity('202.8 microliter'),
)
# Protocol for 1:1 binding analyis
blank_protocol = ITCProtocol(
'1:1 binding protocol',
sample_prep_method='Chodera Load Cell Without Cleaning Cell After.setup',
itc_method=
'ChoderaHostGuest.inj', # TODO Define new protocol with more injections?
analysis_method='Onesite',
num_inj=10,
v_inj=Quantity('3 microliter'),
v_cell=Quantity('202.8 microliter'),
)