Cells as Biosensors - nanoHUB
Transcript of Cells as Biosensors - nanoHUB
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L5.3: Cells as Biosensors II
Prof. Rickus
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In this lecture
• Sensitivity
• Sensitivity Amplification
• Ultrasensitivity
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Recognition Element Transducer Detector
Target
End User
Display
What is a biosensor?
SENSOR
Signal INPUT
OUTPUT Response
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Sensitivity Sensitivity: The differential change in R as a ratio to the differential change in S
Res
pons
e, R
Input Signal, S
Plot the magnitude of the response magnitude as a function of the signal magnitude
slope for a linear response
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slope = unit of response unit of signal
Sensitivity
Signal
sensitivity
R = mS + b
Increase the sensitivity of the sensor response background
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Dynamic Range
Concentration Range for which Response is Predictably Dependent Upon the Signal Level
max min
max – usually some saturation of the response (e.g. saturated binding) min – signal lost in the noise (limit of detection)
Signal
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G protein
1) 1 metarhodopsin catalyzes many GDP/GTP exchanges
2) Each phosphodiesterase can hydrolyze many molecules of cGMP
From Neuron to Brain. 4th ed. Nicholls, Martin, Wallace, Fuchs, chapter 19
Classic Example of Magnitude Amplification - Phototransduction
1 photon event results in the hydrolysis of 105 cGMPs
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Whole Cell Biosensor
Signal Response
commonly genetically encoded
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2008/tsien-slides.pdf
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Whole Cell Biosensor from Simple Activation
Response of the Sensor Circuit at Zero Signal Some circuits can be “leaky”. E.g. still get basal transcription with 0 activator.
Background
Transcription rate of Y
X
βo
Signal
Maximum β1
Simple activation model
response
signal
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Classic Hyperbolic Response (.e. Calibration) Curve
Normalize the response and stimulus parameters Rmax: maximum response S0.5: the concentration of signal where the response is at half maximum r, s: dimensionless response (Y) and signal (X) - divide both sides by Rmax - multiply both sides by S0.5/S0.5
= 1 S0.5
= KXY = level of X signal that results in a half
maximum response (transcription rate of Y) dimensionless form
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Sensitivity Amplification
An increase in the % change in response , R, relative to the % change in stimulus, S.
We define the sensitivity amplification factor, As.
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Hyperbolic sensitivity classic hyperbolic calibration
Ultrasensitivity As > 1 for a range of S
Sub-sensitivity The As is never greater than 1.
Koshland, Goldbeter, Stock Science 1982
R /
R m
ax
Note the trade off between dynamic range and sensitivity.
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Biological Design Approaches to Achieve Ultra-sensitivity
1.Cooperativity
2.Cascades
3.Zero-Order Ultra-sensitivity
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Ultra-sensitivity – Cooperativity
f(x)
x/K
n=1 n=2 n=3 n=4
K: - units conc. - defines functional concentration range of X - may correlate with (but is not formally) the binding affinity of X to the DNA - other factors contribute to K n: - Hill coefficient - increases nonlinearity of function - increases steepness of sigmoidal - greater n, more on/off switch-like
[X] gene
x >> K ON high
x = K 0.5 ON mod
x << K 0 0 OFF
rate prob. Hill function model of gene activation
From Lecture on Simple Models of Gene Expression
hyperbolic sensitivity
Ultra-sensitivity
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Sara Hooshangi et al. PNAS 2005;102:3581-3586
Ultra-sensitivity: Multi-stage Cascades
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W W*
Enzyme 1
Enzyme 2
R = W* / Wtotal
S S is an activator of Enzyme, E1
E1 and E2 are enzymes that follow classic Michaelis Menton Kinetics
Ultra-sensitivity: Zero Order Sensitivity
W is some Response Signal Protein that can exist in 2 states
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W W*
E1
E2
S
Structure is used widely by biology
kinase
phosphatase
P
ATP ADP
Kinases make up 1. 5 – 2.5% of all proteins in most genomes examined.
Quantitative analysis of signaling networks (2004) Herbert M. Sauroa, Boris N. Kh l d k
S
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0o Ultrasensitivity Depends on Certain Conditions:
KM,1 / WT = KM,1 / WT = 0.1 equivalent hill coefficient = 2.9 KM,1 / WT = KM,1 / WT = 0.01 equivalent hill coefficient = 13
Zero Order Regime: The total amount of WT = W + W* must be very high relative to the KM’s of the reactions catalyzed by E1 and E2
W
VE1
W0.5
Zero order regime
high W levels
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Cascades to Enhance 0o Ultra-sensitivity:
W W*
E1
E2
S
Z Z*
E3
E4
R1 = W*/WT R2 = Z*/ZT
1 cycle
2 cycle
Adding the 2nd cycle increases the ultrasensitivity
response Equivalent to hill coeff. of
3.6
7.5
ALBERT GOLDBETER AND DANIEL E. KOSHLAND, JR. PNAS 1981
1st cascade
2nd cascade
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Engineering Design: Analogy to the Transistor
Quantitative analysis of signaling networks (2004) Herbert M. Sauroa, Boris N. Kholodenkoc
View these systems as sensors, amplifiers, or switches
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