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Enzyme Kinetics
Enzymatic reaction
k1 k2
E+S ES E+P
k-1
Conservation of enzyme
(E) = (E0) (ES)
Two Methods to Proceed
Rapid equilibrium assumption: define
equilibrium coefficient
Km = k-1/k1 = [E][S]/[ES]
Vmax [S ] k 2 [E 0 ][S ]
v
K m [S ] K m [S ]
Assumptions:
1. The rate of reaction is first order in
concentration of substrate at relatively low
values of concentration
2. As the substrate concentration is continually
increased, the reaction order in substrate
diminishes form one to zero.
3. The rate of reaction is proportional to the total
amount of enzyme present.
Michaelis-Menten Kinetics
Vmax [S ] k 2 [E 0 ][S ]
v
K m [S ] K m [S ]
Vmax = k2 [E]t
=[E] +[ES]
Experimentally Determining Rate
Parameters for Michaelis-Menten
Kinetics
Lineweaver-Burk
Eadie-Hofstee
Hanes- Woolf
Batch Kinetics
Determining Parameters
Rearrange the equation into a linear form.
Plot the data.
What kind of data would we have for an
experiment examining enzyme kinetics?
Describe an experiment.
The intercept and slope are related to the
parameter values.
Lineweaver-Burk
(double reciprocal plot)
Rewrite Michaelis-Menten rate expression
1 Km 1 1
v Vmax [S ] Vmax
Plot 1/v versus 1/[S]. Slope is Km/Vmax,
intercept is 1/Vmax
Lineweaver-Burk Plot
Graphical Solution
intercept
1/ V
1 Km 1 1 Slope = Km/ Vmax
v Vmax [S] Vmax
1/ Vmax
-1/ Km 1/ [S]
Example: Lineweaver-Burk
-5 -5
[S] x 10 M V, M/min x 10
1.0 1.17
1.5 1.50
2.0 1.75
2.5 1.94
3.0 2.10
3.5 2.23
4.0 2.33
4.5 2.42
5.0 2.50
Resulting Plot
Vmax [S ] k 2 [E 0 ][S ]
v
K m [S ] K m [S ]
Vmax = 1/2.8687 x 10-4 = 3.49 x 10-5 M/min
Km= 0.5686 x Vm = 1.98 x 10-5 M
Other Methods
Eadie-Hofstee plot
v
v Vmax K m
[S ]
Hanes- Woolf
[S ] K m 1
[S ]
v Vmax Vmax
Eadie-Hofstee plot
Hanes-Wilkinson Plot
Another inversion method: multiply MM eq by [S]
v0 = Vmax[S] 1 KM
S/V0 = [S] +
KM + [S] Vmax Vmax
60
50
Vmax is 60 by inspection
40
30
20
10
0
1.00E-05 1.00E-04 1.00E-03 1.00E-02 1.00E-01 1.00E+00
[S]
Example of Michaelis-Menten Enzyme Kinetics
Given this data, what is Vmax? What is KM?
[S] moles/L 1/[S] v (mol/min) 1/v
2.00E-01 5.00 60 0.01666667
2.00E-02 50.00 60 0.01666667
2.00E-03 500.00 60 0.01666667
2.00E-04 5000.00 48 0.02083333
1.50E-04 6666.67 45 0.02222222
1.30E-05 76923.08 12 0.08333333
Since Vmax = 60 we can solve for KM, plug this into MM eq.
0.08
0.07
1/v 0.06
KM 1 1
0.05 1/Vmax 1/V0 = +
0.04
Vmax [S] Vmax
0.03
-1/KM 0.02
Scale is important
0.01
1/[S]
0
- 40000 - 20000 0 20000 40000 60000 80000 100000
Comparison of Methods
Vmax
kcat
ET
For Michaelis -Menton kinetics k2= kcat
When [S] << KM very little ES is formed and [E] = [E]T
and
vo
k2
ET S ES
k cat
KM KM
Kcat/KM is a measure of catalytic efficiency
What is catalytic perfection?
k1k 2
When k2>>k-1 or the ratio is maximum
k 1 k 2
10
8
6 experimental data
regression
4
2
0
0 5 10 15 20 25
S (g/L)
Allosteric Enzyme Kinetics
In an enzyme with more than one substrate
binding site, binding of one substrate
molecule affects the binding of another.
n
d[S ] V max[S]
v n
dt K m [S ]n
Michaelis-Menten
Allosteric
Inhibition of Enzymes
Can be irreversible (metals) or
reversible (product, substrate, salt,
etc.)
1. Competitive
2. Noncompetitive
3. Uncompetitive
Competitive Inhibition
Inhibitor is an analog of the substrate, and
binds to the active site of the enzyme.
[E ][S ]
K m
E S ES P [ES ]
[E ][I ]
KI
I [EI ]
[E 0 ] [E ] [ES ] [EI ]
EI
v k 2 [ES]
Competitive inhibition E
ES
Vmax [S ] Vmax [S ]
v
I [S ]
K m,app
K m 1 [S ]
K I
Competitive Inhibition
1/v I>0
I=0
Vmax is unchanged
1/Vmax
v k 2 [ES]
(b) A noncompetitive inhibitor (I) (green) does
not bind to the substrate binding site and can Noncompetitive
bind to both the free enzyme or the ES E ES
complex.
Usually a noncompetitive inhibitor resembles
one substrate (S2) in a two-substrate reaction, EI
as shown here, where both substrates are
present on the enzyme at the same time.
In the simplest cases, noncompetitive
inhibitors don't change the Km for the first
substrate (S), because they don't affect its
binding.
But providing the concentration of S2 is not
high enough to out-compete all the inhibitor,
the inhibitor does reduce the Vmax for the
reaction.
Noncompetitive Inhibition
Cofactors and Coenzymes
Holoenzymes- three parts
Apoenzyme- Protein portion
Cofactor- inorganic ion (ex: metal ions),
improve the fit of enzyme with substrate
Coenzyme- nonprotein organic molecule
(ex: NAD- nicotinamide adenine
dinucleotide), many synthesized from
vitamins (why vitamins are essential)
Noncompetitive Inhibition
Rate is given by:
Vmax Vmax,app
v
[I ] K m K m
1 1 1
K I
[S ]
[S ]
Noncompetitive Inhibition
1/v I>0
I=0
1/Vmax,app
1/Vmax
-1/Km 1/[S]
Km is unchanged
Uncompetitive Inhibition
Inhibitor binds only to ES complex, and not
to E alone.
E S ES P [E ][S ]
K m
[ES ]
I
[E ][I ]
KI
[EI ]
ESI
[E 0 ] [E ] [ES ] [ESI ]
v k 2 [ES]
Uncompetitive inhibition
Vmax
[S ]
[I ]
1
K I Vmax,app [S ]
v
K m K [S ]
[S ] m ,app
[I ]
1
K I
Uncompetitive Inhibition
1/v
I>0
I=0
1/Vmax,app
1/Vmax
Substrate inhibition
Vmax [S ]
v
[S]2
K m [S ]
KSi
[S ]max. rate K mK Si S
Figure U2-4.1 Competitive, noncompetitive and
uncompetitive inhibition
Enzyme reactions can be slowed by the presence of
inhibitors
A key parameter that can be obtained from such an analysis is the
affinity of the inhibitor for the enzyme, the inhibition constant Ki.
By convention, Ki is given as the dissociation constant for the enzyme-
inhibitor equilibrium:
Ki = [E][I] Ki = [ES][I]
[EI] [ESI]
The lower the value of Ki the tighter the inhibitor binds. In
pharmacology, the value of Ki is often used as a measure of the
effectiveness of a drug.
A compound with a very low Ki, say 10-9 M (nanomolar) or less, can
be given at very low doses and will still be able to bind its target.
Enzyme Inhibitor Classification
1. Competitive inhibitors:
Most common class of reversible inhibitor consists of
compounds that resemble the substrate.
Such molecules can fit into the substrate binding site,
thereby blocking access from substrate molecules.
These inhibitors compete with the substrate for the
active site.
Example: Many HIV protease inhibitors that have
proven to be effective in treatment of AIDS are
competitive inhibitors that were designed to resemble
the peptide substrate of the HIV protease.
Enzyme Inhibitor Classification
Not all inhibitors compete with the substrate for the
active site of the enzyme; other inhibitors bind to a
separate site.
y = 0.5331x + 0.0912
0.25
y = 0.2668x + 0.091
R = 1
0.2 50nM
100nM
200nM
0.15
Linear (50nM)
Linear (100nM)
y = 0.1337x + 0.0909
0.1 Linear (100nM)
Linear (200nM)
0.05
0
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35
The variation in slope and common y-intercept for the
reciprocal plot as a function of MTX concentration
demonstrates that MTX is a COMPETITIVE
INHIBITOR. Best fit by a straight line to the 200 nM
data corresponds to a y-intercept of 0.091mM/s and
slope of 0.535 s.
KI = 3.40 pM
E a
k d t
v Ae RT
[E 0 ]e
Activation energy 10
kcal/mol
Deactivation energy 100
kcal/mol