Binding of ligands to proteins

P+L PL (P: protein; L: ligand)

[P ][L]
K
[P L]

• Simple binding (myoglobin)

• Cooperative binding (hemoglobin)

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Myoglobin

The function of myoglobin is

to store oxygen and transfer
it to mitochondria in muscles

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Fe(II) heme liganded to His
and oxygen

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Myoglobin

O2

O2

O2

[MbO2]
Y=
[Mb]0

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Hemoglobin

Hemoglobin has 4
subunits each
containing a heme
group.

The function of
hemoglobin is to
transport oxygen
from lungs to
tissue (in muscle
to myoglobin)

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Hemoglobin

O2 O2

O2 O2 O2

O2 O2
O2 O2
T R
O2
O2 O2 O2 O2

[HbO2] O2 O2 O2
Y=
[Hb]0 O2

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Hemoglobin and myoglobin

Myoglobin

Hemoglobin

Myoglobin Hemoglobin
Y Y

[O2] [O2]
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Enzyme kinetics

• Michaelis Menten kinetics

• Substrate inhibition
• Cooperativity (Monod-Changeux-Wyman)
• Ion channels

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Time course of reactants

Quasi-
steady state

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 Graph of d[P]/dt (=v0) vs. [S]

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Substrate inhibition

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Cooperativity

• Proteins are (almost) always oligomers, i.e.

at least two (almost) identical subunits
• Several ligand/substrate binding sites
• The protein exists in an inactive (T) and an
active (R) form
• The protein usually also has binding sites
for allosteric activators/inhibitors

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 T R
f
T R (inactive) (active)
b 2k+ k
R+S RS R+P
k-
k+ 2k
RS + S RS2 RS + P
2k-

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 Quasisteady-state approximation

Total no of active sites = [E]0

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 [S ] [S ]
d [ P ] V m ax K ( 1  K ) V m ax  1   
 
dt [ S ] 2 L  1    2
L  (1  )
K
L  1   
2
If then
d [ P ] V m ax
  1   
dt L

L  1   
2
If then
d [ P ] V m ax  1   
 2  V m ax
dt L  1   
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 V
Vmax

Generally for an enzyme with n subunits:

d [ P ] V m ax  1   
n 1
[S ]
 ; 
L  1   
n
dt K
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Michaelis-Menten
vs. MCW kinetics

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Hill plot

Hill
plot

slope  n

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Effect of size of L

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Effect of the size of n

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Allosteric activator

A A
A A A

inactive active active active

T R R R
RS RAS RA2S
RS2 RAS2 RA2S2

Quasisteady-state ………

d [ P ] V m ax  1   1   
2
[S ] [ A]
 2 ;  ;  
dt L  1    1    KS KA
2

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Allosteric inhibitor

I I
I I I
inactive

Quasisteady-state ………

d[ P] V m ax  1    [S ] [I]
 ;  ; 
L 1     1   
2
dt 2
KS KI

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An activator ”decreases” L
An inhibitor ”increases” L

d[ P] 
V m ax  1    n 1
[S ] [I] [ A]
 ;  ;  ; 
L 1  
n
dt KS KI KA
 1  
n

1    n

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 d [ P ] V m ax  1   1   
2
[S ] [ A]
 2 ;  ;  
dt L  1    1    KS KA
2

L  1    1   
2 2
If th e n
d [ P ] V m ax
 1   1    2

dt L

If A is also a product of the reaction we say that

the reaction is autocatalytic because the rate
increases with increasing concentration of the
product

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Receptors and ion channels

A A

Lipid
Recptor
membrane

Yopen
Ion
channel
1.0
A: agonist

[A]

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Action potentials

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Synapse H3C
C
O
O
CH2
H3C
CH2
N
+ CH3 CH3
N
+

H
CH3
Acetylcholine N
Nicotine

H
H O CH2
+ CH3
H3C N
H3C
HO H CH3

Muscarine

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Nicotinic Acetyl Choline Receptor

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Acetyl choline receptor

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Receptor in two conformations

T-form closed, R-form closed,

does not bind A binds 2 A molecules

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Binding of two agonist molecules
opens channel
A

Closed channel Closed channel A

A

A A A

Closed channel A Open channel

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 [ A ]2 [ A ]2
[ R A2 ] 2 [R] 2
Y op en   K  K
[ R ]0 [ A ] 2 [ A] 2
[ R ]( L  ( 1  ) ) L  (1  )
K K

Generally for receptor that binds n molecules

of agonist
Yopen
n
[ A]
n
Yop en  K n small
[ A] n n large
L  (1  ) [A]
K
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 Agonists may be activators, e.g. Acetyl
choline or inhibitors, e.g. g-aminobotyric
acid (GABA)

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Voltage-gated ion channels

Lipid
Recptor
membrane

Yopen
Ion
channel
1.0

Membrane potential

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Nerve cell

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Actions potentials arise from voltage-
sensitive ion channels

http://www.youtube.com/watch?v=ifD1YG07fB8
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