Download enzyme - Clayton State University

Chapter 3
DRUG TARGETS:
ENZYMES
Naming enzymes
• Root + ase
•Classification
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
Reaction Type Catalyzed
Oxidation Reduction Reactions
Group transfer Reactions
Hydrolysis Reactions
Addition or removal of groups to form
double bonds
Intramolecular group transfers
Joining two substrates
Structure and function of enzymes
• Globular proteins acting as the body’s catalysts
• Speed up time for reaction to reach equilibrium
• Lower the activation energy of a reaction
Example:
O
NADH2
+ H3C
O
C
Pyruvic acid
C
LDH
H
HO
O
C
H3C
OH
C
+
OH
Lactic acid
LDH = Lactate dehydrogenase (enzyme)
NADH2 = Nicotinamide adenosine dinucleotide (reducing agent & cofactor)
Pyruvic acid = Substrate
NAD+
Structure and function of enzymes
Lowering the activation energy of reaction
Energy
Energy
Transition state
Act.
energy
Starting
material
Act.
energy
Starting
material
∆G
∆G
Product
Product
WITHOUT ENZYME
New
transition
state
WITH ENZYME
Enzymes lower the activation energy of a reaction but DG remains the same
Structure and function of enzymes
Methods of enzyme catalysis
• Provides a reaction surface (the active site)
• Provides a suitable environment (hydrophobic)
• Brings reactants together
• Positions reactants correctly for reaction
• Weakens bonds in the reactants
• Provides acid / base catalysis
• Provides nucleophilic groups
The active site
• Hydrophobic hollow or cleft on the enzyme surface
• Accepts reactants (substrates and cofactors)
• Contains amino acids which:
- bind reactants (substrates and cofactors)
- catalyse the reaction
Active site
Active site
ENZYME
Substrate binding
Induced fit
Substrate
S
Induced fit
• Active site is nearly the correct shape for the substrate
• Binding alters the shape of the enzyme (induced fit)
• Binding strains bonds in the substrate
• Binding involves intermolecular bonds between functional
groups in the substrate and functional groups in the active site
Substrate binding
Bonding forces
• Ionic
• H-bonding
• van der Waals
Example
vdw
interaction
S
H-bond
Active site
O
Ser
H
ionic
bond
CO2
Asp
Enzyme
Phe
Substrate binding
Bonding forces
• Ionic
• H-bonding
• van der Waals
Example - Binding of pyruvic acid in LDH
O
O
O
C
H3 C
H-Bond H
O
C
O
Possible interactions
H-Bond
van der Waals
Ionic
O
C
H3 C
vdw-interactions
C
O
H3 N
Ionic bond
Substrate binding
Bonding forces
• Induced fit - Active site alters shape to maximise intermolecular
bonding
Phe
S
O
Ser
S
O
H
CO2
Asp
Intermolecular bonds not optimum
length for maximum bonding
Phe
Induced
fit
Ser
H
CO2
Asp
Intermolecular bond lengths optimised
Susceptible bonds in substrate strained
Susceptible bonds in substrate more easily
broken
Substrate binding
Example - Binding of pyruvic acid in LDH
O
H
O
O
C
H3 C
C
O
H3N
Substrate binding
Example - Binding of pyruvic acid in LDH
O
p bond
weakened
H
O
O
C
H3 C
C
H3N
O
Catalysis mechanisms
Acid/base catalysis
•Histidine
+H
NH
N
NH
N
-H
H
Non-ionized
Acts as a basic catalyst
(proton 'sink')
Ionized
Acts as an acid catalyst
(proton source)
Nucleophilic residues
H3N
L-Serine
H
CO2
OH
H3N
H
CO2
SH
L-Cysteine
Catalysis mechanisms
Serine acting as a nucleophile
Substrate
X
H2O
HO
OH
Ser
O
Ser
OH
Ser
Product
Catalysis mechanisms
Mechanism for chymotrypsin to hydrolyses peptide bonds
Catalytic triad of serine, histidine and aspartate
..
:O
Ser
H
:N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
: O:
C
Protein
..
:O
Ser
NH
H
Protein
:N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
:
:O:
Protein
C
:O
Ser
NH
H
Protein
:N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
:
:O:
Protein
C
NH
Protein
H
: O ::
Ser
N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
H
C
:O ::
Ser
:
Protein
:
:
O
:
O
H
:N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
:
:O:
Protein
O
C
:O :
Ser
H
H
:N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
:
:O:
H
O:
Protein
:
C
H
:O : :
Ser
N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
:O:
C
OH
Protein
..
:O
Ser
H
:N
N
H
O
His
Chymotrypsin
Asp
O
Catalysis mechanisms
Mechanism for chymotrypsin
:O:
C
NH protein
:N
H
Ser
C
C
:N
H
Ser
His
:O :
O
Asp
Ser
.. H
:O:
protein
C
:O :
O
..
protein
H
O
Asp
His
O
O
N H
His
O
Asp
O
:O :
Ser
N H
His
protein
C
O
O
Asp
OH
O
C
:N
:N
:O :
Ser
Asp
..
: O : ..
OH
protein
..
H
H
O
C
N H
N
H
O
NH protein
protein
N H
O
:
:O
O
:
..
:O :
NH protein
Ser
His
..
:O :
protein
N H
:
..
:O
:
protein
H
N
N H
His
O
Asp
O
..
: OH
Ser
:N
N H
His
O
Asp
O
Overall process of enzyme catalysis
S
P
S
EE
E+S
E
ES
P
E
EP
E
E+P
• Binding interactions must be strong enough to hold the substrate
sufficiently long for the reaction to occur
• Interactions must be weak enough to allow the product to depart
• Implies a fine balance
• Designing molecules with stronger binding interactions results in
enzyme inhibitors which block the active site
Regulation of enzymes
• Many enzymes are regulated by agents within the cell
• Regulation may enhance or inhibit the enzyme
• The products of some enzymes may act as inhibitors
• Usually bind to a binding site called an allosteric binding site
NH2
Example
N
N
O
O
P
O
O
O
H
H
OH
H
OH
H
O
HO
HO
H
H
H
AMP
H O
H O
HO
N
H OH
H OH
Glycogen
N
OH
OH
Phosphorylase a
H
H
H
OH
O
Glucose-1-phosphate
O
P
HO
OH
n
Regulation of enzymes
Active site
unrecognisable
Active site
ACTIVE SITE
(open)
Enzyme
ENZYME
Allosteric
binding site
Induced
fit
(open)
Enzyme
ENZYME
Allosteric
inhibitor
• Inhibitor binds reversibly to an allosteric binding site
• Intermolecular bonds are formed
• Induced fit alters the shape of the enzyme
• Active site is distorted and is not recognised by the substrate
• Increasing substrate concentration does not reverse inhibition
• Inhibitor is not similar in structure to the substrate
Regulation of enzymes
Biosynthetic pathway
S
P
P’
P’’
P’’’
(open)
Enzyme
ENZYME
Inhibition
Feedback control
• Enzymes with allosteric sites are often at the start of a biosynthetic
pathway
• Enzyme is controlled by the final product of the pathway
• Final product binds to the allosteric site and switches off enzyme
Regulation of enzymes
• External signals can regulate the activity of enzymes
(e.g. neurotransmitters or hormones)
• Chemical messenger initiates a signal cascade which activates
enzymes called protein kinases
• Protein kinases phosphorylate target enzymes to affect activity
Example
Phosphorylase b
(inactive)
Protein
kinase
Signal
cascade
Phosphorylase a
(active)
Glycogen
Glucose-1-phosphate
Cell
Adrenaline