Principles of Enzyme Catalysis
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Principles of Enzyme Catalysis
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Thermodynamics is concerned with only the initial and final states of a process, being independent of the path(s) between the two states.
Kinetics is concerned with the rate at which the process occurs and thus is concerned with the path(s) between the two states.
The parable of the sugar packet
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Wolfenden, R. (2003) Thermodynamic and extrathermodynamic requirements of enzyme catalysis. Biophys. Chem. 105, 559-572.
Time Scale for Selected Biochemically Important Reactions
Carbonic anhydrase
kcat = 20 x 106 s-1
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Collision Theory
k = (gkBT/h) C1-n e-DG‡/RT
The rate constant for the reaction
is inversely proportional to the height of the barrier (DG‡) but proportional to temperature
is proportional to the concentration of reactants
Kinetic energy
Nu
mb
er
of
mo
lec
ule
s
Boltzmann distribution
DG‡
is proportional to the probability of a productive collision
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Encounter Complex
As two reactants diffuse together they become caged by the surrounding water molecules.
In this encounter complex there is a greater probability that the reactants will collide rather than diffuse apart.
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DG = DH -TDS
DG‡ = DH‡ -TDS‡
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Potential Mechanisms for Enzyme Catalytic Efficiency
• By binding substrates in the active site, enzymes can increase the effective local concentrations of reactants (Proximity effects)
• Substrate binding can correctly orient reacting groups in the active site (Orbital steering)
• Enzymes can promote desolvation upon substrate binding
• Enzymes can enhance the inherent reactivity of functional groups by altering the microenvironment within the active site
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Entropy-Enthalpy Compensation
The unfavorable entropy of activation (DS‡) of bringing the reactants together into the encounter complex is compensated by the favorable enthalpy of binding (DH) of the reactants in the active site.
By binding substrates in the active site, enzymes can produce effective concentrations orders of magnitude greater than can be achieved in the absence of the catalyst.
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Proximity Effects
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Induced Fit (Transition State Binding)
Wolfenden, R. (2003) Biophys. Chem. 105, 559-572
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Induced Fit (Transition State Binding)
Methotrexate Aminopterin
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Microenvironment Effects
Mechanism of Acetoacetate Decarboxylase
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Ho et al. (2009) Nature 459, 393-397
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Ramped N-terminus to C-terminus
Lys115
Substrate Schiff base
Arg29
Ho et al. (2009) Nature 459, 393-397
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General Acid-Base Catalysis
Human Pancreatic Ribonuclease
His219
His112
NC
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General Acid-Base Catalysis
Mechanism of Ribonuclease
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C
E35 D52
C
Rings A-D Rings A-D
Induced Fit in the Mechanism of Lysozyme
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Vocadlo et al. (2001) Nature 412, 835-838
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Covalent Catalysis in the Serine Proteases
Ser195
His57
Asp102
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Trypsin Chymotrypsin
Thrombin Subtilisin