Lecture 14: Enzyme-substrate interactions Flashcards
Models of enzyme behaviour‘Michaelis-Menten’ kinetics
Simple models assume the following:
Only one molecule of one substrate binds to the enzyme (One substrate reactions are rare – isomerizations and rearrangements);
Enzyme and substrate form a [ES] complex (rate-limiting step);
Enzyme converts substrate to product and product release occurs (fast);
Products bind weakly to enzymes.
Factors that affect enzyme activity
pH – due to changing ionisation state of side-chains. Grossly inappropriate pH unfolds proteins;
Denaturing reagents (detergents, urea, guanidinium hydrochloride);
Temperature – higher temperatures increase rate until thermal denaturation (unfolding) of the protein occurs;
Activity is proportional to amount of enzyme;
Substrate concentration (Lecture 14; this lecture);
The presence of inhibitors
[E]
concentration of enzyme
[S]
concentration of substrate
[ES]
concentration of enzyme-substrate complex
[P]
concentration of product
v
rate
Vmax
rate when all enzyme active sites are occupied (the enzyme is saturated
Km
[S] at which v = ½ Vmax
At high [S],
ate (v) does not increase with further increases in [S] (zero order). Rate only depends on [ES] and k3 (i.e., saturation has occurred
Assumptions of steady-state model
[E] «_space;[S] (typically nM vs. mM);
[S] remains constant; Measured rate of reaction is linear at beginning of curve (‘initial rate’);
[ES] remains the same throughout course of reaction (‘The steady-state approximation’);
Product binds weakly to enzyme;
Rate of conversion of product to substrate is negligible
The Lineweaver-Burk Plot
Plot 1/v against 1/[S]
Y-intercept = 1/Vmax
X-intercept = -1/Km
Higher precision;
Lower accuracy;
Errors are not equal at all points
(least squares regression is not appropriate
Meaning of kinetic parameters
Km = concentration of substrate at which v = 0.5 Vmax.
Km is NOT a substrate binding constant, but is often interpreted as a crude measure of affinity of enzyme for substrate;
Km often similar to substrate concentration in cell;
Vmax = maximum velocity = limiting rate (e.g., in nmoles product/min);
kcat = Vmax/amount of enzyme in e.g., nmoles. This is the first order rate constant for conversion of substrate to product. In our model kcat = k3
Mode of action of inhibitors
Inhibitors can resemble the substrate in structure;
Inhibitors affect either Km, Vmax or both;
Potency is measured by Ki value (concentration of inhibitor that causes a 2-fold change in Km or Vmax);
Ki values related to binding energy (ΔG);
Smaller Ki numbers mean tighter binding (higher potency);
Kcat
Vmax/moles of enzymes
Competitive inhibition
The most common form of inhibition;
Km increases (X-intercept changes);
Km (I) = Km (1 + [I]/Ki)
No change in Vmax (Y-intercept the same);
Inhibition decreases with increased substrate concentration.
Non-competitive inhibition
Uncommon for single substrate enzymes;
Vmax is reduced;
Vmax/Km (I) = Vmax/Km(1 + [I]/Ki);
Km is not affected;
Inhibition not reduced by increasing substrate.
Mixed competitive inhibitor
Common form of inhibition;
Km is increased (as for competitive inhibition);
Vmax is decreased (as for non-competitive inhibition);
α factor defines the competitive and non-competitive components.
Uncompetitive inhibition
Uncommon mode of inhibition;
Inhibitor binds to the ES complex;
Parallel lines in Lineweaver-Burk plot;
Both Km and Vmax reduced by same amount, (1 + [I]/Ki);
Increasing substrate concentration increases inhibition.
IC50
concentration of drug required for 50% reduction in activity
Tight-binding Inhibitors
Tight-binding inhibition occurs when the concentrations of (active) enzyme and inhibitor are similar;
This means that the concentration of free inhibitor does not approximate to total inhibitor (unlike in the cases above);
The apparent Ki value will increase with increasing enzyme concentration;
Tight-binding inhibition often has very slow onset, and the enzyme inhibitor complex can have a very long half-life (Ki = koff/kon);
This means that infrequent dosing regimens can be used (easier for patient, reduced side-effects etc.). Therefore, many drug discovery programmes aim to develop a tight-binding inhibitor.
