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Abstract−The Michaelis-Menten Formalism based on standard quasi steady state approximation (sQSSA) derived for single
enzyme reaction, described the kinetics of many enzyme catalyzed reactions for a number of years. Based on this sQSSA a
closed form solution for basic enzyme reaction was derived earlier by Schnell and Mendoza. This solution was given in terms of
a relatively new function known as Lambert W function which satisfies the transcendental equation W(x)exp(W(x)) = x. But this
formalism is valid only when enzyme concentration is sufficiently small. Recently Borghans et. al. have introduced the total
quasi steady state approximation (tQSSA) which is valid for a broader range of parameters. In the present work an attempt has
been made to derive an analytical solution for substrate decomposition and product formation with the aid of Lambert W
function for single enzyme-substrate reaction, based on total quasi steady state approximation.
Keywords−Standard quasi steady state approximation, Total quasi steady state approximation, Lambert W function,
Transcendental equation.
—————————— ——————————
1 INTRODUCTION
The kinetics of most of the biochemical reactions in in vivo, and thus advantageous in speeding up the
biochemistry have been described by the formalism simulations. Furthermore, while the rate constants in (1)
developed by Henri [8], [9] and Michaelis and Menten are usually not known, finding the kinetic parameters
[10] and further improved by Briggs and Haldane [4]. characterizing the sQSSA is a standard procedure in in
This formalism assumes a reaction where substrate S vitro biochemistry [2]. But the validity of sQSSA demands
binds reversibly to an enzyme E to form intermediate that the initial enzyme concentration should be much
enzyme‐substrate complex C which irreversibly yields the lower than either the substrate concentration or the
product P and enzyme become free to proceed on another Michaelis‐Menten constant Km [16]. This is usually
substrate molecule. The basic enzyme catalyzed reaction fulfilled for in vitro experiments, but since biological
can be represented as follows media is structure heterogeneous therefore condition
k1
E S C
k2
E P (1)
breaks down in vivo [1], [18]. Therefore sQSSA might be
k1 invalid in simulation of physiologically realistic in vivo
systems. Hence, even if the kinetic constants such as Km
where k1, k‐1 and k2 are the positive rate constants for
and kcat are identical in vivo and in vitro, they need to be
each reaction. Michaelis and Menten [10] assumed the
implemented in some other approximation which must
existence of an equilibrium between reactants and the
be valid for the whole system and initial concentrations
intermediate compound to describe the kinetics of
under investigation.
reaction (1). But rather than accepting the equilibrium
Therefore when enzyme concentration is high in
between substrate, enzyme, and the intermediate
comparison to substrate, the methods based on sQSSA are
compound George Briggs and John Haldane [4] claimed
not expected to be valid. Segel and Slemrod [17] proposed
that the rate at which the concentration of the
a reverse quasi steady state approximation (rQSSA) in
intermediate compound varies is practically zero, except
which the substrate S is in a QSS with respect to the
at the very beginning of the reaction. This assumption is
enzyme–substrate complex. Recently Schnell and Maini
usually referred to as standard quasi steady state
[14] discussed the validity of rQSSA and derived the
approximation (sQSSA) which states that after an initial
solution for it. The total quasi steady state approximation
short transient phase the reactant concentrations vary
(tQSSA) has been introduced by Borghans et al. [3] which
slowly as if in a quasi steady state.
is valid for a broader range of parameters covering both
The application of quasi‐steady‐state approximation
high and low enzyme concentrations. The validity of
reduces the dimensionality of the system which is
tQSSA has been verified by Tzafriri [19] for any set of
essential to numerically simulate large networks as found
parameters.
Although tQSSA proved to be better approximation
————————————————
than sQSSA and rQSSA but still an analytical formalism is
Prashant Dwivedi is with theDepartment of Mathematics, Maulana Azad
National Institute of Technology, Bhopal-462051. needed to describe kinetics of biochemical reactions
Madhvi Shakya is with theDepartment of Mathematics, Maulana Azad under in vivo conditions. However based on sQSSA an
National Institute of Technology, Bhopal-462051. explicit closed‐form solution to the Michaelis‐Menten
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equation has been proposed only recently [13]. This transient phase the enzymatic system enters in a slowly
solution is based on the Lambert W function [5], [6] and changing phase where the reactants can be assumed to be
the accuracy of this solution was independently verified in instantaneous equilibrium. Therefore in this slow time
to be on the order of 10‐15 [7]. But since sQSSA is valid regime the complex C is in a quasi steady state with
only for a short range of parameters this solution failed if regard to substrate and product. From dC dt 0, it
enzyme concentration is not very small compared to follows from (9) that
substrate concentration. In the present paper taking into E0 S
account only the well‐established assumptions of the C (12)
tQSSA, we have been able for the first time to find Km S
analytical solution to describe the variations of the Substituting the value of C from (12) into (8) leads to the
reactant concentrations during the complete time span of ordinary differential equation
the basic enzymatic reaction. dS v S
max (13)
dt Km S
2 Enzyme kinetics with Standard Quasi
Where vmax k 2 E0 is referred to as the maximum
Steady-state Approximation
velocity. Now since during the initial transient phase the
Mathematical formulation of enzymatic system given by
substrate concentration hardly changes, i.e. S S 0 .
(1) is based on the law of mass action which states that
reaction rates are proportional to the concentrations of Therefore during the initial transient phase (9) can be
reactants. Thus by applying the law of mass action we get solved to give
the following system of nonlinear differential equations E0 S0
dS C (t ) [1 exp(k1 ( K m S0 )t )] (14)
k1SE k1C , (2) K m S0
dt Equations (13) and (14) are describing the two time
dE phases of reaction system (1) and the complete time
k1SE (k1 k2 )C , (3) evolution of (1) is described by these two phases namely
dt
initial transient phase and steady state phase. Hence the
dC
k1SE (k1 k2 )C , (4) total solution for complete time evolution of enzymatic
dt system (1) will comprise the solution obtained from (13)
and that of equation (14). But on integrating (13) an
dP
k2 C , (5) implicit expression in substrate concentration S is
dt obtained. However Schnell and Mendoza [13] derived an
With initial conditions explicit closed form solution for equation (13), given in
S (0) S0 , E (0) E0 , C (0) 0 and P(0) 0 (6) terms of Lambert W function and is of the form
Two conservation laws can also be formulated here one S v t S 0
S (t ) K mW 0 exp max (15)
for enzyme concentration and other for substrate K
concentration as follows m K m
E0 E C and S0 S C P (7) At this point, Segel [16] suggested two time scales, first is
concerned with the time duration of initial fast transient
By applying these two conservation laws the system of phase tC and second is concerned with the time taken for
nonlinear differential equations given by equations (2), a significant change in substrate concentration tS that
(3), (4) and (5) reduces to following pair of coupled characterizes the quasi steady‐state period. From
nonlinear differential equations: equation (14) the initial fast time scale can be given as
dS 1
k1 ( E0 C ) S k1C , (8) tC (16)
dt k1 ( K m S0 )
dC
k1[( E0 C )S K mC ], (9) The slow time scale can be determined by dividing the
dt total change in substrate concentration by the maximum
Where rate of substrate change, i.e.
k1 k2 tS
S0
Km , (10) , (17)
k1 dS dt max
together with the uncoupled equation This in turn gives
dP S0 K m
k2C (11) tS (18)
dt k2 E0
Now sQSSA states that when the reaction is started by Now sQSSA will be valid if tc ts (as suggested by
mixing enzymes and substrates, the enzyme substrate segel, [16]). Therefore from (16) and (18) the necessary
complex builds up at first very rapidly and this phase is condition for the validity of sQSSA is
known as initial transient phase. After this initial fast
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E0 For the sake of simplicity neglecting the square terms of C
1 (19) in (26), we get
S0 K m E0 St
From (19) it is clear that the validity of sQSSA demands C (27)
that initial enzyme concentration should be much less E0 K m St
than either initial substrate concentration or Michaelis‐ Substituting the value of C from (27) into (21),
Menten constant. This condition is usually fulfilled in dSt vmax St
vitro (i.e. in lab condition) but often breaks down in vivo (28)
(i.e in biological conditions) [1], [18]. Therefore in dt E0 K m St
simulation of physiologically realistic in vivo systems where vmax k2 E0 is the maximum velocity.
sQSSA might be invalid. For this kind of situations total
The slow time scale can again be estimated by
quasi steady state approximation (tQSSA) proved to be
considering the maximum change of St divided by the
extremely useful.
maximum rate of change of total substrate after fast
transient, i.e.
3 Enzyme kinetics with Total Quasi Steady- S0
state Approximation tS , (29)
dSt dt max
When enzyme concentration is in access compared to
substrate the sQSSA and therefore (17) are not expected to From equation (21) with C given by equation (27) and
be valid, the total quasi steady state approximation is with St = S0, the expression for the slow time scale ts is
applied. According to tQSSA substrate concentration S is given as follows
replaced by total substrate concentration St, [3] where E0 S0 K m
tS (30)
St S C (20) k2 E0
Substituting St in place of S in equations (8) and (9) the Now total quasi steady state approximation is to be valid
dynamics of the enzymatic system will be governed by if tc ts . Therefore from (25) and (30) condition for the
the following coupled nonlinear differential equations validity of tQSSA can be given as
dSt k2 E0
k2C , (21) 1 (31)
dt k1 ( E0 S0 K m ) 2
dC
k1[( E0 C )( St C ) K mC ] (22) 3.1 Analytical Solution based on tQSSA
dt From the above discussion we can see that the initial
With initial conditions St(0) = S0 and C(0) = 0. The transient phase which is being described by (24), is also
uncoupled reaction given by (11) remains unchanged. valid for post‐transient period (i.e. steady state phase) as
Again the complete course of reaction can be divided into it is taking into consideration the form of (27). Also (28) is
two phases, initial transient phase and steady state phase. describing the steady state phase. In this way the use of
Now during the initial transient phase change in the tQSSA allows us the decoupling of the coupled
substrate concentration is negligible and the complex differential equations (21) & (22) describing the kinetics of
concentration begins from an initial value of zero and enzymatic system (1). Therefore the total solution for the
remains relatively small. Therefore in the equation (22) complete time evolution can be obtained from the
substituting St(t) = S0 and neglecting the terms quadratic equations
in C,
dSt vmax St
dC (32)
k1[ E0 S0 ( E0 S0 K m )C ] (23) dt E0 K m St
dt
Moreover for the initial transient phase equation (23) can be E0 St
C (t ) [1 exp( k1 ( E0 St K m )t )]
solved to give E0 St K m
E0 S0
C (t ) [1 exp(k1 ( E0 S0 K m )t )] (24) (33)
E0 S0 K m Integrating (32) results in the following equation
From (24) it is clear that the time scale corresponding to St (t ) S0 ( K m E0 ) ln St (t ) S0 vmax t (34)
initial transient phase is
This expression is of implicit nature therefore a solution
1
tC (25) of the form S = f(t) cannot be obtained for S(t) from here.
k1 ( E0 S0 K m ) However an explicit analytical solution can be obtained in
Since after the initial transient phase the complex the form of Lambert W function for equation (32), by
concentration remains constant therefore applying steady taking a different approach as follows.
Let f(x) be a function defined as f ( x) xe ; x 0 . Then
x
state assumption dC/dt ≈ 0 in equation (22), we get a
quadratic equation given as
f '( x) (1 x)e x , so f '( x) 0 for every positive x. Then
C ( E0 K m St )C E0 St 0
2
(26) the inverse of f : (0, ) (0, ) will exist. This inverse
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function is known as Lambert W function. Function f(x) mapped onto the interval (0,1) by dividing their
defined above is strictly increasing on [ 1, ) , therefore maximum absolute values as shown in the figure.
W(x) is defined over [ 1 e , ) [5], [6]. However for the
present purpose it is convenient to restrict W to [0, ).
1
Scaled Concentrations
W ( x)eW ( x)
x . Thus 0.6
ln W ( x) W ( x) ln x (35) 0.5
0.4
Now (34) can be rearranged to give
0.3
St (t ) S (t ) S0 vmax t S0
ln t ln
0.2
K m E0 K m E0 K m E0 K m E0 0.1
0
(36) 0 0.1 0.2 0.3 0.4 0.5
Scaled Time
0.6 0.7 0.8 0.9 1
Looking closely at (35) and (36) it seems reasonable to
Fig. 1. Time dependent behaviour of the reactant concentrations for
assume that for any t during the steady state phase of the basic enzyme substrate reaction with the aid of tQSSA. Reactant
reaction there exist a positive number x such that concentrations and time range has been scaled to the interval (0,1)
by dividing their maximum absolute values. Parameters values used
St (t ) S (t ) -1 -1 -1 -1
are k1=10 μM sec , k-1=1 sec , k2=10 sec (Km=1.1 μM) and initial
W ( x) and so ln t ln W ( x) data were S0=10 μM, E0=0.1 μM and C0=0=P0.
K m E0 K m E0
Which in turn gives From the fig. 1. It is clear that the substrate concentration
St (t ) S (t ) decreases exponentially while the product concentration
ln t W ( x) ln W ( x) increases exponentially as expected. Also in the transient
K m E0 K m E0 period which is very small, enzyme substrate complex
Therefore from (36), we get builds at first very rapidly (vertically increases) and
became nearly constant during steady state phase and
S0 vmax t S0
ln W ( x) ln W ( x) then start to decay to zero. The graph for enzyme
K m E0 K m E0 concentration is just opposite to that of enzyme substrate
complex. In fig. 1 since we have taken initial enzyme
Taking antilog on both sides and recalling W ( x)eW ( x ) x concentration less in comparison to that of substrate, the
We obtain results are in agreement to that of results obtained from
S0 S v t tQSSA.
x exp 0 max (37)
K m E0 K m E0
1 1
2(a) For e0=0.1 2(b) For e0=10
0.9 For e0=1 0.9 For e0=100
Now for the x given by (37) under steady state phase it 0.8 0.8
can also be proved that
Scaled Substrate Concentration
Scaled Substrate Concentration
0.7 0.7
S t (t ) S0 v t S 0 0.6 0.6
W exp max
0.5 0.5
( K m E0 ) K m E0 K m E0 0.4 0.4
0.3 0.3
(38)
0.2 0.2
From (38) we are in position to express substrate
0.1 0.1
concentration as a function of time explicitly
0 0
S0 v t S0
0 0.2 0.4 0.6 0.8 1 0 0.2 0.4 0.6 0.8 1
Scaled Time
Scaled Time
St (t ) ( K m E0 )W exp max
K E Fig. 2. Time dependent behaviour of the substrate concentrations
m 0 K m E0 with varying enzyme concentration for basic enzyme substrate
reaction. Reactant concentrations and time range has been scaled to
(39) the interval (0,1) by dividing their maximum absolute values.
-1 -1 -1 -1
Equation (39) provides a better approach to analyze Parameters values used are k1=10 μM sec , k-1=1 sec , k2=10 sec
enzymatic system (1). (Km=1.1 μM). Initial substrate concentration is taken as S0=10 for
both the figures 2(a) and 2(b). In fig. 2(a) time dependent curve for
substrate concentration has been drawn for two different initial
4 Results and Discussion enzyme concentrations E0=0.1 and E0=1 and in fig. 2(b) initial
enzyme concentrations are taken as E0=10 and E0=100.
With equation (36), (33) and conservation laws given in
(7) we are now in position to elegantly construct the time
In fig. 2(a) and 2(b) the graph for substrate concentration
evolution of all the reactant concentrations during the
with respect to time has been drawn for different enzyme
complete duration of the reaction 0 ∞ . Reactant
concentrations. In both the figures initial substrate
concentrations and the infinite time range has been
concentration is taken as 10 while initial enzyme
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concentrations for fig. 2(a) were 0.1 and 1 and for fig. 2(b) advantage of this work is that it provides the solution at
were 10 and 100. From the fig. 2(a) we can see that when each point for the complete course of reaction hence gives
initial enzyme concentration is less in comparison to better insights of enzyme substrate reaction system for
substrate, substrate decays exponentially as in the case of
which numerical techniques had been used previously.
sQSSA and the curve remains almost same for both initial
The solution which has been derived for basic enzyme‐
enzyme concentrations E0=0.1 and E0=1. In fig. 2(b) when
enzyme concentration is comparable or higher in regard substrate reaction is not an exact solution but will be
to substrate, substrate decays almost vertically for little accurate for k 2 E0 k1 ( E0 S 0 K m ) 2 1 and will give
time and then becomes nearly horizontal with time. This better results than the solution based on sQSSA.
phenomenon was obvious because in this situation all the
substrate molecules can bind with enzyme molecules at
once and most of them would have been transformed into APPENDIX A
the product (vertical decay) and remaining would be Lambert W function (also known as Omega function or
transformed afterwards (horizontal decay). Product log function) was first introduced by Euler in
1779 and satisfies the transcendental equation
3(a)
1
For e0=0.1 3(b)
1
For e0=10 W ( x ) exp(W ( x )) x
0.9 For e0=1 0.9 For e0=100
Lambert W function is useful to analyze linear time delay
0.8 0.8
systems. The advantage of using the Lambert W function
Scaled Complex Concentration
0.7 0.7
is that it can algebraically solve the characteristic
0.6 0.6
equations of scalar linear time‐delay systems. This makes
0.5 0.5
one possible to explicitly express the characteristic roots
0.4 0.4
of the systems and easily compute them. Moreover, it
0.3 0.3
helps to study the qualitative features of systems and
0.2 0.2
always supplies an exact analysis for which it is difficult
0.1 0.1
to express solution in terms of independent variable [5].
0
0 0.2 0.4 0.6 0.8 1
0
0 0.2 0.4 0.6 0.8 1 As in present case with the aid of Lambert W function we
Scaled Time Scaled Time
are able to describe the substrate concentration as a
Fig. 3. Time dependent behaviour of the enzyme substrate complex function of time explicitly.
concentrations with varying enzyme concentration for basic enzyme
substrate reaction. Reactant concentrations and time range has Lambert W function has three distinct branches
been scaled to the interval (0, 1) by dividing their maximum absolute depending upon the values of x [6]. For x > 0, W is
-1 -1 -1
values. Parameters values used are k1=10 μM sec , k-1=1 sec , positive and has a unique value (Region above W = 0). For
-1
k2=10 sec (KM = 1.1 μM). Initial complex concentration is taken as
x values in the range of ‐1/e < x < 0, two solutions exist (
zero for both the figures 3(a) and 3(b). In fig. 3(a) time dependent
curve for complex concentration has been drawn for two different First is between W = 0 and W = ‐1 and the other one is
initial enzyme concentrations E0=0.1 and E0=1 and in fig. 3(b) initial below W = ‐1 as shown in the fig. 4.
enzyme concentrations are taken as E0=10 and E0=100.
In fig. 3(a) and 3(b) the graph for enzyme substrate
complex concentration with respect to time has been
drawn for different enzyme concentrations. In both the
figures initial complex concentration is taken as zero
while initial enzyme concentrations for fig. 3(a) were 0.1
and 1 and for fig. 3(b) were 10 and 100. From the fig. 3(a)
we can see that when initial enzyme concentration is less
in comparison to substrate, the behaviour of the graph
remains almost same for both the initial enzyme
concentrations and in agreement to that obtained from
sQSSA. In fig. 3(b) complex concentration increases
vertically in the transient phase as usually but the steady
state phase becomes very small and complex
concentration decays more rapidly (almost exponentially)
after steady state phase.
Fig. 4. Three branches of Lambert W Function (see [5] & [6]).
4 CONCLUSION
In the present work an analytical solution based on REFERENCES
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