It has hitherto not been possible to analyze the control
of oscillatory dynamic cellular processes in other than qualitative ways. The control coefficients, used in metabolic control analyses of
steady states, cannot be applied directly to dynamic systems. We here
illustrate a way out of this limitation that uses Fourier transforms to
convert the time domain into the stationary frequency domain, and then
analyses the control of limit cycle oscillations. In addition to the
already known summation theorems for frequency and amplitude, we reveal
summation theorems that apply to the control of average value,
waveform, and phase differences of the oscillations. The approach is
made fully operational in an analysis of yeast glycolytic oscillations.
It follows an experimental approach, sampling from the model output and
using discrete Fourier transforms of this data set. It quantifies the
control of various aspects of the oscillations by the external glucose
concentration and by various internal molecular processes. We show that
the control of various oscillatory properties is distributed over the
system enzymes in ways that differ among those properties. The models that are described in this paper can be accessed on
http://jjj.biochem.sun.ac.za.
 |
INTRODUCTION |
Periodic phenomena are widespread in biology (for
review see Hess, 2000
), e.g., calcium waves (Rottingen and Iversen,
2000
; Bootman et al., 2001
), oscillations in neuronal signals
(Rabinovich and Abarbanel, 1998
), oscillations in cyclic AMP in the
slime mould Dictyostelium discoideum (Halloy et al., 1998
;
Nanjundiah, 1998
), yeast glycolytic oscillations (Ghosh and Chance,
1964
), the circadian rhythm (Turek, 1998
), and the cell cycle (Johnson et al., 1996
; Mori and Johnson, 2000
; Smaaland, 1996
; Tyson and Novak,
2001
). Periodic signals can be a function of time (glycolytic oscillations), space (striping in Drosophila melanogaster
embryos), or both (D. discoideum, calcium waves, neuronal
oscillations) depending on the mechanism of the oscillator. Some of
these periodic phenomena are crucial for the living system in which
they occur. Consequently, it should be important to identify the
processes that determine these oscillations, if only to understand
which molecular defects result in pathological disturbances in
oscillations. The complexity of what determines biological oscillations
has often been underestimated by attributing all control to a single pace-maker. In recent years it has become clear that the frequency and
amplitude of biological oscillations can be controlled by more than one
enzyme (Teusink et al., 1996a
; Reijenga et al., 2001
). However,
oscillatory properties carry more information than frequency and
amplitude, such as average value, waveform, and phase shift. All of
these properties may be controlled by the molecular biological
processes in the system, and perhaps differentially so. The functional
importance of oscillatory phenomena may reside in any of these
properties or in their combinations. Calcium and endocrine oscillations
appear to function as information-transfer pathways where the
information is frequency rather than amplitude encoded (Goldbeter et
al., 1990
; Goldbeter, 1996
; Bootman et al., 1996
). The importance and
the inherent complexity of the control of biochemical oscillations
suggest that a systematic way of analyzing this control might be useful.
Metabolic Control Analysis (MCA) is a systematic method for analyzing
the control of steady states. It quantifies the extent to which any
parameter, but more notably all molecular processes, controls any
steady-state variable within a metabolic pathway (Kacser and Burns,
1973
; Heinrich and Schuster, 1996
). Oscillations are dynamic and
therefore do not exist in a steady state. Standard MCA cannot be
applied to transient oscillations (but see Heinrich and Reder, 1991
).
An operational definition of a time-dependent control coefficient was
introduced by Acerenza et al. (1989)
as the relative change in a system
variable at time t after a perturbation of a parameter at
time zero, divided by the relative change in that parameter. It
appears, however, that this time-dependent control coefficient is not
useful for the characterization of autonomously oscillating systems,
because its magnitude diverges as time progresses (Kholodenko et al.,
1997
; Demin et al., 1999
). Neither standard MCA nor its extension
proposed by Acerenza et al. and Heinrich and Reder (1991)
can be
applied to the steadily varying concentrations in a limit cycle
oscillation (Kholodenko et al., 1997
; Demin et al., 1999
). In contrast,
the frequency, amplitude, average value, waveform, and phase shift are
time independent in such oscillations, and this should make it possible
to develop an MCA-like approach for those properties. Parts of such an
approach have been developed (Westerhoff et al., 1990
; Bier et al.,
1996
; Kholodenko et al., 1997
; Demin et al., 1999
; Reijenga et al., 2001
), but all but one of these focused on frequency. The principles of
a more general approach have been put forward theoretically (Kholodenko
et al., 1997
), but elaborations of how it should be implemented in
actual systems have been lacking. Here we wish to make the approach
operational by applying it to an actual system, i.e., that of yeast
glycolytic oscillations.
Yeast glycolytic oscillations have been studied both in cell-free
extracts and in whole cells for almost 40 years (e.g., Ghosh and
Chance, 1964
; Richard et al., 1996
; Teusink et al., 1996b
). Yeast cells
show transient oscillatory behavior after starvation of the cells and
subsequent addition of glucose (Chance et al., 1964
). The make-up of
the cells determines the stability of the steady state and the
distinction between transient oscillations and sustained (limit cycle)
oscillations. When cells are harvested at the diauxic shift (shift from
using glucose to using ethanol as a carbon source), the cells are prone
to sustained oscillations, monitored macroscopically by measuring NADH
fluorescence in populations of cells (Richard et al., 1994
, 1996
; Dano
et al., 1999
). To monitor these sustained oscillations, synchronization
of the cells is crucial. The cells are synchronized by acetaldehyde,
provided the latter is partly trapped, e.g., by added cyanide.
Mathematical models of yeast cells with synchronizing glycolytic
oscillations (Bier et al., 2000
; Wolf and Heinrich, 2000
) are realistic
enough to serve as a silicon (Westerhoff, 2001
) replicon of a real and experimentally accessible oscillatory system. This presents us with the
possibility to use the models to develop, illustrate, and, to some
extent, test new metabolic control analysis for realistic biological oscillations.
The aim then is to develop a systematic approach similar to MCA for the
analysis of what controls autonomous oscillations. The notion
elaborated in this paper is that the control of autonomous oscillations
can be analyzed by considering the Fourier spectrum of the individual
fluxes and concentrations. Laws that relate various control properties
are derived and illustrated. Focus is on the five most obvious
characteristics of an oscillating property, i.e., frequency (
),
average value (A0), amplitude
(An), waveform
(A2/A1), and phase (
).
 |
MATERIALS AND METHODS |
Theory and definitions
Metabolic control analysis
MCA quantifies the extent to which an enzyme i
controls a steady-state variable X. Control coefficients are
defined as the relative change in that steady-state variable upon a
relative change in the activity (vi) of the
enzyme i,
The elasticity of an enzyme quantifies the extent to which the
activity of that enzyme is changed by a parameter p, and
reads, in mathematical terms,
Furthermore, the way a variable responds to a change in a
parameter is given by the response coefficient,
Combination of these three properties gives the combined
response theorem,
Here, it is assumed that the parameter p affects the
enzyme i only.
Fourier transformation
Any periodic signal of period T can be expanded into
a trigonometric series of sine and cosine functions:
where A0 is the average value of the
signal, an and bn are the
amplitudes of the cosine and sine, respectively, of the nth component,
is the eigenfrequency of the signal,
An is the absolute amplitude of the
nth component of the signal (An = 

)
and
n is the phase of the nth component of
the signal (
n = arctan(bn/an). For a
virtually sinusoidal oscillation, the Fourier spectrum peaks at
n = 1, and the other components can be disregarded. In
general, the component amplitude in a potentially infinite Fourier
series rapidly decreases with the number n. In this study,
the amplitude will be studied in terms of the absolute amplitudes of
the first and second component of the Fourier spectrum
(A1, A2). The waveform is studied in
terms of the ratio of the first and second components of the Fourier spectrum (A2/A1).
Methods
We used a numerical approach to calculate control coefficients,
because limit cycle oscillations can only be analyzed analytically infinitely close to the Hopf bifurcation. All models were programmed in
the metabolic modeling program GEPASI (Mendes, 1997
). Fourier transformations were carried out and analyzed using MATHEMATICA (Wolfram, 1999
). A data set was generated in GEPASI and imported in
MATHEMATICA. Using Fourier transformations, an estimation of the
average value of the data was made and this value was used to calculate
the exact beginning and end of N number of periods (with
N a natural number, usually ~10). Subsequently, a discrete Fourier transform was carried out on such a subset of the data and the
frequencies and amplitudes calculated. Furthermore, a reverse Fourier
transform was made and compared to the original signal. The three main
components were analyzed in terms of MCA.
To calculate the response of a variable toward a change in a parameter,
that parameter was changed by both +
p and

p around the reference state. For calculation of the
control coefficients, the activities of the enzymes
(Vmax or corresponding rate constants) were also
changed by both +
p and 
p around the
reference state. New limit cycles were computed, and the Fourier
spectrum was taken. The response coefficient equals the slope of the
curve when plotting ln Xj versus ln
p, whereas the control coefficient equals the slope of the
curve when plotting ln Xj versus ln
vi. Here, Xj can be any
element of the Fourier spectrum (
, A0,
A1, A2, A2/A1, and
). The magnitude of the parameter change
p was
balanced between linearity of the ln-ln plot (which usually requires
small changes) and accuracy of determination of the change of the
components in the Fourier spectrum.
Models
In this study, we used three models (Fig.
1, A-C), which are described
below in terms of differential equations. The models can also be
accessed and run on http://jjj.biochem.sun.ac.za. Further details on
the models can be found in the original literature. For comparison, we
have chosen to use the same symbols as used in the original literature.

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FIGURE 1
Reaction schemes for the models (A) 1, (B) 2 and (C) 3. See the text for explanation of
the symbols and the rate equations.
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Model 1: the PFK model by Goldbeter and Lefever (1972)
The phosphofructokinase (PFK) model is a core model that
describes glycolysis solely in terms of the kinetics of the enzyme PFK
(Fig. 1 A). The model consists of two variables
and
, and three reaction rates,
where
includes the most important kinetic details of PFK. The
variables
and
denote the concentrations of substrate (ATP or fructose 6-phosphate) and product (ADP or fructose 1,6-bisphosphate), respectively.
1 denotes the constant injection rate of
substrate,
M is the rate constant (or concentration) of
PFK, and ks is the rate constant for the sink of
the product. Explanation of the other parameters can be found in the
original literature. In the present study, a set of parameter values
was used according to Goldbeter and Caplan (1976)
: L = 106; c = 10
5; e = e' = 0.9090909;
= 1;
1 = 0.7;
M = 4; ks = 0.1.
Model 2: a core model by Bier et al. (2000)
Bier et al. describes glycolysis in terms of two variables,
i.e., (internal) glucose and ATP (Fig. 1 B). The system is
summarized by the following dynamical system:
where G and T denote the internal glucose
concentration and the ATP concentration, respectively.
Vin is the constant influx of glucose and
k1 is the enzyme activity (or concentration) of PFK. There is a positive feedback, i.e., ATP stimulates its own production. Furthermore, ATP is broken down according to
Michaelis-Menten kinetics. In this study, we used the following
parameter set as a reference state: Vin = 0.36; k1 = 0.02; kp = 6.0;
KM = 13.0 (Bier et al., 2000
).
Model 3: the nine-variable model by Wolf et al. (2000)
Wolf et al. have set up a minimum model of glycolysis in yeast
that qualitatively describes the experimental observations of Richard
et al. (1996)
(Fig. 1 C). The model consists of lumped reactions and includes branches to glycerol and ethanol. Furthermore, it accounts for the diffusion of acetaldehyde across the plasma membrane, the trapping of acetaldehyde (the synchronizing agent) by
cyanide, and the presence of more than one cell. Therefore, this model
can describe intercellular synchronization. The one-cell version of the
model contains nine variables and the system is described by the
following differential equations:
with the rate equations,
and two conserved moieties,
Variables and their meanings are: S1,
glucose; S2, fructose-1,6-bisphosphate;
S3, pool of the triosephosphates,
glyceraldehyde-3-phosphate and dihydroxyacetone phosphate;
S4, 3-phosphoglycerate;
S5, pyruvate; S6,
intracellular acetaldehyde; S
,
extracellular acetaldehyde; A2, ADP;
A3, ATP; N1, NAD;
N2, NADH. The parameter values that were used in
this study are listed in Table 1 (Wolf et
al., 2000
).
 |
RESULTS |
Fourier spectra
Fourier analysis is not yet standard in metabolic control
software. Therefore, we first developed a routine in MATHEMATICA that
enabled us to take a Fourier spectrum of a set of data generated in the
metabolic modeling program GEPASI. The bold line in Panel A of Fig.
2 shows an autonomous oscillation in the
concentration of variable
calculated for model 1 of glycolysis. The
filled diamonds in Panel B give the corresponding discrete Fourier
spectrum. The zero frequency component of amplitude 70 mM corresponds
to the time-average value of the concentration variable. The first Fourier component represents a sinusoidal oscillation with an amplitude
of approximately half that average. That the oscillation has a form
that deviates from a simple sinus (cf. Fig. 2 A), is consolidated by the presence of higher-order Fourier components, e.g.,
the one at a frequency near 0.62 min
1 (cf. Fig.
2 B). Because the third and higher-order components were
small, we shall further focus on the ratio of the amplitudes of the
second- and the first-order Fourier components as a measure of the
waveform of the oscillations.

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FIGURE 2
Output of the PFK model by Goldbeter and Lefever
(1972) . See the text for parameter values. (A) The
concentration of metabolite in time. (B) The
corresponding Fourier spectrum. The bold line and the filled diamonds
reflect the oscillation at [Glc]ext = 1 mM, the thin
line and the open diamonds reflect the oscillation at
[Glc]ext = 1.5 mM.
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In the original model by Goldbeter and Lefever (1972)
the substrate
injection rate was constant (
1). To determine the
response of the system to external glucose, the kinetics of this first reaction were adapted to reflect mass action of the external glucose (
1 = k1 * [Glc]ext). The external glucose concentration was
then increased by 50% and the resulting oscillations calculated (Fig. 2 A, thin line). In accordance with experimental
expectations (Hess and Boiteux, 1973
; Reijenga et al., 2001
), the
frequency of the oscillations increased. The Fourier spectrum (in Fig.
2 B, diamonds) reflected the change in frequency
and revealed that, also, the waveform had been changed slightly, which
was less noticeable in the time domain representation of Fig.
2 A.
The effect of the external glucose concentration on the oscillation
depended (nonlinearly) on the extent to which the glucose concentration
was changed. To move away from this effect, we decided to focus on the
effects of small modulations of the glucose concentration, much in the
vein of MCA. Therefore, the glucose concentration was increased by a
mere 5%. The elements of the two Fourier spectra are listed in Table
2. This table testifies to a change in
both frequency and amplitude of the different Fourier components, and in the average value of the variables upon a change in external glucose.
Response of the oscillation to external glucose in terms of Fourier
response coefficients
From the time domain representation of Fig. 2 A, it is
not immediately obvious how to describe the response of the oscillation to an increase in external glucose concentration. If one were to
determine the change in the concentration variable
and divide that
by the change in external glucose concentration, as should be done for
a traditional response coefficient, a time-dependent result would
appear that, itself, oscillated with a sizable amplitude even for very
small modulations of the glucose concentration (not shown; Kholodenko
et al., 1997
). The frequency domain presentation of Fig.
2 B, however, suggests how to characterize the control external glucose exerted on the oscillations, i.e., in terms of the
effect on frequency and on the amplitudes of the various Fourier components. For model 1, we therefore quantified the response of the
Fourier spectrum to a change in external glucose in terms of such
response coefficients. The Fourier response coefficient is defined as
where p is a parameter (i.e., external glucose) and
X is a dependent variable (i.e., any of the elements of the
Fourier spectrum;
, A0, A1,
A2, A2/A1, and
). Table
3 shows the response coefficients for the
different elements of the Fourier spectrum, for the two metabolites of
the system (
,
). As quantified by this table, external glucose
affected frequency, average value, amplitude, and waveform of the
oscillations. Frequency and waveform of the oscillations of the two
metabolites were affected to virtually the same extent (even though the
waveforms of the two variables differed considerably), whereas the
response differed for the average value A0 and
the amplitude of the first and second Fourier component. Furthermore,
for the amplitude of the second Fourier component
(A2), the response coefficients were negative,
whereas, for the other elements of the Fourier spectrum, the response
coefficients were positive.
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TABLE 3
Response coefficients of the external substrate on the
Fourier spectrum for the dynamic behavior of the concentrations of
metabolites of model 1
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Dependence of the oscillation on kinetic parameters
We calculated the control of the enzymes on the oscillations for
the three models. We changed the kinetic parameters (i.e., the
activity) of the individual enzymes and determined the Fourier spectra.
The control coefficients are listed in Tables
4, 5, and 6. The tables show that, for
all three models, the control by the enzymes on all different Fourier
elements was distributed over the various processes. Negative control
coefficients were calculated for each model, for various steps, and for
all Fourier amplitudes. For the glucose influx step, the control
coefficient for the frequency was positive for both core models, model
1 and model 2 (0.51 and 0.78, respectively) and negative for the more detailed model 3 (
1.54). Recently, we determined experimentally a
control coefficient for the glucose transporter on the frequency of the
limit cycle oscillations of +0.5 (Reijenga et al., 2001
). A multitude
of various molecular mechanisms can bring about the oscillations in
glycolysis. A large difference in the frequency control exerted by the
glucose transporter demonstrates that these mechanisms differ for the
core models and a detailed model. It should also be noted that, for
model 3, it was more difficult to choose a parameter change that was
small enough for (local) linearity of the ln-ln plot of
Xj versus vi and large
enough for an accurate change in the variables. Both the average values
and the amplitudes of the oscillations in the metabolites were small, and therefore numerical error was high.
Summation properties
Because of time scaling properties, the sums of the control
coefficients with respect to frequency and amplitude have been shown to
equal 1 and 0, respectively (Giersch, 1988
; Westerhoff and Van Dam,
1987
; Westerhoff et al., 1990
; Acerenza, 1990
; Kholodenko et al.,
1997
). This is confirmed by Tables 4-6.
The same tables suggest that the sum of the control coefficients with
respect to the higher-order Fourier components should also equal zero, as should the sum of the control with respect to the waveform. The
minor deviations from one and zero were in line with numerical error.
We further tested the summation theorems by increasing all kinetic
parameters simultaneously by 10%. As was expected, the frequency of
the oscillations increased by 10%, whereas the average value, the
amplitudes of the different Fourier components, and the waveform of the
oscillations did not change. The sums of the changes after increasing
all kinetic parameters simultaneously by 10%, are also listed in Table
6 (sum*).
Illustration of summation theorems
The summation theorems and the control coefficients are
illustrated on model 2. For three different parameter sets, a Fourier spectrum of intracellular glucose was made. The first parameter set
acted as the reference state (Vin = 0.36;
k1 = 0.02; kp = 6.0;
KM = 13.0). For the second parameter set, all
kinetic parameters were increased simultaneously by 10%, and, for the
third parameter set, only the kinetic parameter for the second reaction
(k1) was increased by 10%. The first- and
second-order Fourier components and the sum of the two components were
plotted. The average concentration (A0) was not
taken into account. It is shown that, when all the rate constants were
increased simultaneously by 10%, the amplitudes did not change (Fig.
3). This implies that the waveform
(defined as A2/A1) did not change
either. This illustrates the summation theorem for the waveform. In
contrast, the frequency of both Fourier components increased by 10%
(Fig. 3). When only the rate constant for the second reaction was
increased by 10%, amplitude and frequency changed as calculated by the
control coefficients for that step (Fig.
4). Here also the waveform of the signal
was altered.

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FIGURE 3
Output of the glycolytic model by Bier et al. (2000) A
Fourier spectrum of the oscillating internal glucose concentration was
taken and the individual components were plotted. Curves have been
shifted relative to each other to separate the different components.
First-order Fourier component (1), second-order Fourier
component (2), and the sum of the two components
(3). Bold line, control; thin line,
all rate constants were increased by 10%. See the text for further
explanation.
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FIGURE 4
Output of the glycolytic model by Bier et al. (2000) A
Fourier spectrum of the oscillating internal glucose concentration was
taken and the individual components were plotted. Curves have been
shifted relative to each other to separate the different components.
First-order Fourier component (1), second-order Fourier
component (2), and the sum of the two components
(3). Bold line, control; thin line,
the rate constant of the second reaction (k1)
was increased by 10%. See the text for further explanation.
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Control of the Fourier spectrum of the flux
In oscillating systems, not only the concentrations of metabolites
vary in time, the fluxes through the enzymes are not constant either.
As for the concentrations, these fluxes can be analyzed using the
Fourier transform. In Table 7, we
demonstrate such an analysis on the flux through PFK for model 1. The
control on the average flux was completely determined by the (constant)
input of substrate (cf. Teusink et al., 1996a
) but the control on the amplitude of the oscillating flux and on the waveform of the
oscillation was distributed. For the amplitude of the two Fourier
components, the total control added up to one, as it did for the
control on the frequency and on the average value of the flux. However,
the control on the waveform of the oscillation summed to zero.
Summation theorem for the phase of the oscillation
The Fourier spectrum also contains information on the phases of
the individual Fourier components and on the phase differences among
these components. The control coefficients for the individual enzymes
could not be calculated because of the Fourier routine we used (i.e.,
the analysis was always started at the average value of the
oscillation). However, for model 1, it was shown that, when all enzymes
were increased by 10%, the phase difference between the second and
first Fourier component did not change. This suggested that the sum of
all the control coefficients on this phase difference should add up to zero.
Combined response theorem
For steady-state phenomena, response coefficients can be linked to
control coefficients and elasticities. The combined response theorem
quantifies the relation between the response of a variable toward a
change in an external clamped substrate, the control of the linking
enzyme (the enzyme for which the parameter is the substrate) on this
variable, and the sensitivity of the enzyme toward the substrate. For
the response of steady-state properties to external glucose, the
combined response theorem reads
For dynamic phenomena, the metabolite concentrations are
oscillating, and, therefore, this theorem can, at most, hold
approximately. We set out to see to what extent the combined response
theorem might still apply to oscillating phenomena. In model 1, the
kinetics of the lumped reaction including glucose influx are defined as mass action (k * [S]). Therefore, the elasticity (
)
for this step toward glucose is 1 and constant. This implies that, in
this model, the response of the system toward a change in glucose
(R
) equals the control of the system
by the glucose transport step (C
).
Trivially the combined response theorem applies.
To examine the more general case, we changed the kinetics of the
glucose transport step for model 3 to reversible Michaelis-Menten kinetics (Vmax = 60;
KMs = 2; KMp = 2). We
calculated the elasticity of the enzyme for external glucose using the
equation,
Because the internal glucose concentration oscillated, we
calculated vi and 
during
one period. The internal glucose concentration ranged from 0.18 to 1.75 mM, the glucose transport rate ranged from 46 to 55 mM
min
1, and the elasticity ranged from 0.11 to 0.25. Furthermore, we determined the response coefficients by changing the
external glucose concentration and the control coefficients by changing the Vmax of the glucose transport step (Table
8). The values for the ratio
R
/C
fell within the range of values for the elasticity (0.11-0.25), but
differed among the various Fourier characteristics. This shows that,
although, for oscillating phenomena, the combined response theorem can
be approximately true, it does not hold precisely, not even if written
in terms of some sort of time average of the elasticity coefficient.
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TABLE 8
Response of the Fourier spectrum to changes in external
glucose concentration, control coefficients of glucose transport on the
Fourier spectrum, and their ratio for model 3
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Response of the Fourier spectrum to changes in affinity of the
enzymes and conserved moieties
For model 3 with reversible Michaelis-Menten kinetics for the
glucose transport step, we determined the response of the Fourier spectrum to changes in affinity of the glucose transport step, as well
as to changes in conserved moieties. The response and control
coefficients, as well as the ratios between the response toward the
KM for external glucose and the control of
glucose transport on the Fourier spectrum are listed in Table
9. The combined response theorem for the
KM value (Chen and Westerhoff, 1986
) held
approximately for oscillating phenomena,
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TABLE 9
Response coefficients of Fourier spectrum to changes in
KM and conserved moieties, control coefficients
of glucose transport on Fourier spectrum, and ratio of response toward
KM and control of glucose transport for model 3
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 |
DISCUSSION |
Dynamical systems are of great interest in both mathematics and
the natural sciences. Jules Henri Poincaré founded the modern qualitative theory of dynamical systems (Sarkaria, 1999
)
emphasizing issues such as whether, and for which parameter values,
systems are stable, and what type of dynamics they exhibit. There is
comparatively little attention for the precise dependence of the
quantitative properties, such as material concentrations or fluxes of
dynamic systems on molecular properties when the system remains within a single basin of attraction. For biological systems, precision and
minor increases in functionality are important. Moreover, through
molecular genetics and modern biochemistry, biological dynamic systems
have become amenable to subtle manipulation of, in principle, each
molecular (enzyme catalyzed) process (Jensen et al., 1993
). In this
way, biology is becoming a prime field for the further subtle analysis
of dynamic systems (Westerhoff, 2001
).
In view of the complexity of biological dynamic systems, a systematic
way of analyzing them should then be useful. With some theoretical
background behind us (Bier et al., 1996
; Demin et al., 1999
; Kholodenko
et al., 1997
, and references therein), we here operationalized such an
analysis method. We did this through numerical experiments on a model
of yeast glycolytic oscillations, because these are already relatively
well defined, both theoretically and experimentally (Chance et al.,
1964
; Ghosh and Chance, 1964
; Richard et al., 1994
; Teusink et al.,
1996a
; Dano et al., 1999
; Bier et al., 2000
; Wolf et al., 2000
). By
describing a time-dependent periodic signal as a function of
frequencies, using a Fourier transformation, again, a stationary
description was obtained that was amenable to control analysis.
Often, periodic signals are described in terms of frequency, amplitude,
and average value. Here, we also studied the waveform of the signal
quantitatively by defining it as the ratio of the amplitudes of Fourier
components. The phase difference between components gave additional
information on the waveform of the signal. Therefore, questions such
as, Is a periodic signal sinusoidal or not? and What controls the
waveform of a signal? can now be answered in a quantitative way, both
for measured and calculated signals.
As an example, the control of the different enzymes on the dynamics of
the variables was determined for three different models of the same
important process, i.e., glycolysis. Control was distributed among the
enzymes. Distributive control of dynamics still has limited
experimental validation. Perhaps the most germane experimental study
has been the determination of the control of frequency of glycolytic
oscillations, the system also studied theoretically in this paper. The
control of the glucose transport system on the frequency was shown to
be +0.5. By implication, control of the frequency should be distributed
among at least two molecular processes (Reijenga et al., 2001
).
For frequency and amplitude, the distributive nature of control had
already been shown by us for models of glycolysis (Teusink et al.,
1996a
). Here, this has now also been shown for waveform and phase
difference. Moreover, the present paper constitutes a substantial
improvement on the earlier approach in which we simulated the system
and then tediously measured the effect on frequency and overall
amplitude by direct inspection of the calculated data. Here we made
this procedure systematic and objective by implementing a Fourier
transformation, which then automatically led us to frequency and
amplitudes. Only with this method could we reliably discuss the control
of the waveform of the oscillations. The new approach is also more
amenable to application to larger data sets. However, the empirical
nature of our study does not provide us with an overall theory to aid
in the understanding of oscillating phenomena. For recent developments
in this, we refer to Kholodenko et al. (1997)
and Demin et al. (1999)
.
The study of the control of the waveform was gratifying, because it
showed, contrary to our expectations, that control on the form of the
oscillations can be quite strong, even though the sum of the
corresponding control coefficients is zero. This suggests that a living
cell may not only regulate itself by adjusting the rate of its
glycolytic flux or the frequency of oscillations therein (or in its
cell cycle for that matter), but also by adjusting the form of the
oscillations (or the time dependence of any dynamic phenomenon).
Amplitude and form of oscillations can have strong implications for
functionality and even for the thermodynamics thereof (Westerhoff et
al., 1986
; Berridge et al., 1998
). More, in general, the possibility of
identifying quantitatively which molecular players control dynamic
games in the living cell may become crucial to progress in cell
biology. The control and response coefficients introduced here to
intracellular dynamics may serve as criteria. More and more the vast
connectivity and multiplicity of the intracellular processes causes
problems of analysis. When searching hard enough, any process seems to
be influenced by almost any other process in the living cell. We have
shown that some processes can be more important than others, i.e., not
all control coefficients are the same in Tables 4-6. In contrast, the
importance of molecular factors for a dynamic process may depend on the
particular aspect of that process that is being considered. Enzymes
that exert a strong control on frequency may not do so on average
concentration or on the amplitude of the second Fourier component.
Having shown this for models of yeast glycolysis, we anticipate that
similar conclusions will emerge for the control of the cell cycle
(Tyson and Novak, 2001
) and calcium oscillations (Höfer et al.,
2001
).
An important asset of the metabolic control analysis of steady-state
systems has been that it exposed laws that should be obeyed by control
coefficients. Of these laws the summation theorems have a counterpart
in the control analysis of oscillatory systems. For the control of
frequency, amplitude, and average value, the summation theorems had
already been derived (e.g., Westerhoff et al., 1990
; Bier et al., 1996
;
Giersch, 1988
; Kholodenko et al., 1997
). In the present paper, we came
up with additional summation theorems on waveform and on phase
difference, confirmed in three different mathematical models for yeast
glycolytic oscillations.
These summation theorems are of considerable importance. First, where
intuition may have suggested control to be constrained to a single
pace-making step, the theorems show what the correct phrasing of the
intuition should be. Control on frequency should indeed amount to a
total of 1, but may well be distributed among all participating
catalytic activities. Second, the theorems show that, with respect to
the control of amplitude or waveform, the intuition is plainly
misleading: control should not add up to 1, but to zero. Therefore, a
system without any key step that controls the amplitude of an
oscillation, may well exist. And, a system with a single such step
cannot exist; if one step exerts a control of 1, then there must be
other steps with control summing up to minus 1. Third, the theorems
provide a prime rationalization for the observation that genes rarely
have strong phenotypes. Also for dynamics, control is distributed and
partial inactivation of a single process should, on average, have
little effect (cf. Kacser and Burns, 1973
).
Oscillations contain more information than steady-state phenomena. In
view of the search for functions for silent genes (Raamsdonk et al.,
2001
), a focus on dynamic phenomena may become helpful, because
analysis of steady-state variables does not always reveal phenotypes.
The quantitative analysis of dynamic systems may provide information,
answers, and additional biological problems. Discussing only the more
regular of such systems, this operational analysis of steady
oscillations is, perhaps, a first step toward a more general analysis
method for such dynamical systems. It may well be possible to
generalize the approach described here to other time dependent systems,
such as those that arise upon perturbation of a steady system, e.g.,
when a growth factor is added to a mammalian cell (Acerenza et al.,
1989
; Heinrich and Reder, 1991
; Kholodenko et al., 1999
).
This work was supported by the Netherlands Organization for
Scientific Research, by the Technology Foundation and by the National Institutes of Health grant GM59570 (B.K.). We thank Martin Bier for
critical reading of the manuscript and valuable comments.
Address reprint requests to Hans V. Westerhoff, Dept. of Molecular Cell
Physiology, Vrije University, De Boelelaan 1087, NL-1081 HV Amsterdam,
The Netherlands. Tel.: +31-20-4447-228; Fax: +31-20-4447-229; E-mail:
hw{at}bio.vu.nl.