Lecture 2

Modeling of Biochemical Reactions
Dr. Carlo Cosentino

School of Computer and Biomedical Engineering
Department of Experimental and Clinical Medicine
Università degli Studi Magna Graecia
Catanzaro, Italy
carlo.cosentino@unicz.it
http://bioingegneria.unicz.it/~cosentino
Dr. Carlo Cosentino 1 Carnegie Mellon University, Pittsburgh, 2008

Outline
Ó Modeling of biochemical reactions

Ô Deterministic models
Õ Michaelis–Menten model
Õ The Quasi–Steady–State Approximation
Õ Allosteric reaction
Õ Regulation of enzymatic reactions
Ô Stochastic models
Õ Stochastic derivation
Õ The Gillespie algorithm

Biochemical Energy
Ó The equilibrium of a reaction is linked to the variation of biochemical

standard free energy, ∆G’0
Ó The velocity, instead, depends on the activation energy, ∆GS → P

‡

Reaction Rate
Ó The reaction rate is determined by

Ô The concentration of the reactants
Ô The kinetic constant, usually denoted by k
Ó The reaction rate for S ⎯

⎯→
k
P is
V = k [S ]
Ó From transition-state theory it is possible to derive the relation

kT − ∆G ‡ RT
k= e k: Boltzmann constant
h: Planck constant
h

Reaction Equilibrium
Ó Let us consider the following basic reversible reaction S ⎯⎯→

k1
P
Ó It can be described by the system S ←⎯⎯
k −1
P
d [S ]
= − k1 [S ] + k −1 [P ]
dt ′ =
K eq
[P ] = k1
d [P ] [S ] k−1
= k1 [S ] − k −1 [P ]
dt
Ó The equilibrium constant is a function of ∆G’0

R=8.315 J/mol·K (gas constant)
′
∆G ′° = − RT ln K eq
T=temperature [K]

Enzymatic Reaction Kinetics
Ó Enzymes are a family of proteins specialized in the catalysis of reactions
Ó Catalysts do not react and do not affect the reaction equilibrium, however
they increase the reaction rate by decreasing the activation energy
Ó The basic mechanism is the formation of an enzyme-substrate complex,

which creates a more favorable condition for the formation of the product
Ó After the substrate has been transformed

into product, the complex dissociates
and the enzyme is free to catalyze the
next reaction

The Role of Enzymes
Ó Enzymes play a central role in all the biological processes (metabolism,

regulation, signaling)
Ó Many diseases are caused by deficiency of some enzyme
Ó Many drugs act by interacting with enzymes

Outline


Michaelis-Menten Model
Ó The basic model of enzymatic reaction was proposed by

Michaelis and Menten in 1913
Ó The law of mass action (LMA) states that the reaction rate is L. Michaelis (1875-1949)
proportional to the product of the concentrations of the
reactants
d [C ]
A+ B ⎯k
⎯→ C = k [A][B ]
dt
k d[C]
mA + nB −→ C = k[A]m[B]n M. Menten (1879-1960)
dt

Michaelis-Menten Model (cont’d)
Ó Applying the LMA to the model reaction scheme, we obtain
s& = − k1es + k −1c, e& = − k1es + (k −1 + k 2 )c

c& = k1es − (k −1 + k 2 )c, p& = k 2 c
s := [S ], e := [ E ], c := [ES ], p := [P ]
with initial conditions s(0)=s0, e(0)=e0, c(0)=0, p(0)=0
Ó Note that the equation of p(t) is decoupled and yields

t
p(t ) = k 2 c(τ )dτ
∫
0

Simplified M-M Model
Ó The total amount of enzyme (free+bound) remains constant over time,

indeed, summing the equations of e(t) and c(t)
e& + c& = 0 ⇒ e(t ) + c(t ) = e0

from which we can derive e(t) and substitute into the other eqs, obtaining
s& = − k1e0 s + (k1s + k −1 )c, s (0 ) = s0

c& = k1e0 s − (k1s + k −1 + k 2 )c, c(0 ) = 0

Simplified M–M Model (cont’d)
Ó Typically, the initial formation of the complex ES is much faster than the
product formation, hence it can be assumed to be instantaneous
Ó This assumption lets us pose dc/dt ≅ 0, that is
e0 s (t ) k 2 e0 s
c(t ) = ⇒ s& = −
s (t ) + K m s + Km
where the positive constant
k −1 + k 2
Km =
k1
is the Michaelis–Menten constant

Simplified M–M Model (cont’d)
Ó Furthermore, the amount of enzyme is typically much less than that of

substrate (at least in metabolic reactions), so one can assume that s(0)=s0
also in the simplified model

Adimensionalization
Ó A change of variables is often used in biochemical models, in order to

obtain adimensional normalized parameters
Ó This helps in analyzing the behavior of the system for different values of the
parameters
Ó Furthermore, the adimensionalization typically reduces the number of

parameters
Ó For the M–M reaction we can use the following change of variables
s(t ) c(t )
τ = k1e0 t , u (τ ) = , v(τ ) = ,
s0 e0
k2 k +k K e
λ= , K = −1 2 = m , ε = 0
k1s0 k1s0 s0 s0

Adimensional M–M model
Ó By applying the change of variable above, the simplified model reduces to

u& = −u + (u + K − λ )v, u (0 ) = 1
ε v& = u − (u + K )v, v(0 ) = 0
Ó If the amount of enzyme is much less than that of substrate, then ε ¿ 1

Analysis of the Time Constants
Ó Assuming that s0 does not undergo a significant variation during the initial
transient, it is possible to evaluate the length of such interval by the eq.
c& = k1e0 s0 − k1 (s0 + K m )c
Ó The time constant of this first-order system is
1
tc =
k1 (s0 + K m )
Ó An estimate for the substrate transformation time constant can be derived

by using the maximum derivative
s0 s + Km
ts ≈ ≈ 0
ds dt max k 2 e0

Analysis of the Time Constants
Ó Finally, we can give analytical conditions for the validity of the simplified
model in terms of tc and ts
k 2 e0
<< 1
k1 (s0 + K m )
2
Ó The amount of s consumed during the initial transient has to be negligible,

that means |∆ s/s0| ¿ 1
e0
ε= << 1
s0 + K m
Ó Actually, even in the case when e0/s0=O(1), the latter assumption is satisfied
for large values of Km (that is when the reaction is slow)

Experimental Parameters
Ó In the experimental practice, not all the kinetic parameters of the reaction
are measured, but rather
Ô the M–M constant, Km
Ô the maximum reaction rate,
Q = [R0 ]max = k 2 e0
k 2 e0 s 0 Qs0
R0 = =
s0 + K m s 0 + K m

Outline


Quasi–Steady–State Approximation
Ó The assumptions exploited in the derivation of the simplified M–M model

take the name of quasi steady-state approximation (QSSA)
Ó Large differences in the time-scales of the reactions may create huge

difficulties both in terms of simulation and of understanding the basic
principles of operation
Ó To overcome this limitations, theoreticians (especially in the biochemistry

community) often use QSSA to eliminate the fastest (and the slowest)
equations in the system of ODE

Validity of the QSSA
Ó The validity of the QSSA depends on

Ô How large is the difference in the time–scales of the reactions
Ô How large is the difference between the amount of enzyme and that of
substrate
Ó In the case of protein interaction networks (PINs) the QSSA assumptions

are not satisfied, indeed
Ô Enzymes have multiple substrates
Ô Substrates are acted upon by multiple enzymes
Ô Enzymes and substrates often swap roles (e.g. two kinases can
phosphorylate each other)

Use and Abuse of the QSSA
Ó An enlightening work concerning the validity of the QSSA

E.H. Flach, S. Schnell, Use and abuse of the quasi-steady-state
approximation, IEE Proc.–Syst. Biol. 153(4), 187–191, 2006
Ó The authors performed a compared analysis of the Van Slyke–Cullen

mechanism, a special case of the M–M reaction, with and without applying
the QSSA

Van Slyke–Cullen Model
Ó By exploiting the conservation of the total amount of enzyme, we obtain
Ó Which can be rescaled, in order to get rid of the parameters k1 and k2, by
applying the change of variable
In the next slides we will not make use of the bars to refer to the new variables
Consideration on the Fluxes
Ó The mass is conserved within the system over time, therefore

ṡ + ċ + ṗ = v = v1 − v2
Ó If v is constant the system can be reduced to a second-order system
ṡ = v1 (p) − k1 s(e0 − c)
ċ = k1 s(e0 − c) − k2 c
Ó When vi=0, the system is said to be in closed form, since there is neither
input nor output
Ó If v1(p) is constant, the equation of p(t) is decoupled (as in the M–M model)

Stability Analysis of the Closed System
Ó Having a second-order system, it is possible to visualize the trajectories on a

phase-plane
Ó The first step consists of finding the null surfaces, by setting to zero the
derivatives, which yields
Ó The intersection of the null surfaces gives the steady state
which depends on k1 and k2, as can be seen by substituting for the original
state variables

Stability Analysis of the Simplified Model
Ó Once the equilibrium point has been computed, analysis of the linearized
system provides information about the local stability in the neighborhood of
that point
Ó In the case of constant v the eigenvalues of the linearized system are real
and negative; this corresponds to a so–called stable–node in the phase plane
ċ = 0 surface
Ó The trajectories are attracted by a slow
invariant manifold, which is confined to the
region bounded between the null surfaces
(the null surface of s is not shown)

Stability Analysis of the Full Model
Ó We can repeat the stability analysis for the full third–order model, in order
to check if the two models have always the same behavior
Ó In this case, linearization around the equilibrium point and computation of

the eigenvalues can lead to different cases:
Ô The system is still locally ċ = 0 surface

asymptotically stable
Ô For certain values of v1 and v2,
complex eigenvalues arise, leading
to a so–called stable focus in the
phase plane

QSSA Model of the Open System
Ó We will now assume v1(p) ≠ v2(p), that is the open system
Ó Assume that, after the initial transient, the amount of complex changes very
slowly, such that dc/dt≈ 0
Ó It is therefore possible to express c as a function of s
Ó Then, substituting in the other equations, we get

e0 s
ṡ ≈ v1(p) −
1+s
e0 s
ṗ ≈ − v2(p)
1+s

Comparison of QSSA and Full Model
Ó Also in this case the systems behavior can be very different
Ó The two phase plane below have been obtained using the same parameters
and fluxes, with the full model (a) and QSSA model (b)
Ó The full model exhibit a limit cycle, whereas the trajectories of the reduced
one follow a spiral stable mode

QSSA is not Always Reliable
Ó The QSSA is probably the most frequently used method for reducing the
complexity of biochemical pathways models
Ó Nonetheless it has been shown, also in other works, that it can conceal
some aspects of the transient dynamics or even alter the long-term
dynamics, and thus the qualitative behavior, of the original system

total Quasi-Steady-State Approximation
Ó A possible way to overcome the limitations of QSSA in enzyme-catalyzed

reactions has been proposed in
JAM Borghans, RJ De Boer, LA Segel, Extending the Quasi-Steady-State
Approximation by Changing Variables, Bull. Math. Biol. 58(1), 43–63, 1996
Ó They simply proposed that, for conditions when ET and S0 have comparable
values, the proper intermediate timescale variable is
Ŝ(t) = S(t) + C(t)
Ó This yields

Validity of tQSSA
Ó Tzafriri and Edelman (J. Theor. Biol., 2004) derived sufficient conditions
for the validity of tQSSA, which can be summarized by
k−1 À k2
that is, the dissociation rate of the enzyme–substrate complex is much faster
than the catalytic conversion of substrate into product
Ó Thus, the tQSSA is likely to be an excellent approximation for any ratio of

enzyme to substrate and for any ratio of timescales
Ó An interesting reading for applications of tQSSA to several kinds of PINs is

A Ciliberto, F Capuani, JJ Tyson, Modeling Networks of Coupled Enzymatic
Reactions Using the total Quasi–Steady State Approximation, PLOS
Computational Biology 3(3), 463–472, 2007

Outline


Cooperative Reactions
Ó In the basic model of enzymatic reaction we have assumed that each

molecule of enzyme binds only one substrate molecule
Ó It is quite common to have multiple binding sites, e.g. the hemoglobin has
four binding sites for oxygen
Ó An enzymatic reaction is said to be cooperative if the binding of one

molecule to one site affects the binding affinity at other sites

Allosteric Effect
Ó The mechanism causing such

phenomenon is named allosteric effect
Ó A substrate can be an activator or

inhibitor, depending on whether it
increases or decreases the binding affinity
at other sites
Ó If the substrate and the modulator are the

same species, then the interaction is called
homotropic, otherwise heterotropic

Cooperative Reaction – Example
Ó The simplest cooperative mechanism is shown below
Ó By applying the law of mass action and then the QSSA, analogously to what
done for the M–M model it is possible to derive the maximum reaction rate
ds k 2 K m′ + k 4 s0
R0 (s0 ) = = e0 s0
dt t =0 K m K m′ + K m′ s0 + s02
k −1 + k 2 k + k −3
Km = , K m′ = 4
k1 k3

Hill Plot
Ó Plotting the reaction rate as a function of s0 it is possible to observe the

difference with respect to standard reactions
Ó For the sake of simplicity, we plot the case when k2=0, which yields
Ó In this case the behavior is usually

described by a Hill curve s0 → 0 ⇒ R0 ∝ s02
Qs0n
R0 (s0 ) = , n>0
s0n + Km

Hill Coefficient
Ó The quantity n is termed the Hill coefficient
Ó The same term can be found by considering an ideal reaction, with an

enzyme binding n substrate molecules at the same time (complete
cooperativity)
Ó In real cases, the value of n has not to be an integer, rather it is a real

number, because usually the substrates do not bind contemporaneously to
different sites, thus
Ô n>1 F positive cooperation
Ô n<1 F negative cooperation
Ô n=1 F no cooperation
Ó Therefore the Hill coefficient is a measure of the cooperativity of the

reaction

Outline


Lineweaver–Burk Plot
Ó The L–B plot (or double reciprocal is a common tool in biochemistry

analysis of enzyme kinetics
Ó It is easily derived by inverting the equation of S in the M–M model
1 K m + [S ]
=
V0 Vmax [S ]
1 Km 1
= +
V0 Vmax [S ] Vmax
Ó It is very useful because it enables

linear regression of experimental data

Regulation of Enzymatic Reactions
Ó Enzymes can increase the rate of a reaction by several orders of magnitude,

but they can also be used for fine regulation of reaction pathways
Ó The production and degradation are often adapted to the current

requirements of the cell
Ó Furthermore, the may be targets of effectors, both inhibitors and activators
Ó The effectors are proteins or other molecules that can modify the enzymatic
reaction rate

Enzyme Inhibition
Ó Different types of inhibition mechanism exist, depending on

Ô the state in which the enzyme can bind the effector
Ô the ability of different complexes to release the product
Ó The general pattern of inhibition is shown in the figure below; the several
subcases derive by eliminating some of the reactions

Competitive Inhibition
Ó The inhibitor competes with the substrate for the binding site (or inhibits
substrate binding by binding elsewhere to the enzyme)
d [P ] V [S ]
= max
dt αK m + [S ]
α = 1+
[I]
, KI =
[E ][I ]
KI [EI ]

Competitive Inhibition L–B Plot
Ó The competitive inhibition can be characterized experimentally by means of

the L–B plot

Uncompetitive Inhibition
Ó The inhibitor binds only to the ES complex
Ó This may be due to conformational changes of the enzyme caused by the

substrate binding (allosteric effect), which makes a new binding site
accessible
d [P ] Vmax [S ]
=
dt K m + α ′[S ]
α′ = 1+
[I ] , K I′ =
[ES ][I ]
K I′ [ESI ]

Uncompetitive Inhibition L–B Plot
Ó The L–B significantly differs from the previous case

Mixed Inhibition
Ó The inhibitor can bind both to the enzyme and to the ES complex
Ó Therefore it binds to a different site than that used by the substrate
d [P ] Vmax [S ]
=
dt αK m + α ′[S ]
α = 1+
[I ] , KI =
[E ][I ]
KI [EI ]
α ′ = 1+
[I ] , K I′ =
[ES ][I ]
K I′ [ESI ]

Mixed Inhibition L–B Plot
Ó Also in this case the L – B plot can be used to distinguish from the other
types of inhibition mechanism

Noncompetitive and Partial Inhibition
Ó Noncompetitive inhibition can be viewed as a special case of mixed

inhibition, when the parameters α and α’ are equal
Ó In this case the inhibitor has the same affinity to the enzyme with or
without bound substrate
Ó It is rarely encountered in experimental practice
Ó If the product can also be formed from the enzyme–substrate–inhibitor

complex, the inhibition is said to be partial
Ó If the production rate from ESI complex is high, the effect of this latter
mechanism can even yield an activating instead of an inhibiting effect

Dependence on Environmental Factors
Ó It is worth pointing out that enzymatic reactions are strongly dependent on

factors like pH and temperature, as shown in the two examples below

Outline


Stochastic Models
Ó The models considered so far are deterministic, i.e. given the initial
conditions (the state at t0) and the exogenous signals perturbing the model,
the response is univocally determined
Ó A stochastic model, on the contrary, involves random variables, therefore its

behavior cannot be predicted a priori, although it can be statistically
characterized
Ó The figure shows two realization of

the same stochastic process, starting
from the same initial condition

Biological Systems are Stochastic
Ó Certainly biological ones fall in the category of stochastic systems, indeed

the very basic steps of every molecular reaction can be described only in
terms of its probability of occurrence
Ó Moreover, the diffusion of molecules is a realization of a random walk

process (Brownian motion)
Ó So, why deterministic model are so widespread?

Ô Usually the phenomena under consideration involve a large number of
molecules, therefore the average effect is well described through
deterministic equations
Ó When is it necessary to use stochastic models/simulations?

Ô When the mechanism to be described is based on the interaction of few
molecules, or we want to simulate the functioning of a little pool of cells

Gillespie Algorithm
Ó The algorithm has been first presented in

DT Gillespie, A General Method for Numerically Simulating the Stochastic Time Evolution
of Coupled Chemical Reactions, J. of Computational Physics 22, 403–434, 1976
Ó The purpose is to simulate chemical reactions with limited computational

resources
Ó The outcome is a realization of the underlying stochastic process

Basic Principles
Ó The basic working principles of the Gillespie algorithm derive from the
description of the collision of particles in a vessel
Ó When two molecules collide, the reaction happens only if they have proper
orientation and kinetic energy
Ó A first hypothesis is that the frequency of non–reacting collisions is much

larger than that of reacting ones
Ó Secondly, the algorithm assumes that each reaction involves no more than
two molecules

Sketch of the Derivation
Ó The method starts from the observation of the volume occupied by a

molecule A that is in relative motion with respect to another molecule B

Sketch of the Derivation
Ó Assuming a random uniform distribution of the molecules in the volume V,

the probability of collision can be computed as
Probability of collision of two
δVcoll V = V −1π r122 v12δ t molecules in the interval t
Ó If in such volume we have X1 molecules of the species S1 and X2 of the

species S2, the probability of collision is
X 1 X 2V −1π r122 v12δ t

Stochastic Reaction Constant
Ó In this framework, the reactions can be characterized by means of a

probability of reaction per unit time, instead of a kinetic rate as in ODE
models
Ó For instance, given the reaction

R1 : S1 + S 2 → 2 S1
we can define a constant c1, dependent on the chemo–physical properties of

the molecules and on the temperature, such that
X1 X2 c1dt = Probability that the reaction happens in the volume V

within the interval dt
Ó In general, given a system of N molecules and M reactions, each reaction

is characterized by a specific stochastic reaction constant cµ (µ=1,…,M)

Stochastic and Deterministic Constants
Ó Intuitively, the stochastic reaction constant, cµ, must be linked to the kinetic
constant of the corresponding determinist equation, kµ
Ó In the validity ranges of the deterministic models, it is possible to establish

the simple relation
k1 = Vc1
Ó The presence of the factor V depends on the fact that deterministic models
take as state variables the concentrations, whereas stochastic ones use the
number of molecules

Stochastic Simulation
Ó There are two main approaches to solve the stochastic system and compute
the system evolution
Ô Master Equation Approach
Ô Stochastic Simulation Algorithm (SSA) with Gillespie method

Master Equation Approach
Ó The key element in this approach is the probability function
P( X 1 , X 2 ,K, X N ; t )
Probability that at time t there are X1
molecules of species S1, …, XN of
species SN
Ó The master equation describes the evolution of the function P
Ó The probability P(X1,…,XN;t+dt) can be derived as a combination of the

probability of all the possible reactions that can happen within dt
Ó The differential equation that is derived by this argument does not usually
have analytical solution, nor it admits a computationally efficient solution

Outline


Stochastic Simulation Algorithm
Ó Disregarding the formalism of the master equation, looking for a more

practical approach, we need to answer two questions
Ô Starting at time t, which is the next occurring reaction
Ô When this reaction will occur
Ó Clearly, the answer can be given only in terms of probability, thus let us
define the pdf of the reaction, P(τ,µ), such that
P(τ , µ )dτ Probability that, given X1,…, XN at time t,

the next reaction in V will be Rµ and that it
will occur within (t+ τ,t+ τ +dτ)

Ó In order to find an analytical expression for P(τ,µ) let define

Ô hµ → number of possible distinct combinations of reactants in Rµ in the
state (X1,…,XN), µ=1,…,M
Õ If Rµ has two–reactants (of the type S1+S2 → …), then
hµ =X1X2
Õ If Rµ has one reactant (of the type 2S1 → …), then
hµ =1/2 X1(X1-1)
Ô aµdt = hµcµdt → probability that a reaction Rµ occur in the interval
(t,t+dt) starting from the state (X1,…,XN), µ=1,…,M at time t

Ó From this quantities it is possible to derive the following expression
⎧aµ exp(− a0τ ) 0 ≤ τ ≤ ∞ and µ = 1, K , M

P(τ , µ ) = ⎨
⎩ 0 altrimenti
where
aµ = hµ cµ (µ = 1,K, M )
M M
a0 = ∑ aν = ∑ hν cν
ν =1 ν =1
Ó Having a random number generator with uniform distribution, it is possible

to generate the exponential distribution above

Steps of the Gillespie Algorithm
Ó Step 0 (Initialization) – Define the number of molecules of each species, the

kinetic constants and the random number generator
Ó Step 1 (Monte Carlo) – Generate random numbers, to determine which is

the next reaction and the length of the interval dt
Ó Step 2 (Update) – Increase time by dt and update the number of molecules

of each species on the basis of the occurred reaction
Ó Step 3 (Iterate) – If the number of reactants is greater than zero and the
simulation stop time has not yet been reached, iterate from Step 1

Drawbacks of the Stochastic
Ó High computational load
Ó Not possible to derive reduced order model (like M–M or Hill terms)

References
Ó DL Nelson, MM Cox, Lehninger Principles of Biochemistry, WH Freeman, 2004
Ó JD Murray, Mathematical Biology, Springer, 2007
Ó E.H. Flach, S. Schnell, Use and abuse of the quasi-steady-state approximation, IEE Proc.–Syst. Biol.
153(4), 187–191, 2006
Ó A Ciliberto, F Capuani, JJ Tyson, Modeling Networks of Coupled Enzymatic Reactions Using the total
Quasi–Steady State Approximation, PLOS Computational Biology 3(3), 463–472, 2007
Ó DT Gillespie, A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled
Chemical Reactions, J. of Computational Physics 22, 403–434, 1976

Lecture 2

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Lecture 2

Uploaded by

Copyright:

Available Formats

Modeling of Biochemical Reactions

Dr. Carlo Cosentino

Dr. Carlo Cosentino 1 Carnegie Mellon University, Pittsburgh, 2008

Ó Modeling of biochemical reactions

Dr. Carlo Cosentino 2 Carnegie Mellon University, Pittsburgh, 2008

Ó The equilibrium of a reaction is linked to the variation of biochemical

Ó The velocity, instead, depends on the activation energy, ∆GS → P

Dr. Carlo Cosentino 3 Carnegie Mellon University, Pittsburgh, 2008

Ó The reaction rate is determined by

Ó The reaction rate for S ⎯

Ó From transition-state theory it is possible to derive the relation

Dr. Carlo Cosentino 4 Carnegie Mellon University, Pittsburgh, 2008

Ó Let us consider the following basic reversible reaction S ⎯⎯→

Ó The equilibrium constant is a function of ∆G’0

Dr. Carlo Cosentino 5 Carnegie Mellon University, Pittsburgh, 2008

Ó Enzymes are a family of proteins specialized in the catalysis of reactions

Ó The basic mechanism is the formation of an enzyme-substrate complex,

Ó After the substrate has been transformed

Dr. Carlo Cosentino 6 Carnegie Mellon University, Pittsburgh, 2008

Ó Enzymes play a central role in all the biological processes (metabolism,

Ó Many diseases are caused by deficiency of some enzyme

Ó Many drugs act by interacting with enzymes

Dr. Carlo Cosentino 7 Carnegie Mellon University, Pittsburgh, 2008

Ó Modeling of biochemical reactions

Dr. Carlo Cosentino 8 Carnegie Mellon University, Pittsburgh, 2008

Ó The basic model of enzymatic reaction was proposed by

Dr. Carlo Cosentino 9 Carnegie Mellon University, Pittsburgh, 2008

Ó Applying the LMA to the model reaction scheme, we obtain

s& = − k1es + k −1c, e& = − k1es + (k −1 + k 2 )c

with initial conditions s(0)=s0, e(0)=e0, c(0)=0, p(0)=0

Ó Note that the equation of p(t) is decoupled and yields

Dr. Carlo Cosentino 10 Carnegie Mellon University, Pittsburgh, 2008

Ó The total amount of enzyme (free+bound) remains constant over time,

e& + c& = 0 ⇒ e(t ) + c(t ) = e0

s& = − k1e0 s + (k1s + k −1 )c, s (0 ) = s0

Dr. Carlo Cosentino 11 Carnegie Mellon University, Pittsburgh, 2008

Ó This assumption lets us pose dc/dt ≅ 0, that is

is the Michaelis–Menten constant

Dr. Carlo Cosentino 12 Carnegie Mellon University, Pittsburgh, 2008

Ó Furthermore, the amount of enzyme is typically much less than that of

Dr. Carlo Cosentino 13 Carnegie Mellon University, Pittsburgh, 2008

Ó A change of variables is often used in biochemical models, in order to

Ó Furthermore, the adimensionalization typically reduces the number of

Dr. Carlo Cosentino 14 Carnegie Mellon University, Pittsburgh, 2008

Ó By applying the change of variable above, the simplified model reduces to

Dr. Carlo Cosentino 15 Carnegie Mellon University, Pittsburgh, 2008

Ó An estimate for the substrate transformation time constant can be derived

Dr. Carlo Cosentino 16 Carnegie Mellon University, Pittsburgh, 2008

Ó The amount of s consumed during the initial transient has to be negligible,

Dr. Carlo Cosentino 17 Carnegie Mellon University, Pittsburgh, 2008

Dr. Carlo Cosentino 18 Carnegie Mellon University, Pittsburgh, 2008

Ó Modeling of biochemical reactions

Dr. Carlo Cosentino 19 Carnegie Mellon University, Pittsburgh, 2008

Ó The assumptions exploited in the derivation of the simplified M–M model

Ó Large differences in the time-scales of the reactions may create huge

Ó To overcome this limitations, theoreticians (especially in the biochemistry

Dr. Carlo Cosentino 20 Carnegie Mellon University, Pittsburgh, 2008

Ó The validity of the QSSA depends on

Ó In the case of protein interaction networks (PINs) the QSSA assumptions

Dr. Carlo Cosentino 21 Carnegie Mellon University, Pittsburgh, 2008

Ó An enlightening work concerning the validity of the QSSA

Ó The authors performed a compared analysis of the Van Slyke–Cullen