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Bio/Chemical Kinetics Made Easy
A Numerical ApproachPetr Kuzmič, Ph.D.
BioKin, Ltd.
1. Case study: Inhibition of LF protease from B. anthracis
2. Method: Numerical Enzyme Kinetics
ier
Bio/Chemical Kinetics Made Easy 2
Anthrax bacillus
CUTANEOUS AND INHALATION ANTHRAX DISEASE
Bio/Chemical Kinetics Made Easy 3
Lethal Factor (LF) protease from B. anthracis
CLEAVES MITOGEN ACTIVATED PROTEIN KINASE KINASE (MAPKK)
Inhibitor?
Bio/Chemical Kinetics Made Easy 4
Neomycin B: an aminoglycoside inhibitor
PRESUMABLY A "COMPETITIVE" INHIBITOR OF LF PROTEASE
Fridman et al. (2004) Angew. Chem. Int. Ed. Eng. 44, 447-452
Bio/Chemical Kinetics Made Easy 5
Competitive inhibition - Possible mechanisms
Segel, I. (1975) Enzyme Kinetics, John Wiley, New York, p. 102
MUTUALLY EXCLUSIVE BINDING TO ENZYME
Bio/Chemical Kinetics Made Easy 6
Competitive inhibition - Kinetics
AT VERY HIGH [SUBSTRATE], ANZYME ACTIVITY IS COMPLETELY RESTORED
log [S]
-3 -2 -1 0 1 2 3
enzy
me
acti
vity
0.0
0.2
0.4
0.6
0.8
1.0
[I] = 0 [I] = 1 [I] = 2 [I] = 4 [I] = 8 [I] = 16
same V !
increase [I]
Bio/Chemical Kinetics Made Easy 7
Non-competitive inhibition - A possible mechanism
Segel, I. (1975) Enzyme Kinetics, John Wiley, New York, p. 126
NON-EXCLUSIVE BINDING, BUT TERNARY COMPLEX HAS NO CATALYTIC ACTIVITY
Bio/Chemical Kinetics Made Easy 8
Non-competitive inhibition - Kinetics
EVEN AT VERY HIGH [SUBSTRATE], ANZYME ACTIVITY IS NEVER FULLY RESTORED
log [S]
-3 -2 -1 0 1 2 3
enzy
me
acti
vity
0.0
0.2
0.4
0.6
0.8
1.0
increase [I]
Bio/Chemical Kinetics Made Easy 9
Compare saturation curves
DIAGNOSIS OF MECHANISMS: SAME OR DIFFERENT RATE AT VERY LARGE [S]?
[S]
0 2 4 6 8 10
activ
ity
0.0
0.2
0.4
0.6
0.8
1.0
[S]
0 2 4 6 8 10
activ
ity
0.0
0.2
0.4
0.6
0.8
1.0
?
COMPETITIVE NON-COMPETITIVE
Bio/Chemical Kinetics Made Easy 10
Compare "double-reciprocal" plots
DIAGNOSIS OF MECHANISMS: STRAIGHT LINES INTERCEPT ON VERTICAL AXIS?
1 / [S]
0.0 0.5 1.0 1.5 2.0
1 / a
ctiv
ity0
5
10
15
20
25
30
[I] = 0[I] = 1[I] = 2[I] = 4[I] = 8
1 / [S]
0.0 0.5 1.0 1.5 2.0
1 / a
ctiv
ity
0
5
10
15
20
[I] = 0[I] = 1[I] = 2[I] = 4[I] = 8
COMPETITIVE NON-COMPETITIVE
Bio/Chemical Kinetics Made Easy 11
Traditional plan to determine inhibition mechanism
THE TRADITIONAL APPROACH
1. Measure enzyme activity at increasing [S]
Collect multiple substrate-saturation curves at varied [I]
2. Convert [S] vs. activity data to double-reciprocal coordinates
3. Perform a linear fit of transformed (double-reciprocal) data
4. Check if resulting straight lines intersect on the vertical axis
If yes, declare the inhibition mechanism competitive
Fridman et al. (2004) Angew. Chem. Int. Ed. Eng. 44, 447-452
Bio/Chemical Kinetics Made Easy 12
Collect experimental data at varied [S] and [I]
THE RAW DATA
[S] (M)
0 20 40 60 80
V (
a.u.
/sec
)
0.0
0.2
0.4
0.6
0.8
[I] = 0
[I] = 0.5 M
[I] = 1.0 M
[I] = 2.0 M
Bio/Chemical Kinetics Made Easy 13
Check for intersection of double-reciprocal plots
[I] = 0
[I] = 0.5 M
[I] = 1.0 M
[I] = 2.0 M
1 / [S]
0.00 0.02 0.04 0.06 0.08 0.10 0.12
1 / V
0
2
4
6
8
10
12
DO LINEWEAVER-BURK PLOTS INTERSECT?
COMPETITIVE
Bio/Chemical Kinetics Made Easy 14
Doubts begin to appear...
[I] = 0
IS THIS A STRAIGHT LINE?
1 / [S]
0.00 0.02 0.04 0.06 0.08 0.10 0.12
1 / V
1.0
1.2
1.4
1.6
1.8
2.0
2.2
Bio/Chemical Kinetics Made Easy 15
Mysterious substrate saturation data
[I] = 0
MICHAELIS-MENTEN KINETICS IS NOT SUPPOSED TO SHOW A MAXIMUM !
[S] (M)
0 20 40 60 80
V (
a.u.
/sec
)
0.4
0.5
0.6
0.7
0.8
Throw these out?
Bio/Chemical Kinetics Made Easy 16
Repeat substrate experiment at higher [S]
[I] = 0
SEE IF MAXIMUM HOLDS UP AT HIGHER [S]
[S] (M)
0 20 40 60 80 100 120
V (
a.u.
/sec
)
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1 / [S]0.0 0.1 0.2 0.3 0.4
1 /
V
0
1
2
Bio/Chemical Kinetics Made Easy 17
Substrate inhibition in LF protease is real
HAS ANYONE ELSE SEEN IT?
Tonello et al. (2003) J. Biol. Chem. 278, 40075-78.
Bio/Chemical Kinetics Made Easy 18
Rate equation for inhibition by substrate
WHAT DOES THE "BIG BLUE BOOK" SAY?
Segel, I. (1975) Enzyme Kinetics, John Wiley, New York, p. 126
Bio/Chemical Kinetics Made Easy 19
Rate equation for inhibition by substrate + inhibitor
WHAT DOES THE "BIG BLUE BOOK" SAY?
?
Bio/Chemical Kinetics Made Easy
A Numerical ApproachPetr Kuzmič, Ph.D.
BioKin, Ltd.
ier
1. Case study: Inhibition LF protease from B. anthracis
2. Method: Numerical Enzyme Kinetics
Bio/Chemical Kinetics Made Easy 21
The task of mechanistic enzyme kinetics
SELECT AMONG MULTIPLE CANDIDATE MECHANISMS
concentration
initial rate
DATAcomputer
Select most plausible model
MECHANISMS
competitive ?
E + S E.S E + P
E + I E.I
uncompetitive ?
mixed type ?
competitive ?
Bio/Chemical Kinetics Made Easy 22
From mechanistic to mathematical models
DERIVE A MATHEMATICAL MODEL FROM BIOCHEMICAL IDEAS
concentration
initial rate
DATA
computer
MATHEMATICAL MODEL
E + S E.S E + P
E + I E.I
k +1
k -1
k +2
k +3
k -3
])[(][)(
][][
21313213
312 IkkkSkkkkk
SkkEkv
MECHANISM
Bio/Chemical Kinetics Made Easy 23
Problem: Simple mechanisms ...
MERELY FIVE REACTIONS ...
• 2 reactants (A, B)• 1 product (P)
• 5 reversible reactions• 10 rate constant
E + A E.A
E + P
E + B E.B
E.A.B
+ B
+ A
"RANDOM BI-UNI" MECHANISM
Bio/Chemical Kinetics Made Easy 24
... lead to complex algebraic models
Segel, I. (1975) Enzyme Kinetics.John Wiley, New York, p. 646.
E + A E.A
E + P
E + B E.B
E.A.B
+ B
+ A
"RANDOM BI-UNI" MECHANISM
MERELY FIVE REACTIONS ...
Bio/Chemical Kinetics Made Easy 25
A solution: Forget about algebra
POSSIBLE STRATEGY FOR MECHANISTIC MODEL BUILDING
• Do not even try to derive complex algebraic equations
• Instead, derive systems of simple, simultaneous equations
• Solve these systems using numerical methods
Bio/Chemical Kinetics Made Easy 26
Theoretical foundations: Mass Action Law
RATE IS PROPORTIONAL TO CONCENTRATION(S)
A products
MONOMOLECULAR REACTIONS
rate is proportional to [A]
A + B products
BIMOLECULAR REACTIONS
rate is proportional to [A] [B]
- d [A] / d t = k [A]
monomolecular rate constant1 / time
- d [A] / d t = - d [B] / d t = k [A] [B]
bimolecular rate constant1 / (concentration time)
“rate” … “derivative”
Bio/Chemical Kinetics Made Easy 27
Theoretical foundations: Mass Conservation Law
PRODUCTS ARE FORMED WITH THE SAME RATE AS REACTANTS DISAPPEAR
- d [A] / d t =A P + Q
EXAMPLE
COMPOSITION RULE ADDITIVITY OF TERMS FROM SEPARATE REACTIONS
mechanism:
d [B] / d t =A B
B C
k1
k2
+ d [P] / d t = + d [Q] / d t
- k2 [B]+ k1 [A]
Bio/Chemical Kinetics Made Easy 28
Composition Rule: Example
E + Ak+1
k-1
EA
EA + Bk+2
k-2
EAB
E + Bk+3
k-3
EB
EB + Ak+4
k-4
EAB
EABk+5
E + P + Q
EXAMPLE MECHANISM RATE EQUATIONS
d[P] / d t =
d[EAB] / d t =
Similarly for other species...
+ k+5 [EAB]
- k+5 [EAB]
+ k+2 [EA][B]
- k-2 [EAB]
+ k+4 [EB][A]
- k-4 [EAB]
Bio/Chemical Kinetics Made Easy 29
Program DYNAFIT (1996)
http://www.biokin.com/dynafit
Kuzmic P. (1996) Anal. Biochem. 237, 260-273.
0
50
100
150
200
250
300
350
400
1997 1999 2001 2003 2005
DYNAFI T paper - cumulative citations
375
Bio/Chemical Kinetics Made Easy 30
A "Kinetic Compiler"
E + S ---> ES : k1
ES ---> E + S : k2
ES ---> E + P : k3
Input (plain text file):
d[E ] / dt = - k1 [E] [S]
HOW DYNAFIT PROCESSES YOUR BIOCHEMICAL EQUATIONS
E + S E.S E + P
k1
k2
k3
k1 [E] [S]
k2 [ES]
k3 [ES]
Rate terms: Rate equations:
+ k2 [ES]+ k3 [ES]
d[ES ] / dt = + k1 [E] [S]- k2 [ES]- k3 [ES]
Similarly for other species...
Bio/Chemical Kinetics Made Easy 31
System of Simple, Simultaneous Equations
E + S ---> ES : k1
ES ---> E + S : k2
ES ---> E + P : k3
Input (plain text file):
HOW DYNAFIT PROCESSES YOUR BIOCHEMICAL EQUATIONS
E + S E.S E + P
k1
k2
k3
k1 [E] [S]
k2 [ES]
k3 [ES]
Rate terms: Rate equations:
"The LEGO method"
of deriving rate equations
Bio/Chemical Kinetics Made Easy 32
Initial rate kinetics
TWO BASIC APPROXIMATIONS
1. Rapid-Equilibrium Approximation
2. Steady-State Approximation
E + S E.S E + P
k1
k2
k3
assumed very much slower than k1, k2
• no assumptions made about relative magnitude of k1, k2, k3
• concentrations of enzyme forms are unchanging
New inDynaFit
Bio/Chemical Kinetics Made Easy 33
Initial rate kinetics - Traditional approach
DERIVE A MATHEMATICAL MODEL FROM BIOCHEMICAL IDEAS
concentration
initial rate
DATA
computer
MATHEMATICAL MODEL
E + S E.S E + P
E + I E.I
k +1
k -1
k +2
k +3
k -3
])[(][)(
][][
21313213
312 IkkkSkkkkk
SkkEkv
MECHANISM Think!
Bio/Chemical Kinetics Made Easy 34
Initial rate kinetics in DynaFit
GOOD NEWS: MODEL DERIVATION CAN BE FULLY AUTOMATED!
[task] task = fit data = rates approximation = Steady-State
[mechanism]
E + A <==> E.A : k1 k2 E.A + B <==> E.A.B : k3 k4 E + B <==> E.B : k5 k6 E.B + A <==> E.A.B : k7 k8 E.A.B <==> E + P : k9 k10
[constants] ...
DynaFit input file
computer
concentration
initial rate
MATHEMATICAL MODEL
MECHANISM
DATA
0 = [E] + [E.A] + [E.B] + [E.A.B] – [E]tot
0 = [A] + [E.A] + [E.A.B] – [A]tot
0 = [B] + [E.B] + [E.A.B] – [B]tot
0 = + k1[E][A] – k2[E.A] – k3 [E.A][B] + k4 [E.A.B]
0 = + k5[E][B] – k6[E.B] – k7 [E.B][A] + k8 [E.A.B]
0 = + k3 [E.A][B] + k7 [E.B][A] + k10 [E][P] – (k4+k8+k9)[E.A.B]
CRANK!
Bio/Chemical Kinetics Made Easy 35
Initial rate kinetics in DynaFit vs. traditional method
WHICH DO YOU LIKE BETTER?
[task] task = fit data = rates approximation = Steady-State
[reaction] A + B --> P
[mechanism]
E + A <==> E.A : k1 k2 E.A + B <==> E.A.B : k3 k4 E + B <==> E.B : k5 k6 E.B + A <==> E.A.B : k7 k8 E.A.B <==> E + P : k9 k10
[constants] ...
[concentrations] ...
E + A E.A
E + P
E + B E.B
E.A.B
+ B
+ A
Bio/Chemical Kinetics Made Easy
A Numerical ApproachPetr Kuzmič, Ph.D.
BioKin, Ltd.
ier
1. Case study: Inhibition LF protease from B. anthracis
2. Method: Numerical Enzyme Kinetics
Bio/Chemical Kinetics Made Easy 37
DynaFit model for inhibition by substrate
ENZYME KINETICS MADE EASIER
[reaction] | S ---> P[enzyme] | E[modifiers] | I
[mechanism]
E + S <===> E.S : Ks dissociation E.S + S <===> E.S.S : Ks2 dissociation E.S ---> E + P : kcat...
Bio/Chemical Kinetics Made Easy 38
DynaFit model for inhibition by substrate + inhibitor
ENZYME KINETICS MADE EASIER
[reaction] | S ---> P[enzyme] | E[modifiers] | I
[mechanism]
E + S <===> E.S : Ks dissoc E.S + S <===> E.S.S : Ks2 dissoc E.S ---> E + P : kcat E + I <===> E.I : Ki dissoc E.S + I <===> E.S.I : Kis dissoc [constants]
Ks = 1 ?, Ks2 = 1 ?, kcat = 1 ? Ki = 1 ?, Kis = 1 ?
...
...
initial estimate
optimization flag
Bio/Chemical Kinetics Made Easy 39
How do we know which mechanism is "best"?
COMPARE ANY NUMBER OF MODELS IN A SINGLE RUN
[task] task = fit | data = rates model = mixed-type ?
[reaction] | S ---> P[enzyme] | E[modifiers] | I
...
[task]
task = fit | data = rates model = competitive ?
...
[task]
task = fit | data = rates model = uncompetitive ?
...Akaike Information CriterionReview: Burnham & Anderson (2004)
Bio/Chemical Kinetics Made Easy 40
The best model: mixed-type noncompetitive
NEOMYCIN B IS NOT A COMPETITIVE INHBITOR OF LETHAL FACTOR PROTEASE
Kuzmic et al. (2006) FEBS J. 273, 3054-3062.
Bio/Chemical Kinetics Made Easy 41
Direct plot: maximum on dose-response curves
Kuzmic et al. (2006) FEBS J. 273, 3054-3062.
[S] (M)
0 20 40 60 80 100
V (
a.u.
/sec
)
0.0
0.2
0.4
0.6
0.8
Bio/Chemical Kinetics Made Easy 42
Double-reciprocal plot is nonlinear
Kuzmic et al. (2006) FEBS J. 273, 3054-3062.
1 / [S]
0.00 0.02 0.04 0.06 0.08 0.10
1 / V
0
2
4
6
8
Bio/Chemical Kinetics Made Easy 43
DR plot obscures deviations from the model
Kuzmic et al. (2006) FEBS J. 273, 3054-3062.
1 / [S]
0.00 0.02 0.04 0.06 0.08 0.10
1 / V
0
2
4
6
8
Bio/Chemical Kinetics Made Easy 44
Direct plot makes model departures more visible
Kuzmic et al. (2006) FEBS J. 273, 3054-3062.
[S] (M)
0 20 40 60 80
V (
a.u.
/sec
)
0.0
0.2
0.4
0.6
0.8
Bio/Chemical Kinetics Made Easy 45
Summary: Enzyme kinetics made (almost) easy
HOW DO I BUILD A MATHEMATICAL MODEL FOR AN ENZYME MECHANISM?
• Let the computer derive your model - don't bother with algebra.
• For many important mechanisms, algebraic models don't exist anyway.
• The theoretical foundation is simple and well understood:
- mass action law - mass conservation law
• The same set of -like rules apply to all types of kinetic models:
- reaction progress curves - initial reaction rates
Bio/Chemical Kinetics Made Easy 46
Acknowledgements: Lethal Factor protease work
Hawaii Biotechcurrently
Panthera BioPharma
Mark GoldmanSheri Millis
Lynne Cregar
Aiea, Island of Oahu, Hawaii
National Institutes of HealthGrant No. R43 AI52587-02
U.S. Army Medical Research and Materials CommandContract No. V549P-6073