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Welcome to
Integrated Bioinformatics
Friday, 18 November 2016
Metabolic Modeling
Welcome to
Integrated Bioinformatics
Friday, 18 November 2016
Metabolic Modeling
Welcome to
Integrated Bioinformatics
Friday, 18 November 2016
Metabolic Modeling
What to do today, tomorrow,...?
I would like to work in industry .
My career goal is to be a part
of a health care organization
Industrial analysis work
I would like some return on my educational
investment…working as bioinformatican
or as a scientific software engineer.
[From a graduate now in industry]
[From a graduate now in industry]
I’ve been working in the biotech industry as a
Bioinformaticist for 2 years. In that time frame I’ve
learned many things school didn’t and probably
couldn’t teach me... What I didn’t know was how to ...
Develop an automated downstream analysis for...
how to... how to....
Without guidance except my brain and my intuition...
I was able to pull this stunt off.
I can honestly say I know a lot and yet I feel like
I know nothing, but typically I do know where I can
find the answer...
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
3. Metabolism can be modeled mathematically
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
3. Metabolism can be modeled mathematically
4. Problems can be modeled computationally
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
3. Metabolism can be modeled mathematically
4. Problems can be modeled computationally
5. Models can tell you when your understanding is faulty
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
3. Metabolism can be modeled mathematically
4. Problems can be modeled computationally
5. Models can tell you when your understanding is faulty
No, I am so confused.
Please help!
Sample Question
• General frame
I’m confused about the
coordinate system.
Sample Question
• General frame
• Specific frame
I’m confused about the
coordinate system.
Sample Question
• General frame
• Specific frame
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences.
Sample Question
• General frame
• Specific frame
• Specific example
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences.
Sample Question
• General frame
• Specific frame
• Specific example
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
Sample Question
• General frame
• Specific frame
• Specific example
• Attempt to resolve
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
Sample Question
• General frame
• Specific frame
• Specific example
• Attempt to resolve
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
I tried counting from coordinate
1 but that led me to the letters
GAT when I believe the gene
should begin ATG.
Sample Question
• General frame
• Specific frame
• Specific example
• Attempt to resolve
• Optional rant
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
I tried counting from coordinate
1 but that led me to the letters
GAT when I believe the gene
should begin ATG.
Sample Question
• General frame
• Specific frame
• Specific example
• Attempt to resolve
• Optional rant
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
I tried counting from coordinate
1 but that led me to the letters
GAT when I believe the gene
should begin ATG. What kind of
idiot would invent such a nonintuitive system?!?!?
Sample Question
• General frame
• Specific frame
• Specific example
• Attempt to resolve
• Optional rant
• Specific request
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
I tried counting from coordinate
1 but that led me to the letters
GAT when I believe the gene
should begin ATG. What kind of
idiot would invent such a nonintuitive system?!?!?
Sample Question
• General frame
• Specific frame
• Specific example
• Attempt to resolve
• Optional rant
• Specific request
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
I tried counting from coordinate
1 but that led me to the letters
GAT when I believe the gene
should begin ATG. What kind of
idiot would invent such a nonintuitive system?!?!? I wonder if
you could give some insight as
to why my experiment failed.
Sample Question
• General frame
• Specific frame
• Specific example
• Attempt to resolve
• Optional rant
• Specific request
• Polite closing
I’m confused about the
coordinate system. Specifically,
I don’t understand how to use
the numbers near genes to find
their sequences. I tried with the
first number for Ava0001 (119),
but that number doesn’t exist
amongst the coordinates shown.
I tried counting from coordinate
1 but that led me to the letters
GAT when I believe the gene
should begin ATG. What kind of
idiot would invent such a nonintuitive system?!?!? I wonder if
you could give some insight as
to why my experiment failed.
Thanks.
Why Metabolic Modeling
Rational drug design
Trypanosoma brucei
Causative agent of sleeping sickness
Life Cycle
Central Nervous System
Death
Trypanosoma brucei
How to stop it?
Standard antibiotic targets
Cell wall
e.g. penicillins
Bacterial ribosomes
e.g. neomycin
Bacterial RNA polymerase
e.g. rifampicin
Bacterial DNA gyrase
e.g. nalidixic acid
Trypanosomes have eukaryotic machinery, like us
Trypanosoma brucei
How to stop it?
Them
ATP
Glucose
Us
Glycolysis
Glycolysis
Pyruvate
Pyruvate
Citric Acid
Cycle
ATP
ATP
Trypanosoma brucei
How to stop it?
Glucose
Them
ATP
Us
Glycolysis
Glycolysis
Pyruvate
Pyruvate
Citric Acid
Cycle
ATP
ATP
Alternative to exhaustive lab testing
Glycolysis
Symbolically
Glucose Hexokinase Glucose-6-P
+ ATP
+ ADP
Mathematically
dG6P/dt = kf [Glc][ATP]
Computationally
dG6P.dxdt = kf*glc*atp
… exhaustive
computational modeling
Alternative to exhaustive lab testing
Glycolysis
dGlc/dt = +kf1 [Glcx] -kr2[Glc]
-kf2[Glc][ATP]
dG6P/dt = +kf2 [Glc][ATP]
-kf3[G6P]
dF6P/dt = +kf3 [G6P]-kr3[F6P]
-kf4[F6P][AT]
dFDP/dt = +kf4 [F6P][ATP]-kf5[FDP]
dDHAP/dt = +kf5 [FDP]+kr6[G3P] -kf6[DHAP]
dG3P/dt = +kf5 [FDP]+kf6[DHAP] -kr6[G3P]
-kf7[G3P][NAD]+kry[13PGA][NADH]
d13PGA/dt = kf7[G3P][NAD]-kry[13PGA][NADH]
-kf8[13PGA][ADP]+kr8[3PGA][ATP]
...
inhibitor1
Alternative to exhaustive lab testing
Everything
dGlc/dt = +kf1 [Glcx] -kr2[Glc]
-kf2[Glc][ATP]
dG6P/dt = +kf2 [Glc][ATP]
-kf3[G6P]
dF6P/dt = +kf3 [G6P]-kr3[F6P]
-kf4[F6P][AT]
dFDP/dt = +kf4 [F6P][ATP]-kf5[FDP]
dDHAP/dt = +kf5 [FDP]+kr6[G3P] -kf6[DHAP]
dG3P/dt = +kf5 [FDP]+kf6[DHAP] -kr6[G3P]
-kf7[G3P][NAD]+kry[13PGA][NADH]
d13PGA/dt = kf7[G3P][NAD]-kry[13PGA][NADH]
-kf8[13PGA][ADP]+kr8[3PGA][ATP]
...
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
3. Metabolism can be modeled mathematically
4. Problems can be modeled computationally
5. Models can tell you when your understanding is faulty
What is glycolysis
Glucose
Pyruvate
ATP
How do I get to my hotel?
Airport
Hotel
$$$
What is glycolysis
Glucose
Pyruvate
ATP
What is glycolysis
Glucose
Pyruvate
ATP
What is glycolysis
Glucose
Pyruvate
ATP
What is glycolysis
glucose
HO
OH
OH
OH
O
OH
OO
ATP +
OH
pyruvate
What is glycolysis
glucose
OH
HO
OH
OH
HO
methanol
O
OH
OH
OH
OH
O
OH
OO
ATP +
OH
pyruvate
What is glycolysis
glucose
HO
OH
OH
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
O
OH
OO
ATP +
OH
pyruvate
What is glycolysis
glucose
HO
OH
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
O
OH
OH
O
OH
OH
OO
ATP +
OH
pyruvate
What is glycolysis
glucose
HO
OH
OH
OH
blood
cell
O
OH
OO
ATP +
OH
pyruvate
What is glycolysis
glucose
HO
OH
OH
OH
O
permease
OH
blood
cell
OO
OH
pyruvate
What is glycolysis
glucose
HO
permease
OH
OH
OH
blood
cell
OO
OH
pyruvate
O
OH
What is glycolysis
glucose
HO
OH
OH
OH
O
permease
OH
ATP
blood
cell
O O O
O-P-O
O-P-O
O-P-O -Adenosine
O O O
Anhydride (acid + acid)
2
OO
OH
pyruvate
What is glycolysis
glucose
HO
permease
OH
OH
OH
O
OH
ATP
blood
cell
O O O
O-P-O
O-P-O
O-P-O -Adenosine
O O O
Anhydride (acid + acid)
2
OO
OH
pyruvate
What is glycolysis
O
glucose
O-P-O
O
permease
OH
OH
OH
O
OH
ADP
blood
cell
O O
O-P-O
O-P-O -Adenosine
O O
Anhydride (acid + acid)
2
OO
OH
pyruvate
What is glycolysis
glucose
O
permease
OH
OH
OH
O
OH
ADP
blood
cell
O O
O-P-O
O-P-O -Adenosine
O O
Anhydride (acid + acid)
2
OO
OH
pyruvate
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
O
glucose-6P
OH
O
OH
O
OH
OH
OH
Hexokinase
Ketone or aldehyde
O
???
O
2 ATP + 2
OO
OH
pyruvate
Enol
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
O
glucose-6P
OH
O
OH
O
OH
OH
O
OH
???
2 ATP + 2
OH
pyruvate
OHO
OH
Hexokinase
OO
OH
OH
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
O
glucose-6P
OH
O
OH
O
OH
OH
O
OH
OH
Hexose-P
isomerase
Hexokinase
OO
2 ATP + 2
fructose-6P
OH
pyruvate
OHO
OH
O
OH
OH
OHO
OH
OH
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
O
ATP ADP
glucose-6P
OH
O
OH
O
OH
OH
O
OH
OH
Hexose-P
isomerase
Hexokinase
OO
2 ATP + 2
fructose-6P
OH
pyruvate
OHO
OH
fructose-1,6 diP
O
OH
Phospho
fructokinase
OH
OHO
OH
O
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
O
ATP ADP
glucose-6P
OH
O
OH
O
OH
OH
fructose-6P
O
OH
OH
Hexose-P
isomerase
Hexokinase
OHO
OH
fructose-1,6 diP
O
OH
OHO
OH
OH
O
Phospho
fructokinase
Aldolase
O
OH
O
glyceraldehyde
3-P (Gla3P)
2 ATP + 2
OO
OH
pyruvate
OHO
O
Dihydroxy
acetone P
(DHAP)
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
O
ATP ADP
glucose-6P
OH
O
OH
O
OH
OH
fructose-6P
O
OH
OH
Hexose-P
isomerase
Hexokinase
OHO
OH
fructose-1,6 diP
O
OH
OHO
OH
OH
O
Phospho
fructokinase
Aldolase
Triose P
isomerase
2 ATP + 2
OO
OH
pyruvate
O
OH
O
Gla3P
OHO
O
DHAP
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
O
ATP ADP
glucose-6P
OH
O
OH
O
OH
OH
fructose-6P
O
OH
Hexose-P
isomerase
fructose-1,6 diP
O
OH
OH
OH
Hexokinase
OHO
OHO
OH
O
OH
Phospho
fructokinase
Aldolase
Triose P
isomerase
O
OHO
OH
O
O
Gla3P
DHAP
NAD+
O
2 ATP + 2
OO
OH
pyruvate
NADH
Gla 3-P
dehydrogenase
O
OH
O
O
O
ADP
ATP
OH
O
O
3-P-glycerate (3PG)
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
ATP ADP
glucose-6P
O
O
OH
OH
OH
OH
fructose-6P
O
OH
OO
OH
pyruvate
OHO
fructose-1,6 diP
O
OH
OH
OH
Hexose-P
isomerase
Hexokinase
2 ATP + 2
O
OHO
OH
O
OH
Phospho
fructokinase
Aldolase
Triose P
isomerase
O
OHO
OH
O
O
Gla3P
DHAP
NAD+
O
NADH
Gla 3-P
dehydrogenase
O
OH
O
O
O
ADP
ATP
OH
O
O
3-P-glycerate (3PG)
What is glycolysis
ATP ADP
glucose
HO
OH
OH
OH
ATP ADP
glucose-6P
O
OH
O
OH
OH
OH
fructose-6P
O
OH
OO
OH
pyruvate
OHO
fructose-1,6 diP
O
OH
OH
OH
Hexose-P
isomerase
Hexokinase
2 ATP + 2
O
OHO
OH
O
OH
Phospho
fructokinase
Aldolase
Triose P
isomerase
O
OHO
OH
O
O
Gla3P
DHAP
NAD+
O
O
O
O
OH O
NADH
Gla 3-P
dehydrogenase
O
O
O
2-P-glycerate (3PG)
ADP
ATP
OH
O
O
O
O
OH
O
3-P-glycerate (3PG)
Trypanosoma brucei
How to exploit dependence on glycolysis?
blood
cell
Treatment
Arsenate
(AsO4 = Asi)
Periodic Table
Trypanosoma brucei
How to exploit dependence on glycolysis?
blood
cell
Treatment
Arsenate
(AsO4 = Asi)
Competitive
with Pi
Trypanosoma brucei
How to exploit dependence on glycolysis?
Glyceraldehyde-3-P
NAD+
O
O
O-P-O-CH2—CH—C
H
O
NADH
ADP
O
O O
O-P-O-CH2—CH—C- O-P-O
O
O
ATP
3-P-Glycerate
O
O
O-P-O-CH2—CH—C-O
O
O
O-P-O
O
Trypanosoma brucei
How to exploit dependence on glycolysis?
Glyceraldehyde-3-P
NAD+
O
O-As-O
O
O
O
O-P-O-CH2—CH—C
H
O
H2O
NADH
O
O
O
O-P-O-CH2—CH—C- O-As-O
O
O
ADP
ATP
3-P-Glycerate
O
O
O-P-O-CH2—CH—C-O
O
+
O
O-As-O
O
Trypanosoma brucei
How to exploit dependence on glycolysis?
Glyceraldehyde-3-P
O
ADP- O-As-O
O
NAD+
O
O
O-P-O-CH2—CH—C
H
O
H2O
NADH
O
O
O
O-P-O-CH2—CH—C- O-As-O
O
O
ADP
O
ADP + O-As-O
ATP
O
3-P-Glycerate
O
O-As-O
O
O
O
O-P-O-CH2—CH—C-O
O
+
O
O-As-O
O
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
3. Metabolism can be modeled mathematically
4. Problems can be modeled computationally
5. Models can tell you when your understanding is faulty
How to model this reaction?
(Spontaneous)
1
[S]
0.8
0.6
0.4
0.2
0
0
1
2
3
t (sec)
4
5
How to model this reaction?
(Spontaneous)
velocity?
ADP-As
ADP +Asi
[ADP-As]
concentration
k = d[ADP] / dt
rate
constant
rate of change
d[Asi] / dt
rate of change
– d[ADP-Asi] / dt
rate of change
k [S] = – d[Si] / dt
How to model this reaction?
(Spontaneous)
velocity?
ADP-As
A differential equation
Its solution?
ADP +Asi
= d[S] / dt = –k[S]
[S] =
How to model this reaction?
(Spontaneous)
velocity?
ADP-As
A differential equation
Its solution?
Check:
ADP +Asi
= d[S] / dt = –k[S]
[S] = S0 e -k(t-to)
= d[S] / dt = S0 (–k) e -k(t-to)
= -k S0 e -k(t-to)
= -k [S]
How to model this reaction?
(Spontaneous)
1
[S]
0.8
[S] = S0 e -k(t-to)
0.6
0.4
0.2
0
0
1
2
3
t (sec)
4
5
How to model this reaction?
(Spontaneous)
How to model this reaction?
(Spontaneous)
1
If you know the slope…
[S]
0.8
(Do you?)
0.6
0.4
= d[S] / dt = –k[S]
0.2
0
0
1
2
3
t (sec)
4
5
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
2. Metabolism has logic
3. Metabolism can be modeled mathematically
4. Problems can be modeled computationally
5. Models can tell you when your understanding is faulty
How to model this reaction?
(Spontaneous)
How to model this reaction?
(Spontaneous)
1
S0
[S] = S0 + Δt d[S] / dt
[S]
0.8
0.6
Δt
0.4
= d[S] / dt = –k[S]
0.2
0
0
1
2
3
t (sec)
4
5
How to model this reaction?
(Spontaneous)
1
[S] = S0 + Δt d[S] / dt
[S]
0.8
SQ3. Why is it that the predicted levels are
all lower than the calculated levels?
S0
0.6
0.4
Δt
= d[S] / dt = –k[S]
0.2
0
0
1
2
3
t (sec)
4
5
How to model this reaction?
(Spontaneous)
1
[S] = S0 + Δt d[S] / dt
[S]
0.8
SQ4. Modify the two programs to make
S0
produce numbers that bring the two
curves closer together.
Δt
What’s
key trick?
= d[S]
/ dt the
= –k[S]
0.6
0.4
0.2
0
0
1
2
3
t (sec)
4
5
My goals for this module
1. Provide you an opportunity to figure out solutions
to problems outside of your experience
Enymatically
catalyzed
2. Metabolism has logic
V
3. Metabolism can be modeled mathematically
4. Problems can be modeled computationally
5. Models can tell you when your understanding is faulty
How to model this reaction?
(Catalyzed)
How to model this reaction?
(Catalyzed)
What is the rate equation?
Glucose-6-phosphate
[G6P]
concentration
Fructose-6-phosphate
k = = d[F6P] / dt
rate
constant
???
k~0
rate of change
Characteristics of enzymes
Enzymatic reactions
Characteristics of enzymes
Enzymatic reactions
G6P + E
G6P·E
F6P·E
E-complex
F6P + E
How to model this reaction?
(Catalyzed)
G6P + E
G6P·E
F6P·E
E-complex
= d[G6PE] / dt =
F6P + E
How to model this reaction?
(Catalyzed)
How to model this reaction?
(Catalyzed)
What are the units of kf and kr?
How to model this reaction?
(Catalyzed)
G6P + E
G6P·E
F6P·E
F6P + E
E-complex
= d[G6PE] / dt =
= d[F6P] / dt
=
Rates of changes of metabolites
Rates of changes of metabolites
SQ5. Write an expression that gives the
concentration of F6P at time t + dt.
Spontaneous vs Catalyzed
Metabolic Modeling
Metabolic Modeling
Metabolic Modeling