Welcome to Integrated Bioinformatics Friday, 18 November 2011 Scenario 5 Metabolic Modeling The one and only concern I and most of my classmets have is the date of most modules needs to be updated in this website plus they need current informations. This is best viewed as a slide show. To view it, click Slide Show on the top tool bar, then View show. Click to start

New! Friday, 16 November 2012 What I learned from the questionnaires The biological problem Overview of glycolysis Modeling a spontaneous reaction (ADP-As.pl) Vmax and Km Problem Set 5, #3 and maybe #11

How things work At the beginning of each module the general principle is discussed… After this, time is spent more on programming and how to biologically use it. Takes up majority of the time writing/modifying perl programs. Not much time analyzing the output or finding answers to biological questions.

About an hour of lecture, followed by an hour of coding. How things work Lately we have been devoting the first hour to notes and defining a problem. The second hour is spent with Paul and Adam circulating to answer questions as the class works more or less independently. Usually, the first hour is devoted to lecture or going over the concepts of the module, and the next hour is spent working with Perl. About an hour of lecture, followed by an hour of coding.

I learn best by doing, not seeing nor hearing. What things work Lectures so far have been a big part of it. The lectures help me greatly with understanding more of the complex concepts. Sitting and trying to figure out how to solve a problem helps me learn about it more. I learn best by doing, not seeing nor hearing.

What things work I am very weak when it comes to math. I have no formal training in differential equations, but I've been able to work my through some biological scenarios that used them. I didn't understand the math,... I am very weak when it comes to math. I learn best by doing, not seeing nor hearing.

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 Glucose Us ATP Glycolysis Pyruvate Glycolysis ATP Pyruvate Citric Acid Cycle ATP

Trypanosoma brucei How to stop it? Them Glucose Us Glycolysis Pyruvate ATP Glycolysis Pyruvate ATP Citric Acid Cycle ATP

Alternative to exhaustive lab testing Glucose Glucose-6-P + ATP + ADP Hexokinase Symbolically inhibitor1 dG6P/dt = kf [Glc][ATP] Mathematically $dG6P_dt = $kf*$glc*$atp Computationally … exhaustive computational modeling

Glycolysis dG6P/dt = +kf2 [Glc][ATP] -kf3[G6P] dFDP/dt = +kf4 [F6P][ATP]-kf5[FDP] dGlc/dt = +kf1 [Glcx] -kr2[Glc] -kf2[Glc][ATP] dF6P/dt = +kf3 [G6P]-kr3[F6P] -kf4[F6P][AT] 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] . . . This is a very detailed modeling of glycolysis. It seems not feasible to model the enzyme kinetics when dealing large system of metabolic model.

Modeling Glycolysis I have studied it in a number of classes I learned about the glycolytic pathway in the past Need a little review, but comfortable with the basics. I understand the concept but I am definitely not an expert at it. Glucose->->->Pyruvate ===free energy

Modeling Glycolysis

electronegativity O > C > H What is glycolysis glucose O OH HO blood cell Oxidation state OH O < electronegativity O > C > H O OH 2 pyruvate 2 ATP +

What is glycolysis glucose O OH HO permease blood cell O OH 2 pyruvate

What is glycolysis glucose O OH HO permease blood cell O OH 2 pyruvate

Anhydride (acid + acid) What is glycolysis glucose O OH HO permease ATP O O-P-O -Adenosine blood cell Anhydride (acid + acid) O OH 2 pyruvate

Anhydride (acid + acid) What is glycolysis glucose O OH HO permease ATP O O-P-O -Adenosine blood cell Anhydride (acid + acid) O OH 2 pyruvate

Anhydride (acid + acid) What is glycolysis O O-P-O glucose O OH permease ADP O O-P-O O O-P-O blood cell -Adenosine Anhydride (acid + acid) O OH 2 pyruvate

Anhydride (acid + acid) What is glycolysis glucose O OH permease ADP O O-P-O O O-P-O blood cell -Adenosine Anhydride (acid + acid) O OH 2 pyruvate

What is glycolysis ??? 2 2 ATP + glucose glucose-6P Ketone or aldehyde ATP ADP glucose O OH HO glucose-6P O OH Ketone or aldehyde O Hexokinase ??? O Enol O OH 2 pyruvate 2 ATP +

What is glycolysis ??? 2 2 ATP + glucose glucose-6P Hexokinase ATP ADP glucose O OH HO glucose-6P O OH O OH Hexokinase ??? O OH 2 pyruvate 2 ATP +

What is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP glucose O OH HO glucose-6P fructose-6P O OH O OH O OH Hexose-P isomerase Hexokinase O OH 2 pyruvate 2 ATP +

What is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase O OH 2 pyruvate 2 ATP +

What is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase Aldolase O O OH OH O O glyceraldehyde 3-P (Gla3P) Dihydroxy acetone P (DHAP) O OH 2 pyruvate 2 ATP +

What is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase Aldolase O Triose P isomerase O OH OH O O Gla3P DHAP O OH 2 pyruvate 2 ATP +

What is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase Aldolase O Triose P isomerase O OH OH O O Gla3P DHAP NAD+ O O OH NADH ADP ATP O OH 2 pyruvate Gla 3-P dehydrogenase 2 ATP + O OH 3-P-glycerate (3PG)

What is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP Ketone or aldehyde O Enol O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase pyruvate Aldolase O O O 2 Triose P isomerase 2 ATP + O OH OH OH O O Gla3P DHAP NAD+ O O OH NADH ADP ATP Gla 3-P dehydrogenase 2-P-glycerate (3PG) O OH O OH P-Gla mutase 3-P-glycerate (3PG)

What is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP Ketone or aldehyde O Enol O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase pyruvate Aldolase O O O 2 Triose P isomerase 2 ATP + O OH OH OH O O Gla3P DHAP Pyr Kinase NAD+ O O O OH NADH ADP ATP Enolase Gla 3-P dehydrogenase H2O OH O O OH H O P-Gla mutase O 2-P-glycerate (3PG) 3-P-glycerate (3PG)

Why is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase pyruvate Aldolase O O O 2 Triose P isomerase 2 ATP + O OH OH OH O O Gla3P DHAP Pyr Kinase NAD+ O O O OH NADH ADP ATP Enolase Gla 3-P dehydrogenase H2O O OH OH O H O P-Gla mutase O 2-P-glycerate (3PG) 3-P-glycerate (3PG)

Why is glycolysis 2 2 ATP + glucose glucose-6P fructose-6P ATP ADP ATP ADP glucose O OH HO glucose-6P fructose-6P fructose-1,6 diP O OH O OH O OH Hexose-P isomerase Phospho fructokinase Hexokinase pyruvate Aldolase O O O 2 Triose P isomerase 2 ATP + O OH OH OH O O Gla3P DHAP Pyr Kinase NAD+ O O O OH NADH ADP ATP Enolase Gla 3-P dehydrogenase H2O O OH OH O H O P-Gla mutase O 2-P-glycerate (3PG) 3-P-glycerate (3PG)

Trypanosoma brucei How to exploit dependence on glycolysis? Treatment blood cell Arsenate (AsO4 = Asi) Competitive with Pi

Trypanosoma brucei How to exploit dependence on glycolysis? O-P-O O OH O O-P-O-CH2—CH—C Glyceraldehyde-3-P H O NAD+ NADH O-P-O-CH2—CH—C- O O-P-O OH ADP ATP O-P-O-CH2—CH—C-O O 3-P-Glycerate OH

Trypanosoma brucei How to exploit dependence on glycolysis? OH O O-As-O O-P-O-CH2—CH—C Glyceraldehyde-3-P O H O NAD+ NADH H2O O-P-O-CH2—CH—C- O O-As-O OH ADP ATP O-P-O-CH2—CH—C-O O 3-P-Glycerate OH O O-As-O +

How to model this reaction?

How to model this reaction?

Characteristics of enzymes Chemical reactions AMP-P-As AMP-P +Asi [AMP-P-As] k rate constant = d[AMP-P ] / dt concentration rate of change = = d[Asi] / dt rate of change = – = d[AMP-P-Asi] / dt rate of change

Characteristics of enzymes Chemical reactions AMP-P-As AMP-P +Asi [AMP-P-As] k rate constant = – = d[AMP-P-Asi] / dt rate of change concentration [S] k = – = d[S] / dt A differential equation

Characteristics of enzymes Chemical reactions AMP-P-As AMP-P +Asi [AMP-P-As] k rate constant = – = d[AMP-P-Asi] / dt rate of change concentration A differential equation = d[S] / dt = –k[S] = [S] Its solution?

Characteristics of enzymes Chemical reactions AMP-P-As AMP-P +Asi [AMP-P-As] k rate constant = – = d[AMP-P-Asi] / dt rate of change concentration A differential equation = d[S] / dt = –k[S] = S0 e -k(t-to) [S] Its solution? = d[S] / dt Check: = S0 (–k) e -k(t-to) = -k S0 e -k(t-to) = -k [S]

Characteristics of enzymes Chemical reactions Write an equation for the rate of increase of a rabbit population over time. (ignore all environmental effects) [R] = R0 2t/D A differential equation = d[S] / dt = –k[S] = S0 e -k(t-to) [S] Its solution? = d[S] / dt Check: = S0 (–k) e -k(t-to) = -k S0 e -k(t-to) = -k [S]

Characteristics of enzymes Chemical reactions AMP-P-As AMP-P +Asi [AMP-P-As] k rate constant = – = d[AMP-P-Asi] / dt rate of change concentration A differential equation = d[S] / dt = –k[S] = S0 e -k(t-to) [S] Its solution? = d[S] / dt Check: = S0 (–k) e -k(t-to) = -k S0 e -k(t-to) = -k [S]

Characteristics of enzymes Chemical reactions = S0 e -k(t-to) = d[S] / dt = –k[S]

Characteristics of enzymes Chemical reactions

Characteristics of enzymes Chemical reactions = S0 e -k(t-to) S0 Δt

Characteristics of enzymes Chemical reactions + Δt d[S] / dt [S] = S0 S0 = d[S] / dt = –k[S] Δt

Characteristics of enzymes Chemical reactions SQ1. Let’s try it. Link to ADP-As.pl Upload and plot results in Excel. For comparison, calculate on the same graph the analytical solution, using constants provided in ADP-As.pl

Characteristics of enzymes Chemical reactions = S0 e -k(t-to) = d[S] / dt = –k[S]

Characteristics of enzymes Chemical reactions

Characteristics of enzymes Chemical reactions = d[S] / dt = –k[S] [S] = S0 + Δt d[S] / dt Slope0 = -k[S0] [S1] = + Δt d[S] / dt S0 Slope1 = -k[S1] S0 Use average of Slope0 and Slope1 Δt

Characteristics of enzymes Chemical reactions = d[S] / dt = –k[S] [S] = S0 + Δt d[S] / dt Slope0 = -k[S0] [S1] = S0 + Δt d[S] / dt Slope1 = -k[S1] S0 Use average of Slope0 and Slope1 Runge-Kutta method Δt

Characteristics of enzymes Enzymatic reactions inhibitor1

Characteristics of enzymes Enzymatic reactions What is the rate equation? Glucose-6-phosphate Fructose-6-phosphate ??? [G6P] k rate constant = = d[F6P] / dt rate of change concentration k ~ 0

Characteristics of enzymes Enzymatic reactions

Characteristics of enzymes Enzymatic reactions E-complex G6P + E G6P·E F6P·E F6P + E [S] VMax [S] + Km v (velocity) = d[product] / dt = [product] = S0 + Δt d[S] / dt

Characteristics of enzymes Enzymatic reactions velocity [S] [S] VMax [S] + Km v (velocity) = d[product] / dt =

Modeling systems of metabolic reactions Spontaneous vs Enzyme-catalyzed Spontaneous reaction v = k [AMP~P~As] product [S]