LSM3241: Bioinformatics and BiocomputingLSM3241: Bioinformatics and Biocomputing

Lecture 9: Biological Pathway Simulation Lecture 9: Biological Pathway Simulation

Prof. Chen Yu ZongProf. Chen Yu Zong

Tel: 6874-6877Tel: 6874-6877Email: Email: yzchen@cz3.nus.edu.sgyzchen@cz3.nus.edu.sg

http://xin.cz3.nus.edu.sghttp://xin.cz3.nus.edu.sgRoom 07-24, level 7, SOC1, NUSRoom 07-24, level 7, SOC1, NUS

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Biomolecular Interaction: Enzyme + SubstrateBiomolecular Interaction: Enzyme + Substrate

E + S ==> E + P

• This is a generalization of how a biochemist might represent the function of enzymes.

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Biomolecular Interaction: Enzyme + SubstrateBiomolecular Interaction: Enzyme + Substrate

E + S ==> E + P

kinase-ATP complex + inactive-enzyme ==> Kinase + ADP + active enzyme

K

ATP ADP

P

• Here is an example of the generalization represented by two different ways.

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Biomolecular Interaction: Enzyme + SubstrateBiomolecular Interaction: Enzyme + Substrate

• This is another representation.

Kinase-ATPcomplex

Activeenzyme

inactiveenzyme

ADP

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Spoke and Matrix Models of Protein-Spoke and Matrix Models of Protein-Protein InteractionsProtein Interactions

Vrp1 (bait), Las17, Rad51, Sla1, Tfp1, Ypt7

SpokeMatrixPossible Actual

Topology

Bader&Hogue Nature Biotech. 2002 Oct 20(10):991-7

Simple model

Intuitive, more accurate, but canmisrepresent

Theoretical max. no. of interactions, but many FPs

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Synthetic Genetic Interactions in Yeast

Tong, Boone

Cell PolarityCell Wall Maintenance Cell StructureMitosisChromosome StructureDNA Synthesis DNA RepairUnknownOthers

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• Glycolysis– Phosphorylation– Pyruvate

• Anaerobic respiration• Lactate production• 2 ATPs produced

Metabolic Pathway: ATP ProductionMetabolic Pathway: ATP Production

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Cyclic Metabolic Pathway

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Methods of Metabolic Engineering

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Generic Signaling PathwayGeneric Signaling PathwaySignal

Receptor (sensor)

Transduction Cascade

Targets

Response Altered

Metabolism

MetabolicEnzyme

Gene Regulator Cytoskeletal Protein

Altered Gene

Expression

Altered Cell Shape or Motility

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Components of SignalingWhat can be the Signal?External message to the cell

• Peptides / Proteins- Growth Factors• Amino acid derivatives - epinephrine, histamine• Other small biomolecules - ATP• Steroids, prostaglandins• Gases - Nitric Oxide (NO)• Photons• Damaged DNA• Odorants, tastants

Signal = LIGANDLigand- A molecule that binds to a specific site on another molecule, usually a protein, ie receptor

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Components of SignalingWhat are Receptors?Sensors, what the signal/ligand binds to initiate ST

Cell surface

Intracellular

Hydrophillic LigandCell-Surface Receptor

Plasma membrane

Hydrophobic Ligand

Carrier Protein

IntracellularReceptor

Nucleus

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Generic Signal Transduction

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RTK Signal Transduction

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Signal TransductionDownstream effectors

Protein Signaling Modules (Domains)

SH2 and PTB bind to tyrosine phosphorylated sitesSH3 and WW bind to proline-rich sequencesPDZ domains bind to hydrophobic residues at the C-termini of target proteinsPH domains bind to different phosphoinositidesFYVE domains specifically bind to Pdtlns(3)P (phosphatidylinositol 3-phosphate)

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Mechanisms for Activation of Signaling Proteins by RTKs

Activation by membrane translocation

Activation by a conformational change

Activation by tyrosine phosphorylation

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Mechanisms for Attenuation & Termination of RTK Activation

1) Ligand antagonists2) Receptor antagonists3) Phosphorylation and dephosphorylation4) Receptor endocytosis5) Receptor degradation by the ubiquitin-proteosome pathway

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Activation of MAPK Pathways by Multiple Signals

Growth, differentiation, inflammation, apoptosis -> tumorigenesis

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Overview of MAPK Signaling Pathways

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The MAPK Pathway Activated by RTK

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RTK ST- PI3K pathway

P

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Apoptosis Pathways

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TGF Pathway

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Constructing a pathway model:Constructing a pathway model:things to considerthings to consider

1. Dynamic nature of biological networks.Biological pathway is more than a topological linkage of molecular networks.

Pathway models can be based on network characteristics including those of invariant features.

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Constructing a pathway model:Constructing a pathway model:things to considerthings to consider

2. Abstraction Resolution:

• How much do we get into details?

• What building blocks do we use to describe the network?

High resolution

Low resolution

(A) Substrates and proteins

(B) Pathways

(C) “special pathways”

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Constructing a pathway modelConstructing a pathway modelStep I - DefinitionsStep I - Definitions

We begin with a very simple imaginary metabolic network represented as a directed graph:

Vertex – protein/substrate concentration.

Edge - flux (conversion mediated by proteins of one substrate into the other)

Internal flux edge

External flux edge

How do we define a

biologically significant

system boundary?

Constructing a pathway modelConstructing a pathway modelStep II: Interaction KineticsStep II: Interaction Kinetics

E + S ==> E + P

kinase-ATP complex + inactive-enzyme ==> Kinase + ADP + active enzyme

K

ATP ADP

P

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Reversibility of Chemical Reactions: Reversibility of Chemical Reactions: EquilibriumEquilibrium

• Chemical reactions are reversible• Under certain conditions (concentration, temperature)

both reactants and products exist together in equilibrium state

H2 2H

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Reaction RatesReaction Rates

Net reaction rate = forward rate – reverse rate

• In equilibrium: Net reaction rate = 0• When reactants “just” brought together: Far

from equilibrium, focus only on forward rate• But, same arguments apply to the reverse rate

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The Differential Rate LawThe Differential Rate Law

• How does the rate of the reaction depend on concentration? E.g.

3A + 2B C + Drate = k [A]m[B]n

(Specific reaction)

rate constant

Order of reaction

with respect

to A

Order of reaction

with respect

to B

m+n: Overall order of

the reaction

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Rate Constants and Reaction OrdersRate Constants and Reaction Orders

• Each reaction is characterized by its own rate constant, depending on the nature of the reactants and the temperature

• In general, the order with respect to each reagent must be found experimentally (not necessarily equal to stoichiometric coefficient)

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Elementary Processes and Rate LawsElementary Processes and Rate Laws

• Reaction mechanism: The collection of elementary processes by which an overall reaction occurs

• The order of an elementary process is predictable

Unimolecular A* B K+ [A] First order

Bimolecular A + B C + D K+ [A] [B] Second order

Trimolecular A + B + C D + E K+ [A] [B] [C] Third order

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Elementary Processes and Rate LawsElementary Processes and Rate Laws

• Reaction mechanism: The collection of elementary processes by which an overall reaction occurs

• The order of an elementary process is predictable

Unimolecular A* B K+ [A] – K- [B] First order

Bimolecular A + B C + D K+ [A] [B] – K- [C] [D] Second order

TrimolecularA + B + C D + E

K+ [A] [B] [C] – K- [D] [E]

Third order

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dxS v

dt

Stoichiometry Matrix

Flux vectorConcentration vector

Constructing a pathway modelConstructing a pathway modelStep III - Dynamic mass balanceStep III - Dynamic mass balance

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A ‘simple’ ODE model of yeast glycolysis

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A model pathway system and its time-dependent behavior

Positive Feedback Loop

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A model pathway system and its time-dependent behavior

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A model pathway system and its time-dependent behavior