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Lecture #12
Building Networks
Outline
• AMP biosynthesis and degradation– A dynamic balance (before the input is fixed)
• Genetic defects– Quite common in this pathway
• The AMP sub-network– Formulation, balancing, QC/QA, simulation
• Integration with coupled pathways– Integration issues are many, many points of contact
• Dynamic simulation for 50% in rate of ATP use• Path towards whole cell models
SOME BIOCHEMISTRYCofactors represent low flux but important pathways
Nucleotide metabolism:
associated with many diseased
states
Table of mutations & associated pathology
AMP metabolismForming a sub-network
AMP Salvage Network
AMP Salvage: S Matrixinternal exchange
AMP Salvage: pathway vectors
AMP Salvage Network:dynamic simulation to AMP increase
AMP Salvage: Dynamic Simulation
One of the degradation routes is activated
Adding AMP Salvage: Forming Integrated Networks
Glycolysis, PPP, & AMP: a metabolic network
Glycolysis, PPP, & AMP: S matrix
Glycolysis, PPP, & AMP: pathway vectors
Glycolysis
Integrated PPP AMP degradation
Pyr/Lac exchange
Futile cycleSalvage pathway
AMPdegradation
AMPdegradation
Integrated Model: Simulation
• Comparing responses from two models, glycolysis + PPP +/- AMP metabolism
• The AMP I/O behavior• More damped than
before
Toward a whole cell simulation: Metabolic demands and the ‘machine’ that meets them
Summary• Purine nucleotide metabolism is complicated and has many
pathological states associated with it• Nucleotides are synthesized and degraded to be in a steady
state that is dynamic and can respond to perturbations• A sub-network for AMP metabolism can be built and
synthesized, and its responses simulated• It can be integrated with the coupled glycolysis+PP
pathways to form a network model• Several integration issues show up• The number of pathways characterizing the null space
grows• The model can be simulated and the dampening effect of
the response to increased ATP rate of utilization demonstrated
• This network model can be expanded to a whole cell model
genotype
Variation (SNP) in
DNA sequence
Hexokinase: Chromosome
10 p11.2 (1667 T -> C)
model
Decrease in rate of glycolysis and ATP
production
Affects systemic functioning of
cell
Unable to maintain osmotic balance under stringent
ATP loads -> cells lyse
Phenotypic expression of
SNP
normal
pathological
GLU
ATP
G6PHK
ADP
0
V’max
0.5 V’max
S’=K’m SConcentration
0
V’max
0.5 V’max
S’=K’m SConcentration
Change in enzyme kinetic
properties
Vmax and Km values altered
by SNP
reconstruction