lecture #10 metabolic pathways. outline glycolysis; a central metabolic pathway fundamental...
TRANSCRIPT
Lecture #10
Metabolic Pathways
Outline
• Glycolysis; a central metabolic pathway• Fundamental structure (m x n = 20 x 21)
• Co-factor coupling (NAD, ATP, Pi)
• The stoichiometric matrix– Its null spaces
• Setting up a simulation model– Steady state
• Interpreting the results from simulation– Concentrations, fluxes, pools, ratios
GLYCOLYSIS: AN OPEN SYSTEM
Glycolysis as an Open System
Compounds: the nodes
pathwayintermediates
cofactorscarriers
Reactions: the links
THE STEADY STATE
The Stoichiometric Matrix
mxn=20x21, Rank(S)=18 dim(Null)=21-18=3dim(Left Null)=20-18=2
3 pathways2 conserved moieties
Glycolysis: ‘annotated’ S matrix
ES=0
Glycolysis: Pathways in Null(S)Selected basis based on biochemical intuition
~P synthesis redox coupling inventory of AMP
The Steady State Fluxes (mM/hr):fluxes have to balance the network
upperglycolysis
lowerglycolysis
exchange & demandfluxes
AMP
The Steady State Concentrations (mM);determined by flux map and kinetic constants
Reactions: the links
pseudo el
emen
tary
rate
consta
nts
distance
from
equili
brium
DYNAMIC SIMULATIONModel defined and ready for:
Simulation: 50% increase in kATP:dynamic responses of the concentrations
ADP ATP
load=k[ATP]
50% increase at t=0
Key Concepts1. Time constants2. Pools3. Transitions
Glycolysis: 0-10 mins
Tiled Phase Portrait:fluxes
fluxes of
interest
Glycolysis: 10-infinity
mins
Tiled Phase Portrait:fluxes
fluxes of
interest
drai
nac
cum
ulat
ion
Dymamic Responses of the Fluxes
drainaccumulation
Secr
etio
n>
sts
tSe
cret
ion
<st
st
Secr
etio
n>
sts
tSe
cret
ion
<st
st
Glycolysis: 0-10 mins
Tiled Phase Portrait:concentrations
Glycolysis: 10-infinity
mins
Tiled Phase Portrait:concentrations
Simulation: 50% increase in kATP:dynamic responses of the concentrations
fast intermediate slow
ADP ATP
load=k[ATP]
50% et=0Key Concepts1.Time constants2.Pools3.Transitions
STRUCTURAL PROPERTIESTowards systems biology
Glycolysis:the system with symbolic representation
Structural Properties:redox trafficking in glycolysis
(#): Redox value
#: Flux value
Structural Properties:high-energy bond trafficking in glycolysis
(#): High-energy bond “value”
x: Flux value
Structural Properties:The Trafficking of Phosphate Groups in
Glycolysis
“through”
“cycle”
Pools:from structural properties
Redox Value of Intermediatesreduce glycolytic
intermediates
oxydized glycolyticintermediates
met
abol
ites
carr
ier
Energy Value of Intermediates
Phosphate Bond Trafficking
Incorporation:
Recycled:
Recycleratio:
Pool Map:shows their
interconnections and steady state
concentrations by area of square
Dynamic Responses of the Pools
2(ATP+ADP+AMP)
2ATP+ADP
Pi
~Pi
capacity
occupancy
GP+ and GP-
RATIOSTowards physiology
Dynamic Responses of the ratios
Adenosine E.C
Glycolytic E.C
Phosphate recycle ratio
Property rations or
charges and their dynamic
responses
Summary• First draft dynamic models can be obtained from using
measured concentration values, elementary reactions, and associated mass action kinetics.
• This first draft can be used as a scaffold to build more complicated models that include regulatory effects and interactions with other pathways.
• Dynamic simulation can be performed for perturbation in environmental parameters and the responses examined in terms of the concentrations and the fluxes.
• A metabolic map can be analyzed for its stoichiometric texture to assess the co-factor coupling
• Such breakdown of the biochemistry helps define pools that are physiologically meaningful from a metabolic perspective, and are context dependent.
Summary• The raw output of the simulation can be post processed
with a pooling matrix that allows the pools and their ratios to be graphed to obtain a deeper interpretation of dynamic responses.
• Some of the responses are built into the topological features of a network and require no regulatory action.
• The identification of the reactions that move the key pools is possible by the use of the stoichiometric matrix.