Tools for modeling metabolism
Guest Lecture
Graduate level course MCB221b - Mechanistic Enzymology
Tobias Kind
UC Davis Genome Center - Metabolomics
November 2007
• How far are we away (light years or light seconds?)
• How we apply reductionist concepts for modeling metabolism
• Computer tools and in-silico models
This document is hyperlinked (pictures and green text).
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In silico modeling of complex systems
What is a complex system?
 Ant hill, a cell, humans,
Source: Nancy Moran
Candidatus Carsonella ruddii
(smallest genome n=182)
Source: WIKI
What means - to model?
Candidatus Carsonella ruddii
symbiont in plant lice (yellow)
 Select level of complexity:
Philosophical description, molecular level, model dynamics,
mathematical equations, implementation of algorithm
Problems?
 Non existing input variables; 2D metabolic pathways (reduced interactions);
lack of good software; model output can become extremely complex
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Reductionism vs. Holism and Emergence
Holism
Reductionism
Aristotle in the
Metaphysics: "The whole
is more than the sum of
its parts."
Emergence
Descartes held that
non-human animals
could be reductively
explained as automata
— De homines 1622.
Emergence refers to the
way complex systems and
patterns arise out of a
multiplicity of relatively
simple interactions.
Source: ALL WIKIPEDIA
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Metabolic engineering/molecular breeding
Alterations in metabolism by A) classical breeding
B) genetic engineering
Source: WIKI
Source: UC Davis News
 MIX : breeders use colchicine to double chromosomes
and produce tetraploid plants (breeders become are genetic engineers)
Breeder + German Giant
(obtained by breeding)
click for more
Titan arum in Stuttgart
(Amorphophallus titanum)
Ernesto and Titan Ted
@ UC Davis
gardening  cultivating  breeding
Polyploid gigantism, tetraploid gigantism
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Modeling complex (bio)-chemical systems
Generic all purpose environments:
• can model or simulate almost everything (like a space shuttle, traffic control)
• Rational Rose Real Time (IBM), Mathematica, MatLab-Simulink and others
• use markup languages (XML) like Unified Modeling Language (UML)
Specialized simulation environments: for biochemistry or systems biology
• rely on biological data like pathway maps
• use kinetic databases and enzyme model databases
• use a specialized markup language like Systems Biology Markup Language (SBML)
A) Stoichiometry models – use reaction based system with stoichiometric matrix
B) Kinetic models – use kinetics data and stoichiometry data (in vivo/in vitro data differs)
C) Hybrid models use a combined subset of several (other) approaches
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Metabolic engineering approaches
• Metabolic control analysis (MCA) – mathematical framework how enzymes control
or obtain an optimal flux
• Metabolic flux analysis (MFA)- quantifies metabolic fluxes
• Metabolic pathway analysis (MPA) – investigates entire flux distributions
Stochastic models – using random generators and Monte-Carlo techniques to cover
all possible concentration ranges (high/low/mixed) for more realistic models
Deterministic models – using discrete concentrations and kinetic equations for being
as accurate as possible
FLUX - Rate of turnover of molecules through a reaction pathway.
Elasticity coefficients – epsilon(i) = d ln(v(i)/d ln(p) ; v(i) is the rate of the enzyme in question and p is the parameter of the perturbation.
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SBML (Systems Biology Markup Language)
Source: Akira Funahashi – Cell Designer Tutorial
• List of supported SBML programs (more than 200) from sbml.org
• List of curated and published SBML models (around 200) from biomodels DB
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Mathematical description representing a metabolic pathway
Aim: simulate the dynamic behavior of the intracellular compounds of a single
cell
•
•
•
mass balances for each compound, i. e. reactions producing and consuming the
compound;
enzyme kinetic equations that represent the rate of production and consumption of
the compounds;
transport equations for uptake and excretion of substrate and products.
Ċ - derivative of the compound
concentrations with respect to time.
N - stoichiometric matrix
v - the vector of kinetic rate equations
C -the vector of intracellular and extracellular
compounds
E - the vector of enzyme concentrations,
MMT - A pathway modeling tool for data from rapid sampling experiments
Jochen Hurlebaus, Arne Buchholz, Wolfgang Alt, Wolfgang Wiechert and Ralf Takors,*
In Silico Biology 2, 0042 (2002)
P - the kinetic parameters of the rate
equations.
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CellDesigner
•
Structured diagram editor for drawing gene-regulatory and biochemical
networks
•
Uses Systems Biology Markup Language (SBML), a standard for representing
models of biochemical and gene-regulatory networks.
•
Networks are able to link with simulation and other analysis packages through
Systems Biology Workbench (SBW)
•
Runs under LinuX, WIN, MacOS
•
Connects to large repositories (BioModels, CellML and other) which provide
pre-defined models and reaction networks
Download CellDesigner
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CellDesigner - exchange of GTP for GDP
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CellDesigner simulation result
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Virtual Cell
•
Open source model (plug-in architecture) supported by NIH
•
Modeling and simulation of biochemical pathways coupled with electrophysiology,
membrane transport, and diffusion/advection
•
Workflow for modeling and simulation which abstracts unnecessary complexity of the
underlying math and physics
•
Around 200 models available (via server login) example:
Kinetic analysis of receptor-activated
phosphoinositide turnover
RUN VCell with JAVA Webstart
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JWS Online – kinetic models and MCA online
• simulation of multiple kinetic models for several organisms
• simulation of enzyme rates or metabolite concentrations
• metabolic control analysis (MCA)
• direct JAVA webstart out of web browser, client server model
Start JWS Online
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COPASI (GEPASI)
• Stochastic and deterministic time course simulation
• Steady state analysis (including stability)
• Metabolic control analysis / sensitivity analysis
• Elementary mode analysis; Mass conservation analysis
• Import/export of SMBL, can create C source code
Download Copasi
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General use of in-silico models for metabolic engineering
• Visualization and modeling of complex interactions can lead to better understanding
• Idea generation + exploration of combinatorial space + design of experiment
• Hypothesis testing and experimental validation of predictions
Example (A): Increasing Bio-Ethanol production
Aim: decrease glycerol content and increase ethanol yield by 10%
Result: 40% decrease in glycerol and 3% increase in ethanol
Approach: genome-scale metabolic model + gene insertion, gene deletion
Example (B): Increase fermentation production of succinic acid
Aim: increase succinic acid production
Result: nine-fold increase of succinic acid
Approach: genome and pathway analysis & flux analysis + combinatorial gene knockout
A) In silico aided metabolic engineering of Saccharomyces cerevisiae for
improved bioethanol production; Metabolic Engineering 8 (2006) 102–111
B) Metabolic Engineering of Escherichia coli for Enhanced Production
of Succinic Acid, Based on Genome Comparison and In Silico
Gene Knockout Simulation; APPLIED AND ENVIRONMENTAL
MICROBIOLOGY, Dec. 2005, p. 7880–7887
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•
Well established tools based on Qualitative StructureActivity Relationships (QSAR) and model based algorithms
or rule base expert systems
•
Used for prediction of organic reactions, drug metabolism
(cytochromes P450), environmental degradation and
toxicity estimations, important for OECD large volume chemicals
Flammarion (WIKI)
Tools for modeling metabolism outside the
Systems Biology world
Source: TIMES and CATABOL program: OASIS Bourgas
Sabcho Dimitrov, Ovanes Mekenyan in METABOLISM in-silico simulation
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Outlook
1) Standardized and open XML languages (SBML) most likely successful
2) Community driven tools most likely successful in the future because
number of people involved is high; data sharing of models important
3) Lots of room for commercial exploitation (better support)
4) Do not expect Artificial Intelligence aka Star Trek “Computer tell me…”
expect to do your homework first,
then use software models to model it.
5) More than 120 modeling programs exist,
expect more to come.
Colossus computer. Source (WIKI)
6) The lack of super-integration of experimental data
from transcriptomics, proteomics and metabolomics
experiments currently hinders in-silico modeling and limits predictive space of
developed in-silico models - hence the ultimate systems biology dream:
complete modeling of metabolism, cells and whole organisms
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Homework for homework discussion III (1h)
1)
Play the game of life in JAVA (webstart) explain why it was a milestone development.
2)
Name three problems during model implementation
(for example: no stoechiometry data existing, only in vitro kinetics available)
3)
Tell three reasons why we should be able to model simple a bug
like Candidatus Carsonella ruddii (182 genes only!)
4)
Tell three reasons why we are not able to model simple a bug like CC ruddii.
5)
Download one of the tools discussed here or one from SBML.ORG and report on the usefulness.
6)
Tell three reasons why metabolic engineering will solve the world hunger problem.
7)
Tell three reasons why metabolic engineering will not solve the world hunger problem.
8)
Name three vitamins and three drugs which can be obtained by metabolic engineering
9)
Explain why successful metabolic engineering requires a systems biology approach.
10) +++ Additional question (after solving all others) +++
You are the head of the newly founded Metab. Eng. Dept. in XYZ. You need to perform and present
a strategic decision in front of the board of directors which three of the 120 tools from SBML.ORG
will be used during the next five years in your department (total fund of 300K is provided for that).
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Reading List (all DOI linked) (25 min)
Experimental and mathematical approaches to modeling plant metabolic networks
Predictive Metabolic Engineering: A Goal for Systems Biology
MMT - A pathway modeling tool for data from rapid sampling experiments
Mathematical modelling of metabolism
The production of fine chemicals by biotransformations
Additional reading just for interest (prediction power of in-silico models):
In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions
Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid,
Based on Genome Comparison and In Silico Gene Knockout Simulation
Here is the evidence, now what is the hypothesis? The complementary roles of
inductive and hypothesis-driven science in the post-genomic era
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Link List 1
Substrate, competitive, uncompetitive, noncompetitive inhibition
http://en.wikipedia.org/wiki/Enzyme_inhibitor
Reductionism
http://en.wikipedia.org/wiki/Reductionism
Emergenz
http://de.wikipedia.org/wiki/Emergenz
Complex Systems and origin of life
http://books.google.com/books?ct=title&psp=1&q=modeling+complex+systems+emergence
Tools
http://www.google.com/search?q=Tools+for+modeling+metabolism
In vivo modeling
http://www.google.com/search?hl=en&q=in+vivo+metabolic+modelling&btnG=Search
MMT – tool for metabolic modeling
http://www.bioinfo.de/isb/2002/02/0042/
MMT
http://www.bioinfo.de/isb/gcb01/poster/hurlebaus.html
ALSYSTA
http://stephanopoulos.openwetware.org/
Tools search
http://www.google.com/search?hl=en&q=ERATO%2C+BioSpice%2C+DBSolve%2C+ECell%2C+Gepasi%2C+Jarnac%2C+StochSim%2C+and+Virtual+Cell&btnG=Search
Modeling cells and metabolism
http://www.mas.ncl.ac.uk/~ncsg3/hackathon07/participants/
Colchicine and algae
http://www.google.com/search?q=Susceptibility+of+Colchicum+and+Chlamydomonas+to+Colchicine
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Link List 2
SBML model repository (for CellDesigner and others)
http://www.systems-biology.org/001/
Systems Biology Markup Language (org) has hundreds of software tools listed
http://sbml.org/index.psp
US GOV network for metabolic engineering
http://www.metabolicengineering.gov
The ultimate goal of Systems Biology
http://www.google.com/search?hl=en&q=%22ultimate+goal+of+systems+biology
Stoechiometry models and power law models
http://www.google.com/search?q=e-cell++gepasi+Stoichiometric+models
Catabol, Meteor, Lhasa
http://www.google.com/search?hl=en&q=catabol+metabolism+lhasa+meteor&btnG=Search
Thank you!
Thanks to Wikimedia! Thanks to the FiehnLab!
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