Tools for modeling metabolism Guest Lecture Graduate level

Tools for modeling metabolism Guest Lecture Graduate level course MCB 221 b - 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). To use WWW links in this PPT switch to slide show mode. 1

In silico modeling of complex systems What is a complex system? à 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; 2 D metabolic pathways (reduced interactions); lack of good software; model output can become extremely complex 2

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 3

Metabolic engineering/molecular breeding Alterations in metabolism by A) classical breeding B) genetic engineering Source: WIKI Source: UC Davis News à 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 4

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, Mat. Lab-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 5

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. 6

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 7

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. 8

Cell. Designer • 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 Linu. X, WIN, Mac. OS • Connects to large repositories (Bio. Models, Cell. ML and other) which provide pre-defined models and reaction networks Download Cell. Designer 9

Cell. Designer - exchange of GTP for GDP 10

Cell. Designer simulation result 11

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 12

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 13

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 14

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 15

• Well established tools based on Qualitative Structure. Activity Relationships (QSAR) and model based algorithms or rule base expert systems • Used for prediction of organic reactions, drug metabolism (cytochromes P 450), 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 16

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 17

Homework for homework discussion III (1 h) 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 300 K is provided for that). 18

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 19

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&btn. G=Search MMT – tool for metabolic modeling http: //www. bioinfo. de/isb/2002/02/0042/ MMT http: //www. bioinfo. de/isb/gcb 01/poster/hurlebaus. html ALSYSTA http: //stephanopoulos. openwetware. org/ Tools search http: //www. google. com/search? hl=en&q=ERATO%2 C+Bio. Spice%2 C+DBSolve%2 C+ECell%2 C+Gepasi%2 C+Jarnac%2 C+Stoch. Sim%2 C+and+Virtual+Cell&btn. G=Search Modeling cells and metabolism http: //www. mas. ncl. ac. uk/~ncsg 3/hackathon 07/participants/ Colchicine and algae http: //www. google. com/search? q=Susceptibility+of+Colchicum+and+Chlamydomonas+to+Colchicine 20

Link List 2 SBML model repository (for Cell. Designer 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=%22 ultimate+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&btn. G=Search Thank you! Thanks to Wikimedia! Thanks to the Fiehn. Lab! 21