Kim “Avrama” Blackwell George Mason University

1. Modelling Biochemical Reactions - Tutorial Second Latin American School on Computational Neuroscience Kim “Avrama” BlackwellGeorge Mason University

2. Three Types of Objects • Pools of molecules • Keep track of concentration • Uni- and Bi-molecular Reactions • Transformation of one or more molecules into equal number of another molecule • Enzyme reactions • One enzyme molecule can transform multiple copies of substrate into equal number of product

3. Compartment-Like Objects • Keep track of molecule quantities and concentrations • Similar to compartment calculating voltage • Requires geometry/morphology values • length • radius • area of outer surface • area of inner surface (can be zero) • area of side surface • volume

4. Compartment-Like Objects • Keep track of molecule quantities and concentrations • rxnpool (Chemesis) • dC/dt =  A -  B C • A = change in quantity independent of present quantity • B = rate of change • Receives messages with quantities A and/or B from other objects (enzymes, reactions, also calcium influx) • RXN0 (A), RXN1 (B), RXN2 (A and B)

5. Compartment-Like Objects • Keep track of molecule quantities and concentrations • conservepool (Chemesis) • C = Ctot - Ci • Quantity is remainder after all other forms of molecule accounted for • pool (Kinetikit) • dC/dt =  A -  B C • Or C = Ctot - Ci(if flag is set to conserve) • Can also implement stochastic reactions

6. Concentration Pools • chemesis • genesis #1 > showobject rxnpool • genesis #2 > showobject conservepool • genesis #3 > showobject pool

7. Enzyme and Reaction objects • Calculate changes due to reactions • mmenz (Chemesis) • Use if MM assumptions are met • Fields: Km and Vmax • Inputs: enzyme, substrate concentration • Calculates Vmax times [Enzyme] times [substrate] divided by ([substrate] + Km) • Send messages RXN0 or RXN0moles to rxnpool • Empirical feedback modification of enzyme activity can be added

8. Enzyme and Reaction objects • Calculate changes due to reactions • Enzyme (Chemesis) • Fields: Kcat, Kf, Kb • Inputs: enzyme, substrate quantity • Calculates amount of Enzyme-Substrate complex • Calculates change in product, enzyme, substrate • Enz (kinetikit) • Fields: Kcat, Kf, Kb • Inputs: enzyme, substrate quantity • Can implement stochastic reactions

9. Enzyme and Reaction objects • Calculate changes due to reactions • reaction (Chemesis) or reac (kinetikit) • Fields: kf, kb • Inputs (messages): substrates and products • Calculates: • forward rate constant times substrate molecules • backward rate constant times product molecules • send messages RXN0 - RXN2 to rxnpool

10. Enzyme and Reaction objects • Genesis #4> showobject mmenz • Genesis #5> showobject enzyme • Compartment dimensions allows membrane bound enzyme to have different volume than substrate and products • Genesis #5> showobject enz • Genesis #6> showobject reaction • Genesis #7> showobject reac

11. Creating Chemesis Simulation • Create rxnpool pool1 • Create conservepool pool2 • Setfield pool1 Cinit initvalue ... • Addmsg pool1 pool2 CONC Conc • mGlu-IP3-enz.g for complete examples

12. Creating Chemesis Simulation • Create reaction rxn1 • Setfield rxn1 kf kfvalue kb kbvalue • Addmsg pool1 rxn1 SUBSTRATE Conc • Addmsg pool2 rxn1 SUBSTRATE Conc • Addmsg pool3 rxn1 PRODUCT Conc • Addmsg rxn1 pool1 RXN2 kbprod kfsubs • To substrate – kbprod is first • Addmsg rxn1 pool3 RXN2 kfsubs kbprod • To product – kfsubs is first

13. Chemesis Example • Metabotropic receptor to PLC to IP3 • Include param.g • Include mGlu-IP3-enz.g • Listglobals • Create neutral purkcell • Create neutral glutamate (under purkcell) • Allow setting a concentration of neurotransmitter • Invoke function (no parentheses or commas) • Include graphs.g (and invoke function) • Step (to run simulation)

14. XPP example • Xppaut mglu-ip3.ode • Evaluate role of aG decay • Evaluate role of IP3 decay