1. Network Dynamics and Cell Physiology John J. Tyson Dept. Biological Sciences Virginia Tech

2. Budapest Univ. Techn. & Econ. Bela Novak Attila Csikasz-Nagy Andrea Ciliberto Virginia Tech Kathy Chen Dorjsuren Battogtokh Collaborators Funding James S. McDonnell Foundation DARPA

3. Computational Molecular Biology DNA mRNA Protein Enzyme Reaction Network Cell Physiology …TACCCGATGGCGAAATGC... …AUGGGCUACCGCUUUACG... …Met -Gly -Tyr -Arg -Phe -Thr... ATP ADP -P XYZ E1E1 E2E2 E3E3 E4E4 Last Step

4. S G1 DNA replication G2 M mitosis cell division The cell cycle is the sequence of events whereby a growing cell replicates all its components and divides them more-or-less evenly between two daughter cells...

5. Cdk1 S G1 DNA replication G2 M mitosis cell division CycB P P Cyclin-dependent kinase Cyclin B

6. P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD Coupled Intra-cellular Networks !

7. R S response (R) signal (S) linear S=1 R rate (dR/dt) rate of degradation rate of synthesis S=2 S=3 Gene Expression Signal-Response Curve

8. R Kinase RP ATP ADP H2OH2O PiPi Protein Phosphorylation RP rate (dRP/dt) 0.25 0.5 1 1.5 2 Phosphatase response (RP) Signal (Kinase) “Buzzer” Goldbeter & Koshland, 1981 1 R 0

9. R S EP E R rate (dR/dt) S=0 S=8 S=16 response (R) signal (S) Protein Synthesis: Positive Feedback “Fuse” Bistability Closed Open Griffith, 1968

10. Example: Fuse response (R) signal (S) dying Apoptosis (Programmed Cell Death) living

11. R S EP E R rate (dR/dt) response (R) signal (S) S=0.6 S=1.2 S=1.8 SN Protein Degradation: Mutual Inhibition “Toggle”Bistability

12. R S EP E X X R Positive Feedback & Substrate Depletion positive substrate signal (S) Hopf response (R) “Blinker” Glycolytic Oscillations Oscillation sss uss Higgins, 1965; Selkov, 1968

13. S X Y YP R RP time X YP RP response (RP) signal (S) Hopf Negative Feedback Loop Goodwin, 1965

14. Example: Bacterial Chemotaxis Barkai & Leibler, 1997 Goldbeter & Segel, 1986 Bray, Bourret & Simon, 1993

15. R S X R rate (dR/dt) S=1 S=3 S=2 S X R time Sniffer Response is independent of Signal (Levchenko & Iglesias, 2002)

16. primed RC fired RC primed MEN fired MEN Cdk1 CycB high MPF low MPF high SPF low SPF Cdk2 CycA Example 2: Cell Cycle (Csikasz-Nagy & Novak, 2005)

17. LALA Response = F L Signal = CDK Cock-and-Fire LALA L + Cdk2 CycA F +

18. Signal = MPF Response = B A TATA T TATA BABA B + + Cdk1 CycB Cock-and-Fire-2

19. P Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD bistable switch oscillator Cdc25

20. P Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD G1 M S/G2 M mass/nucleus M Fission Yeast

21. 012345 0 0.4 0.8 3.0 mass/nucleus Cdk1:CycB G1 S/G2 M Wild type SNIPER

22. Genetic control of cell size at cell division in yeast Paul Nurse Department of Zoology, West Mains Road, Edinburgh EH9 3JT, UK Nature, Vol, 256, No. 5518, pp. 547-551, August 14, 1975 wild-type wee1 

23. P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD

24. wee1  mass/nucleus Cdk1:CycB G1 S/G2 M wee1  cells are about one-half the size of wild type

25. cell mass (au.) Wee1 activity wild-type wee1 - 0 0 50 100 150 200 250 300 350 400 450 500 550 30 60 90 120 150 180 210 240 270 300 period (min) PHYSIOLOGY GENETICS Two-parameter Bifurcation Diagram SNIPER

26. P Cdc25 Wee1 P CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD Cdc25

27. mass/nucleus Cdk1:CycB G1 S/G2 M cki  The Start module is not required during mitotic cycles

28. P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD CycB

29. 0 0.4 0.8 2.0 0 1 2 3 4 5 G1 S/G2 M cki  wee1 ts 1 st 2 nd 3 rd 4 th mass/nucleus Cdk1:CycB Cells become progressively smaller without size control

30. P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD

31. endoreplication Act CycA cdc13  Fission yeast 2 param bifn diag for Cdc13 mitotic cycles endoreplication S G2 G1 M mitotic cycle mass Production of Cdc13 X No production of cyclin B (Cdc13) Wild type cdc13  cdc13 +/  ??

32. The Dynamical Perspective Molecular Mechanism ? ? ? Physiological Properties

33. The Dynamical Perspective Molecular Mechanism Kinetic Equations Vector Field Stable Attractors Physiological Properties

34. References Tyson, Chen & Novak, “Network dynamics and cell physiology,” Nature Rev. Molec. Cell Biol. 2:908 (2001). Tyson, Csikasz-Nagy & Novak, “The dynamics of cell cycle regulation,” BioEssays 24:1095 (2002). Tyson, Chen & Novak, “Sniffers, buzzers, toggles and blinkers,” Curr. Opin. Cell Biol. 15:221 (2003).