Systems biology 9 Signal Transduction

Transcription

1 Humbol- Sommersemester 2 Systems biology 9 Signal Transuction Ea Klipp Humbol- Institut für Biologie Theoretische Biophysi

2 Moeling of Signal Transuction Humbol- Before: Metabolismus - Mass transfer Now: Signal transuction - Information transfer Typical Signals: Hormones, pheromones Heat, col, osmotic pressure concentration of certain substances (K, Ca, camp,..) nutrient availability Interactive Animation of MAP Kinase Signal Transuction

3 Typical Mechanism Signal Humbol- Activation of receptor at membran Internalization of signals G-Protein, Phosphorelay Signal transmission Activation of transcription factors Transcription, Translation, Gen Protein function biochemical response Downregulation of signal mrna Protein

4 Yeast Signaling Pathways Humbol-

5 Signaling Pathway Components Humbol-

6 Receptors Humbol- Ligan Receptor, Bining site Receptor, cytosolic omain inactive active Extracellular space Membrane Intracellular space transmembrane receive signal an transmit it conformation change active or inactive form Simple concept: H + R HR K D = H. R HR H - Hormone R - Receptor HR - Hormone-receptor-complex Typical values : K D = -2 M. -6 M

7 Receptor, Extene Moel Humbol- L v pi v ps v is R i R s R a v si v sa v as v i v s v ai v a Differential equations R R R i s a v v pi ps v v a v i s v v is v sa is v v si v as si v v ai v ai sa v as Rate expressions?? v v v xy sa sa xy sa sa R x R R s s L b n Kb L K L n Mass action Hill inetics

8 Humbol- Receptor, Moel of Yi et al. +L v v v v v R i v v pi v i v is L R i R s R a ps ps s a sa as s a sa as * i v i* v si R s R R R v ps v s a s a L v sa v as v ai v a ps s a sa as Number of Molecules molecules per cell s s 3 s M 2 s s R a R s 2 3 Time

9 G-Proteins: small G-proteins Humbol- e.g. Ras-Protein GEF GTP GDP GDP GTP GDP Ras v GTP Ras GDP + + GTP P i v 2 GAP GEF Guanine nucleotie exchange factor GAP GTPase-activating protein Differential equations Conservation relations GDP GTP Ras v Ras v v v 2 2 Ras total GDP Ras GTP Ras

10 G-Proteins: small G-proteins Humbol- GDP Ras e.g. Ras-Protein GTP P i GEF v v 2 GAP GDP GTP Ras Differential equations GDP Ras v v2 GTP Ras v v2 Ras total GDP Ras GTP Ras Mass action v v 2 2 GDP GTP Ras GEF Ras GAP GTP GEF Ras Ras total GEF 2 GAP 2 ; Rastotal Michaelis Menten v v 2 GEF K 2 K m GAP m2 GDP GDP GTP GTP Ras Ras Ras Ras GTP Ras GTP Ras 2 ; Rastotal ; Km Km2 GEF or GAP = (const.), other varying from to GEF GAP Enzyme concentration GEF GAP Enzyme concentration

11 G-Proteins: small G-proteins Humbol- e.g. Ras-Protein GEF GTP GDP v v v 2 GEF K 2 K m GAP m2 GDP GDP GTP GTP Ras Ras Ras Ras GTP Ras GEF GAP GDP Ras v 2 GTP Ras 2 ; Rastotal ; Km Km Enzyme concentration P i GAP Differential equations GDP Ras v v2 GTP Ras v v2 sigmoial epenence Ultrasensitivity Switch-lie regulation GTP Ras K m K m 2. K m K m 2 Ras total GDP Ras GTP Ras Enzyme: GEF

12 G-Proteins: small G-proteins Humbol- e.g. Ras-Protein GEF GTP GDP GTP Ras K m K m 2. K m K m 2 v GDP Ras v 2 GTP Ras Enzym: GEF P i GAP GEF: x v v 2 K m GEF K 2 K 2 m GAP m2 K GDP GDP GTP GTP ; Ras m2 Ras Ras Ras Ras total. ; GTP Ras Zeit x=2.5 x=2. x=.5 x=. x=.5

13 active receptor GDP G GDP GTP GTP G v h slow GDP G P i v sr v ga v h fast P i RGS G-Protein G signal Number of Molecules GDP GDP G GTP + G GTP G Humbol- + GDP G Differential equations G G v ga v sr GTP v ga v v h h Conservation relations G total G t G G G G GTP G GDP 2 3 Time

14 Phosphorelay-System Humbol- - Transmits iniviual phosphate groups? Sln Asp P i high osmolarity 3 P i P i P His i ADP YpHis Yp-P 4 Ss-P SsAsp 5 2 ATP Sln Sln 3 SlnA P Yp Sln H P Sln SlnH P 2 SlnA P 2 SlnH P 3 SlnA P Yp Yp Yp Ss Ss 3 4 Yp P Ss SlnA P Yp 3 P 4 Yp P Ss SlnA P Yp 4 5 Ss P Yp P Ss 4 P 5 Ss P Yp P Ss Sln total Sln SlnH P SlnA P Example: Sln pathway, Phosphorelay system Yp total Ss total Yp Yp P Ss Ss P

15 Phosphorelay-System Humbol- A-P B C-P A A ATP 2 AP B B 2 B AP 3 BP C C 3 C BP 4 CP A AP A B BP B C CP C ADP ATP total total total P A B-P C Depenence of steay state values Of stress strength Temporal behavior, Stress no Stress A, B, C A, B, C Three component system Two components One component Time

16 Phosphorelay-System Humbol- A-P B C-P total v v 2 v 3 v 4 A B-P C A A ATP 2 AP B B 2 B AP 3 BP C C 3 C BP 4 CP A AP Atotal B BP Btotal C CP C Dynamics Steay State Concentration C Concentration, a.u...8 A B.6 C Time a.u =.4 = Rate constant 4

17 MAP Kinase Cascae = Mitogen activate protein inase cascae Humbol- Alternative: SAP = stress activate protein MAPKKKK MAPKKK inactive MAPKKK active MAPKK inactive MAPK inactive MAPKK active MAPK active Signal

18 Humbol- MAP Kinase Cascae - Equations ATP MAPKKKP ATP MAPKKKK MAPKKK MAPKKKP MAPKKKP ATP MAPKKKK MAPKKK MAPKKK 2 4 MAPKKPP ATP MAPKKKP MAPKKP MAPKKPP MAPKKP MAPKKPP ATP MAPKKKP MAPKKP ATP MAPKKKP MAPKK MAPKKP MAPKKP ATP MAPKKKP MAPKK MAPKK MAPKPP ATP MAPKKPP MAPKP MAPKPP MAPKP MAPKPP ATP MAPKKPP MAPKP ATP MAPKKPP MAPK MAPKP MAPKP ATP MAPKKPP MAPK MAPK 2 9 9

19 MAP Kinase Cascae - Equations Humbol- Kinase, p - Phosphatase A A S p AP APP AP p APP B B AP p BP BPP BP AP p BPP C C BPP p CP CPP CP BPP p CPP A AP APP A MAPKKK B BP BPP B C CP CPP C total total total MAPKKK MAPKKK total total total CPP S 4 Steay state S 4 A 4 total B 2 total C total S... S... S... S... p Sigmoiale epenence of concentration of activate MAP inase on concentration of input signal. CPP p

20 zu MAPK Cascae: Impact of Kinases an Phosphatase Humbol- Berlin MAPK-PP, a.u. MAPK-PP, a.u Time, a.u A B.9.8 = =3 =4 =5 p= p=.3 =2.2. = Time, a.u. MAPK-PP, a.u. MAPK-PP, a.u Time, a.u C D..2 p= p=.3 p=.4 p=.5 Kinase, p - Phosphatase p=.2 p=. = Time, a.u.

21 Humbol- MAP Kinase Cascae Parameter Depenence MAPKKK v v 7 MAPKKK P v MAPKKK P v2... MAPK P v7 v2 v8 2 v8 2 v6 v2 - Sigmoie input/output epenence - Signal amplification Kinase, p - Phosphatase Time courses Steay states MAPKP 2 (t) = =.64 =.36 =.6 = Time MAPKP MAPKKKK=. MAPKKKK= /p

22 Humbol- MAPK Cascae: Control P P, P, P 2 P P2, P2 P3, S v C i v S i S v i P3 3 P 2, P P 3, P 3 6 positive none negative Rates J v C j v J j J v j

23 Humbol- MAPK Cascae: Control with complex formation P P P, 2 P, P P, P PX P2, P P2, P2 P2X P3, P2 P3, P3 P3X positive none negative P, 4 3 P X X phosphatase P 5 6 P 2, P P 2, 8 7 P 2 X P 2 9 P 3, P 2 P 3, 2 P 3 X P Rates

24 MAPK-Cascae with Feebac an Michaelis-Menten Kinetics: Oscillations Humbol-

25 MAP Kinase Cascae Scaffoling Humbol- Ste5 Ste Ste7 Fus3 MAPKKK Scaffol MAPKK MAPK

26 Humbol- MAP Kinase Cascae Scaffoling Double Phosphorylation of each protein 2 2 Ste5 Ste Ste7 Fus

27 Quantitative Measures for Signaling Humbol- (a) P v f P, v r P v 2f P 2, P 2 v 2r v 3f P 3, P 3 v 3r (b) Concentration, a.u max t max P P S Time, a.u. Transition time i t X X i i t t i Signal uration t 2 X X i i t t 2 i S i Amplitue X i t 2 i Heinrich et al., T.A. Mol.Cell, 22

28 Crosstal in Signaling Pathways Humbol- Are signaling pathways linear structures? Are signals transmitte in signaling networs? How can we measure the transfer of signal between ifferent branches of the networ?

29 Crosstal & Signal Integration Humbol- Signal Signal Measures of crosstal Receptor A Receptor B X C X B A A A B B A B X S i X, X S e X, Target A Target B X function of amplitue, timing or integral of response Pheromone Pathway Filamentous Growth Pathway S e > S e < S i > Mutual signal inhibition Dominance of intrinsic signal Crossactivation Mutual signal amplification Crossinhibition Dominance of intrinsic signal S i < Dominance of extrinsic signal Mutual signal amplification

30 Crosstal Humbol-.3 left cascae.3 right cascae (a) = P A v Af P A, P A v Ar v 2Af P 2A, P 2A v 2Ar v 3Af P 3A, P 3A v 3Ar = P B v Bf P B, P B v Br v 2Bf P 2B, P 2B v 2Br v 3Bf P 3B, P 3B v 3Br Concentration a.u. Concentration a.u P A P 2A P 3A P 3A P A P 2A P B P 2B P 3B i = i = Concentration a.u P A P 2A P 3A Time a.u.3.2. P B P 2B P 3B Time a.u

31 Humbol-.3 Crosstal X S A i A SeA X, A X X A A, = P A v Af P A, P A v Ar v 2Af P 2A, P 2A v 2Ar v 3Af P 3A, P 3A v 3Ar = P B v Bf P B, P B v Br v 2Bf P 2B, P 2B v 2Br v 3Bf P 3B, P 3B v 3Br Concentration a.u. Concentration a.u P 2A P A P 3A P 3A P A P 2A I = P max = t max = I = P max = t max = Integrate Response S i (I) =.9 S e (I) =.97 Mutual amplification Maximal Response S i (P max ) =.97 S e (P max ) =.34 Mutual amplification i = i = Concentration a.u P 2A P A P 3A Time a.u I = P max =.3682 t max = Timing of Response S i (t max ) =.4 S e (t max ) =.97 Dominance of intrinsic signal

32 Integration of Signaling Pathways Humbol- PRE, large Responses: 5,7,9, Response coefficients of PREs FREs m@2d; PRE, meium Responses: 3,4,6,,,4 m@24d; FRE, meium Responses: 9,, m@2d; PRE, meium negative Responses: 7,9,2,8,2 m@24d; FRE, large negative Responses: 6,6,3,3,39 9 m@24d; FRE, plus minus Responses: 2,4,5,2,22 4 -Fus3 phosphorylation in MAPKcascae 6 -repeate Fus3 phosphorylation -Kss phosphorylation in MAPKcascae 2-Kss release from Ste2Tec complex S p R i l p S i l t Si p t l Time/min Time/min

33 Humbol- Yeast Signaling Pathways +Pheromone,,9,8,7,6,5,4,3,2,, Crosstal Opportunities,2,,8 +Pheromone +Salt,6,4,2, Salt,2,,8,6,4,2, Waltermann in prep., Hoffman-Sommer in prep. Fus3 Kss Hog

34 Humbol- Crosstal Moel

35 Humbol

36 Humbol- Hog activity as timer for filamentous ifferentiation uner exposure to simultaneous osmo-stress an nutrient-limitation Nutrient limitation only Nutrient limitation + osmostress Activity Osmo-stress an nutrient-limitation simultaneously: increase of Tec activity elaye (transcriptional activator of filamentation (FRE) genes) Time Nutrient limitation + osmostress Reuce crosstal from Hog to Tec Time Nutrient limitation + osmostress Reuce inhibition of Hog by Kss Activity Time Time In mutants with altere crosstal the timer function of Hog is isrupte or enhance.

37 Humbol- Pathway Interaction upon Cell Cycle Regulation

38 gtow Metho Humbol-

39 Growth Rates for Signal Pathway Mutants Humbol-

40 Humbol- gtow Sensitivity to Overexpression Krantz et a., MSB, 29

41 Ca 2+ oscillations Humbol- Cytosolic Ca2+ oscillations Spatio-temporal ynamics Control variety of cell processes

42 Calcium Oscillation - Equations Humbol-

43 Calcium Oscillation - Simulations Humbol- for ifferent parameter values Thul et al., 29

44 Ca 2+ oscillations Humbol- Interspie interval Calcium oscillations - limit cycle oscillations? - sequences of ranom spies? Problem: Channels form tetramers, tetramers form cluster.

45 Hierarchic stochastic moeling Ca 2+ oscillations Humbol- Thurley & Falce, PNAS, 2