信号传递网络 .ppt

1、Networks of BiologicalSignaling Pathways信号传递网络,康海岐 高方远 马欣荣,一、生物体内的信号传递,1. The sense of signal transduction： intercelluar information exchange,regulation of metobolism, on body level 2. Type of signals： neuroregulation: neurotransmitter(乙酰胆碱,胺类 氨基酸,调节肽类等),neuroregulator chemical signals：cAMP, Ca2+ ,

2、hormone， 3. Mechanisms: 3.1 pr. pr., 3.2 E reaction(p ) 3.3 E activity 3.4 pr. degradation 3.5 intracelluar messager 3.6 seconder messager,E,cell,一、生物体内的信号传递,4. Signaling pathways： 4.1 Ca2+ 4.2 cAMP 4.3 tyrosine kinase: EGFR,insulinR 4.4 other pr. kinase cascade:PKC,PKA,PKG 4.5 intracelluar protease

3、 cascadeSignal transmission occur: i. Pr.pr. Interaction ii. Enzymatic reaction: p iii. Pr. Degradation iiii. Production of intracellular messager,一、生物体内的信号传递,5. cytoplasm membrane receptor： 5.1 neurotransmitter-dependention channel (依赖神经递质的离子通道)： nAChR(烟碱型乙酰胆碱受体) GABA( -氨基丁酸) GlyR(甘氨酸受体) 5.2 recept

4、or connecting to signal transduction protein (G,N protein second messenger activate E.): mAChR(毒蕈碱型乙酰胆碱受体) adrenergic -,-receptor (肾上腺素能 -,-受体) 5.3 growth factor receptor(tyrosine kinase activity)： PDGFR(血小板衍生的生长因子受体)， EGFR(表皮生长因子受体)，insulin R(胰岛素受体),Peptide Signaling in Plants,PNAS, Nov. 6, 2001, v

5、ol.98 no. 23 In plants, only a few peptide have been identified that act as signaling molecules. In contrast, signaling peptides are major players in all aspects of the life cycle in animals and yeast. suggests that signaling mechanisms across the eukaryotic kingdom are fundamentally different.,目前有关

6、植物中信号肽的研究主要基于以下5种：番茄systemin PSK ENOD40 CLV3 SCR 18 aa 10-13 aa 72-75 aa 53-55 aa,2. 最近分离到另外3种活性信号肽：RALF: rapid alkalinization factor, 5 kd; Tobacco systemin: Tob sys I, Tob sys II,1）tomato systemin: 由食草动物损伤后引起的系统 损伤反应( a systemic wounding response) 在悬浮培养细胞中可以激活促细胞分裂蛋白激酶 mitogen-activated protein(MA

7、P) kinase 并诱导培养基地碱化(alkalinization) 诱导蛋白酶抑制蛋白编码基因的表达(induce expression of proteinase-inhibitor protein-encoding genes),3. 功能：,2）tobacco systemin Tob I and Tob II: 激活 MAP kinase，但不诱导蛋白酶抑制蛋白编码 基因的表达3）RALF (rapid alkalinizaton factor): 激活 MAP kinase，但不诱导蛋白酶抑制蛋白编码 基因的表达; 快速引起 medium 碱化,From the followin

8、gs support the idea that peptide and nonpeptide hormone-activated signaling cascades are linked in plants as they are in animals: 植物生长素类似5羟色胺，乙烯类似一氧化碳， 油菜素类固醇是类固醇，茉莉酮酸与前列腺素相关； Systemin-induced wound response is regulated through the octadecanoid pathway, involving jasmonic acid;,4. 信号调控网络,PSK-induce

9、d cell proliferation requires the hormones auxin or cytokinin; Some of the developmental distortions in roots induced on addition of RALF are reminiscent of impaired nonpeptide hormone-controlled processes.,因此，揭开两种信号cascades之间关系，将是非常有趣的事。,一、生物体内的信号传递,6.2 IP3 system,Hermone/neurotransmitter,G protein

10、,PLC,PIP2,IP3+DAG,CaM,mAChR,EGFR,insulinR,adrenergicR ,组胺R,5-羟色胺R,多肽激素R,Ca2+,PKC等蛋白激酶，磷酸酯酶，核苷酸环化酶，离子通道蛋白，肌肉收缩蛋白等依赖Ca2+ /CaM的蛋白。,Ca2+ /CaM,PKC*,使各种受体，膜蛋白，收缩蛋白，细胞骨架蛋白，核蛋白和酶类的丝氨酸或苏氨酸残基磷酸化，从而影响细胞代谢、生长和分化。,AA,GC,cGMP,多种酶及依赖cGMP的蛋白激酶。,激活多种酶和依赖cGMP的蛋白激酶而发挥生理作用。,激活蛋白激酶活性，自身与tyrosine残基磷酸化,促进cell生长和分化。,二、海马趾C

11、A1神经元区室化模型中的15个信号途径,A:EGF,SOSB:GEF,RasC:cAMP,AC1,AC2D:GE: AA, PLA2 F: PLC, PLC G: DAG, IP3 H: MAPK Cascade I: CaMKII J: PKA K: PKC L: Ca, IP3 M: CaM N: CaN O: PP1,Reaction A:EGF,SOS,Reaction B:GEF,Ras,Reaction C:cAMP,AC1,AC2,Reaction D:G,Reaction E: AA, PLA2,Reactions F,G: PLC, PLC, DAG, IP3,Reactio

12、n H: MAPK Cascade,The various phosphorylation states of CaMKII have different enzyme kinetics, and each of these were explicitly modeled. For simplicity the autophosphorylation steps are represented by a single enzyme arrow in this figure, with CaMKII_a as the combined activity of the various phosph

13、orylation states. The individual kinetic terms used in the model are indicated by the multiple rate references on the arrows.,Reaction I: CaMKII,Reaction J: PKA,Reaction K: PKC,Reaction L: Ca, IP3,Reaction M: CaM,Reaction N: CaN,Reaction O: PP1,三、establishing the individual pathways 1. steps,1. Set

14、up model activation of single component.2.generate the model for an individual signaling pathway.3. Obtain a good empirical model which fit the experimental data.4.examine experimentally defined combination of 2 or 3 such individual signaling pathways.5.test these combined models.,2. Materials and m

15、ethord,(1). Hippocampal CA1 neuron(in GENSIS), (2).NMDARon dendritic spine(树突棘) on the model (3).Synaptic input(3 tetanic bursts at 100HZ,1s each) LTP Ca2+ waveforms,3. Computation formulation,Genesis formulation: S + E SE -k3- P + E Vmax = max velocity = k3. Substrate is saturating, so all of E is

16、in SE form. So Vmax.Etot = SE.k3 = Etot.k3 Km = (k3 + k2)/k1 k2 = k3 * 4 Kd=Kb/KfIf A*Bhalf*Kf=Chalf=Bhalf*Kb then A=Kb/Kf=Kd Ka=Kf/Kb=1/Kd,4.verification,(i). Model simple kinetic schemes that could be calculated analytically, compare simulated results with analytical results. (ii). Use the law of

17、mass conservation and microscopic reversibility principles(微观可逆性原理) test accuracy in complex reaction schemes. (iii). Run the same model at different time steps, compare the resulting simulated values.,5. Protein Kinase C modeling example,Simulation parameters: PKC,References,1. Review: Y. Nishizuka

18、, Nature 334, 661 (1988) 2. J. D. Schaechter and L. I. Benowitz, J. Neurosci.13, 4361 (1993) 3. T. Shinomura, Y. Asaoka, M. Oka, K. Yoshida, Y. Nishizuka, Proc. Natl. Acad. Sci. U.S.A. 88, 5149 (1991) U. Kikkawa, Y. Takai, R. Minakuchi, S. Inohara, Y. Nishizuka, J. Biol. Chem. 257, 13341 (1982).,A.

19、Block diagram of activation for PKC pathway by Ca2+, AA and DAG.,built up simulations iteratively: First: matched AA activation of PKC at zero Ca.Then: matched activation of PKC with Ca at zero AA,Third: matched the curves in B with 1 uM Ca and varying AA. Four: test the match for C, with varying Ca

20、 and 50 uM AA.Last:incorporated DAG interactions into the model.,B: Activation of PKC by AA, with (triangles) or without (squares) 1 mM Ca2+.,Open symbols and dashed lines represent simulations, solid symbols and solid lines are experimental data. Shows:Ca2+ is necessary for the activation of PKC.,e

21、xperimental concentration-effect curves from two main sources: J. D. Schaechter and L. I. Benowitz, J. Neurosci. 13, 4361 (1993); T. Shinomura, Y. Asaoka, M. Oka, K. Yoshida, Y. Nishizuka, Proc. Natl. Acad. Sci. U.S.A. 88, 5149 (1991),C: Activation of PKC by Ca2+, with (triangles) or without (square

22、s) 50 mM AA.,The curve in the presence of 50 mM AA (triangles) was predicted from the parameters obtained by matching the curves in B and the curve without AA (squares) in C, without further adjustment.,D: Activation of PKC by DAG, with (triangles) or without (squares) 50 mM AA.,Both curves in D wer

23、e obtained in the presence of 1 mM Ca2+. Due to different methods for estimating DAG concentrations the levels of DAG used in the model are scaled 15-fold up with respect to the experimental conditions from Shinomura et al.,四、develope the network model in stages,First : model individual pathwaysThen

24、: examin experimentally defined combinations of two or three such individual pathways and test these combined models against published data. Third: repeat this process using larger assemblies of pathways until the entire network model of interacting pathways wasformed. Pathways were linked by two ki

25、nds of interactions: (i) Second messengers such as AA and DAG, produced by one pathway were used as inputs to other pathways. (ii) Enzymes whose activation was regulated by one pathway were coupled to substrates belonging to other pathways.,1、one Signaling pathways exampleS(1).EGFs stimulation of MA

26、PK1,2,Fig. 2. EGF receptor signaling pathways.(A). Block diagram of signalingpathways. Rectangles represent enzymes, and circles represent messengermolecules. This model used modules shown in Fig. 1, reaction A(EGF), B(Ca2+/CaM), E(AA,PLA2), H(PKC),F(PLC,DAG,IP3), H(MAPK ascade), K(PKC), I(CaMKII),

27、L(Ca,IP3).,Fig.2B the time course of activation of MAPK by EGF,(B) Predicted (open triangle) and experimental (filled triangles) time course of response of MAPK to a steady EGF stimulus of 100 nM.the y axis represents fractional activation. The fall in the MAPK activity after the initial stimulation

28、 is due to a combination of EGF receptor internalization and MAPK phosphorylationand inactivation of SoS.,1、one Signaling pathways exampleS (2). Activation of PLC by Ca2+ in the presence (triangles) or absence (squares) of EGF.,(C) Concentration-effect curves.Dashed lines are model data, and solid l

29、ines are experimental data. The y axis represents activation.,Three stimulus conditions: 10 min at 5 nM EGF (short bar, circles), 100 min at 2 nM EGF (long bar,squares), 100 min at 5 nM EGF (long bar, triangles). Only the third condition succeeds in causing activation of the feedback loop. Why?,2、Tw

30、o connected pathways(1). Activation of the fractional feedback loop by EGF receptor : (D) Activation of feedback loop by EGF.,B (basal), T (threshold), and A(active).Point A represents high activity forboth PKC and MAPK, whereas point B represents low activity. Both of these points represent distinc

31、t steady-state levels. Such a system with two distinct steady states is a bistable system. The bifurcation point T is important because it defines threshold stimulation.,2.(1) Activation of the fractional feedback loop by EGF receptor : (E) Bistability plot for feedback loop,Bistability is present o

32、vera range comparable to the experimental uncertainty, indicating that thephenomenon is robust. (Horizontal stripes: experimental uncertainty in concentration; diagonalstripes, simulated bistability range for concentrations.) MAPK has a particularly large uncertainty in concentration range because o

33、f large differences in tissue distributions.,2.(1) Activation of the fractional feedback loop by EGF receptor : (F) estimated experimetal uncertainty in E parameters,initially activating: a suprathreshold stimulus, and then one of three inhibitory inputs was applied: 10 min at 8 nM (short bar, circl

34、es), 20 min at 4 nM (long bar, squares), and 20 min at 8 nM (long bar, triangles.).Only the third condition is able to inactivate the feedback loop.The rebound in the first two cases is due to two factors: the persistence of AA due to a relatively slow time course of removal and the time course ofde

35、phosphorylation of activated kinases in the MAPK cascade.,2.(1)Activation of the fractional feedback loop by EGF receptor: (G) Inactivation of feedback loop by MKP-1.,2.(1) Activation of the fractional feedback loop by EGF receptor: (H) Thresholds for inactivation of feedback loop.,MKP was applied f

36、or varying timesand amounts. At high MKP levels, inactivation occurs more quickly, but there is a minimum threshold of nearly 10 min. Conversely, when MKP is applied for very long times, at least 2 nM MKP is required to inactivate the feedback loop.,Some conclusions for EGFR signaling pathways,(1).1

37、00 nM EGF can activate MAPK.(2).Ca2+ activate PLC,which has more high activity under 0.1uM EGF.(3).100 min at 5 nM EGF activated the feedback loop.(4).Activation of MAPK and PKC by EGF has a threshold(point T).(5).The phenomenon is robust as comparing with Sim and Expt on Km and Conc.(6).MPK-1(20 mi

38、n,8nM) can inactivate the feedback loop.(7).High MKP level ,necessary for nearly 10 min. Long time application of MKP requires at least 2nM MKP.,About bistable system,(1). Such a bistable system has the potential to store information. Signaling events the initial stimulation (amplitude and duration)

39、 that push the levels of either activated PKC or activated MAPK past the intersection point T will cause the system to flip from one state to another. This analysis can be generalized to any combination of pathways in a feedback loop.(2). The emergent properties of this feedback system define not on

40、ly the amplitude and duration of the extracellular signal required to activate the system but also the magnitude and duration of processes such as phosphatase action required to deactivate the system. (3). These properties make a feedback system, once activated, capable of delivering a constant outp

41、ut in a manner unaffected by small fluctuations caused by activating or deactivating events. This capability to deliver a stimulus-triggered constant output signal even after the stimulus is withdrawn may have numerous biological consequences.,2.(2) CaMKII (Ca2+/calmodulin-dependent protein kinase I

42、I ) functions in LTP of synaptic responses in the hippocampus.,The cAMP pathway gates CaMKII signaling through the regulationof protein phosphatases.NMDAR and Ca influx are modeled in a compartmental model of a CA1 neuron with a series of three tetanicstimuli at 100 Hz, lasting 1 s each, separated b

43、y 10 min. This model used modules shown in Fig. 1, C,I, J, M, N, and O(B to E).Open squares: full model; Filled triangles:cAMP(fixed at resting concentrations prevent PKA activity ).,2.(2) (B) Activation of CaMKII.,The initial increase in intracellular Ca2+ caused an activation of CaMKII, AC1,and Ca

44、N through CaM binding and of PKA through increase in cAMP produced through activation of AC1-AC8. cAMP PKA activation PP1 CaMKII The presence of a cAMP-operated gate leads to a large increase in the amplitude of the CaMKII response and prolongation of its activity. Nevertheless, it does not lead to

45、a persistent activation of CaMKII.,2.(2) (C) Activation of PKA.,AC1-AC8 binding to Ca/CaM producing cAMP. PKA activity rises sharply Otherwise,its activity: dont rise,2.(2) (D) Activity of PP1., Ca/CaM + cAMP(fixed) CaN activation smalltransientscAMP fixed PKA activationcAMP unfixed PKAactivation PP

46、1 activityActive PP1 dephosphorylate CaMKII(Thr286) CaMKII .,2.(2) (E) CaN (PP2B) activation byCa/CaM elevation.,The full modelcAMP fixed curves overlap almost erfectly. CaN uninfluenced by cAMP,四、3. A model for interaction between 4 signaling pathways: form a network,( PKC、 MAPK pathways + CaMKII、cAMP pathways ),Glu(+postsynaptic depolarization) Ca2+ influx through NMDAR Ca2+ postsynaptic PK(CaMKII,PKC,PKA,MAPK) ,