Signal transduction

Signal transductionMajor definitionsSignal transduction is a basic process in molecular cell biology involving the conversion of a signal from outside the cell to a functional change within the cell.ECB consider 4 general pathways of signal transduction: endocrine, paracrine, synaptic and contact dependentMore generally, signaling can be either via diffused molecules or due to surface-surface interactions

Paracrine signaling occurs between local cells where the signals elicit quick responses and last only a short amount of time due to the degradation of the paracrine ligands.Endocrine signaling occurs between distant cells and is mediated by hormones released from specific endocrine cells that travel to target cells, producing a slower, long-lasting response.

Intracellular signalingIntracellular signaling molecules can relay, amplify, integrate and distribue the incoming signal.Participants of the intrecellular signaling cascades:extracellular signals (soluble ligands, other cell surface receptors)ReceptorsAdaptor proteinsSecond messengers (intracellular soluble ligands)Effector proteins

Key proteins that control intracellular signaling act as molecular switches

Alberts et al. ECBAlberts et al. ECBKinases. KinomeMajor definitionsKinases are enzymes that catalyze the transfer of the -phosphate of ATP (GTP) on a corresponding substrateParticuarly, protein kinases catalyze the transfer on protein alcohol (on Ser and Ther) and/or phenolic (on Tyr) groupsKinases are classified by sequence comparison of their catalytic domains, and in second turn by sequence similarity and domain structure outside of the catalytic domains and biological functionsHuman kinome is a set of all human kinasesIt includes about 500 protein kinase(518 according to Manning et al., 2002) and a lot of kinases specific to non-protenaceus substratesMost of kinase families are conserved in eukaryotes and particularly in multicellular eukaryotes (144 of 189 for PK)

ClassificationGroupFamilyExamplesAGC1770AGCI. Cyclic-nucleotide-regulated PKPKA (cAMP-dependent PK)PKG (Cyclic GMP-dependent PK)AGCII. Diacylglycerol-activated/phsospholipid-dependent PKPKC (protein kinase C) including Ca2+-dependent (cPKC) ,Ca2+-indepdendent (nPKC), atypical (aPKC)AGCIII. Related to PKA and PKCRACAGCIV. G-protein-coupled-receptor phosphorylating PKARK1 and ARK1 (-adrenergic receptor kinases) , GRK5 and GRK6ClassificationGroupFamilyExamplesCAMK3384CAMKI. Ca2+/calmoduline regulated PKCAMKsEG2K (Elongation factor 2 kinase)Phosphorylase kinases (PhK-M)Myosin light chain kinases (MLCK) MAP kinase-activated PK 2(MAPKAP2)CAMKII. AMPK familyAMPK AMP-activated PKCMGCCMGCI. Cyclin-dependent kinases (CDKs)Cdc2, Cdk2 etcCMGCII. MAPK (or Erk) family Erk1, Erk2(extracellular signal regulated kinases, known as p44 MAPK and p42 MAPK)P38 (MPK2, HOG1-related protein)Jnk1, Jnk2 (SAPKs, stress-activated protein kinases)CMGCIII. Glycogen synthase kinase 3 familyGSKs, CKs (casein kinases)ClassificationGroupFamilyExamplesSTEMAPK cascade families, 351Ste7/MAP2K/MEKMEK1, MEK2 (MAP ERK Kinases)Ste11/MAP3KMEKKSte20/MAP4K/Pakp21(CDC42/Rac) activated kinaseClassificationGroupFamilyExamplesTyrosine kinase group3095PTK1. SrcSrc (cellular homolog of Rous sarcoma virus oncoprotein)Yes , Yrk, Fgr, Fyn, Lyn, Lck (Lymphoid T-cell protein-tyrosine kinase)BlkPTKII. Brk familyBreast expressed PKPTKIII. TecTec (Tyrosine kinase expressed in hepatocellular carcinoma)Emt (Itk, Tsk, expressed in mainly in T-cells)PTKIV. CskC terminal Src kinase; negative regulator of SrcPTKVIII. Jak familyJanus kinases (Jaks), Tyk2 )Transducer of interferon signals)PTKIX. AckAck CDC42Hs-associated kinasePTKX. FakFak Focal adhesion kinaseClassificationGroupFamilyExamplesTyrosine kinase group3095PTKXI. EGFR familyEGFR, HER2/c-neu (ErbB-2), Her3 (ErbB-3), Her4 (ErbB-4).

PTKXII. Eph/Elk/Eck receptor familyEph (erythropoeitin-producing hepatoma PK)Eck (epithelial cell linase)Elk (Epl like kinase detected in brain)PTK. TieTiePTKXVI. Fibroblast growth factor receptor familyFGFR1 (Flg, Cek1), FGFR2 (Bek, K-Sam)PTKXVII. Insulin receptor familyInsR, IGF1R (insulin like growth factor receptor)PTKXXII. Hepatocyte growth factor receptorHGFR (Met), Sea, Ron, Stk (stem cell derived tyrosine kinase)ClassificationGroupFamilyExamplesTKL tyrosine kinaselike , 748MLK mixed-lineage kinaseLISK (LIMK/TESK)IRAK interleukin-1 (IL-1) receptorassociated kinase], RafRaf (cellular homolog of retroviral oncogene product)RIPK receptor-interacting protein kinase (RIP)], STRKactivin and TGF- receptorsRGCReceptor guanylate cyclase, 15Platelet-derived growth factor receptor PDGFR, CSF1R (Colony stimulating factor 1 receptor)ClassificationGroupFamilyExamplesOthers37106Activin/TGF receptor familyActRAtypical PKs1340Kinase domain structureFunctional activities of the kinaseBinding and orientation of ATP (GTP) as a complex with divalent cationBinding of a target proteinEnzymatic transfer of the -phosphate group to the acceptor hydroxyl residueCatalytic kinase domain consists of 300-350 aa and is organized in 12 dubdomainThe catalytic activity depends on cation (Mg2+ or Mn2+ ) binding, often on phosphorylaton within the VIII subdomain and sometimes on binding of a ligand or a catalytic subunit

Hanks and Hunter, 1995

Figure 1. Two Views of the Structure of PKA [70]Scheeff ED, Bourne PE (2005) Structural Evolution of the Protein KinaseLike Superfamily. PLoS Comput Biol 1(5): e49. doi:10.1371/journal.pcbi.0010049http://127.0.0.1:8081/ploscompbiol/article?id=info:doi/10.1371/journal.pcbi.0010049

Figure 1 Dendrogram of 491 ePK domains from 478 genes.

G. Manning et al. Science 2002;298:1912-1934Other kinasesEnzymeTargetFunctional roleAminoglycoside phosphotransferase APH(3)-IIIa 3 and/or 5 hydroxyl of aminoglycoside antibiotics

Antibiotic inactivationCholine kinase (CK)Phosphatidylcholine precursorPhosphatidylcholine synthesisPhosphoinositide 3 kinases (PI3Ks)Phosphatidylinositol (PI) or its formsPtdIns(3)P, PI(3,4,5)P3

Type II phosphatidylinositol phosphate kinase (PIPKII)phosphatidylinositol 5-phosphate (PI5P)PI(4,5)P2

Figure 4. Proposed Phylogeny for the Kinase-Like Superfamily, Based on a Unified Bayesian Analysis of Both the Sequence Alignment in Figure 3 and the Structural Character Matrix in Table 2Scheeff ED, Bourne PE (2005) Structural Evolution of the Protein KinaseLike Superfamily. PLoS Comput Biol 1(5): e49. doi:10.1371/journal.pcbi.0010049http://127.0.0.1:8081/ploscompbiol/article?id=info:doi/10.1371/journal.pcbi.0010049

Regulatory GTP-binding proteins=regulatory GTPases=G-proteinsMajor classes of regulatory GTP-binding proteins

Trimeric G- proteins associated with GTPbinding protein coupled receptorsSmall (monomeric) G proteins

inactiveactiveHeterotrimeric guanine-nucleotide binding proteins (G-proteins)

alpha- subunit is myristoylated and can be palmytolatedGamma-subunitc is prenylatedG-proteins are peripheraly proteins of the plasma membraneG-proteins provide signal coupling to seven-transmembrane-surface-receptors known as G-protein couplde receptors (GPCR). G proteins are composed of monomers of alpha, beta, and gamma subunits. The alpha-subunit is a GTPaseThe beta- and gamma-subunits are tightly associated. Receptor phosphorylation upon signal binding mediate GDP/GTP exchange .The GTP bound alpha-subunit dissociate from beta- and gamma-subunits Dissociated subunits initiate cellular response by altering the activity of effectorsG-protein coupled receptors (GPCRs)GPCRs IS the largest family of integral membrane proteins About 800 GPCR genes are identified in the human genome GPCRs are comprised of seven transmembrane a-spirals (TM), an extracellular N-terminus and an intracellular C-terminal domain.GPCR are activated by ligand binding that causes conformation changesLigand-bound GPCR affects the G-protein alpha-subunit decreasing its affinity to GDPGDP/GTP exchange take place due to a decreased affinity to GDP and higher intracellular concentrations of GTPApproximately 30% of all current therapeutic agents acting directly on GPCRs

Alberts et al., ESB

GPCR ligands and effectorsLigandsEffectorsHormones:epinephrine, acetylcholine, noradrenaline, dopamine, histamineLipids: prostaglandins, leukotriens, Lysophosphatidic acid (LPA) ChemokinesRegulatory peptides: thrombin, bombesin, bradykininNucleotidesAdenylyl cyclase, PKA, PKC, Phospholiases (PLC), Rho GTPase, PI3K, ion channels

Biological functionsCell proliferaion, differentiation, migration, angiogenesis, cancerG-protein functionsThe -adrenergic receptor is the GPCR for the hormone epinephrine. epinephrine and glucagon binding activates -adrenergic receptor -adrenergic receptor stimulate GTP/GDP transition in a stimulatory G-protein (Gs with alpha subunit Gsa ). Gs activates adenylyl cyclases to switch on cyclic-AMP formation that results in PKA activation etc.GTP/GDP degradation stop the cascade

GPCR regulatory proteinsGPCR kinases (GRKs) and arrestins causes receptor desensitization (uncoupling) from hetereotrimeric G-proteins (fast recycling) or CME (slow recycling)Receptor activity-modifying proteins (RAMPS) modify the expression, and pharmacology of calcitonin receptor and calcitonin-like receptor (CRLR)Regulators of G-protein signalling (RGS) act as GTPase activating proteins

British Journal of PharmacologyVolume 165, Issue 6, pages 1717-1736, 22 FEB 2012 DOI: 10.1111/j.1476-5381.2011.01552.xhttp://onlinelibrary.wiley.com/doi/10.1111/j.1476-5381.2011.01552.x/full#f1Ion channels as integrators of G-protein mediated signaling: Sympathetic stimulation in the heartNoradrenalin intecrats with AR, activates Gs

Atsushi Inanobe , Yoshihisa KurachiBiochimica et Biophysica Acta (BBA) - Biomembranes, Volume 1838, Issue 2, 2014, 521 - 531increased heartbeatHoe to stop and what happens if it isnt gonna stop ?A, B (cholera toxin subunits); GM1 (GM1 ganglioside receptor); Gsa (G protein alfa subunit); AC (adenylate cyclase); Gi (G protein); cAMP (cyclic AMP); CFTR (cystic fibrosis transmembrane conductance regulator).Cholera toxin blocks Gsa in the GTP-bound state via a reaction of ADP-ribosylation

Clemens, J. et al. (2011) New-generation vaccines against choleraNat. Rev. Gastroenterol. Hepatol. doi:10.1038/nrgastro.2011.174

Figure 2 Cholera pathogenesis and cholera toxin actionSmall regulatory GTPases = small G proteins = small GTP binding proteins =Ras superfamily

GDISmall GTPAses are monomeric proteinsGTP-bound form is active, GDP-bound form is inactiveThree types of regulatory proteins control small G-protein activityGAP- GTPase activating proteins increase its low intrinsic hydrolase activity to trasfser G-protein into an INACTIVE formGDI- GTPase dissociation inhibitors stabilize the GDP-bound, inactive state of G proteinsGEF- guanine nucleotide exchange factors accelerate nucleotide exchange in response to cellular signals to transfer G-protein into an ACTIVE formSmall G-protein familiesFamilyControl of RasGene expressionRhoGene expression; Cytosceleton rearrangementsRabVesicular transportSar1/ArfVesicular transportRanNuclear transportCell cycleSecond messengersSecond messengersSmall intracellular molecules that amplify incoming signalcAMPProducts of PtdIns2P degradation: Ins3P and DAGcGMPPhospholipid signaling