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SIGNAL
TRANSDUCTION
THIRD EDITION
IJsbrand M. Kramer
University of Bordeaux
European Institute of Chemistry and Biology, INSERM U1045
Talence, France
This book and the individual contributions contained in it are protected under
copyright by the Publisher (other than as may be noted herein).
Notices
Knowledge and best practice in this field are constantly changing. As new research
and experience broaden our understanding, changes in research methods, professional
practices, or medical treatment may become necessary.
Practitioners and researchers may always rely on their own experience and knowledge in
evaluating and using any information, methods, compounds, or experiments described
herein. In using such information or methods they should be mindful of their own safety
and the safety of others, including parties for whom they have a professional responsibility.
To the fullest extent of the law, neither the Publisher nor the authors, contributors, or
editors, assume any liability for any injury and/or damage to persons or property as a
matter of products liability, negligence or otherwise, or from any use or operation of any
methods, products, instructions, or ideas contained in the material herein.
ISBN: 978-0-12-394803-8
xiii
Preface
The third edition differs considerably from the earlier editions in that
the book is no longer separated in two parts, the first providing the nuts
and bolts of what might be termed classical signal transduction. In fact,
this classification does not really apply for two reasons. First, for students
everything is as new as the latest scientific article is for a teacher and
dividing between classical or nonclassical is not really making the subject
clearer and might even pretend that cells employ classical (important) and
not-so classical (less important) mechanisms that bring about changes in
their metabolism, gene expression, secretion rate, contraction state, and
so on. Second, with the recent structural revelations of G protein-coupled
receptor and the action of biased agonists, classical signal transduction has
suddenly lost its classical touch and has become very modern. Instead, an
introductory chapter has been added in which a number of principles are
outlined common to many signal transduction events, and these are placed
in the context of the most “Nobel”, the most classic, of all pathways: adren-
aline to glycogen phosphorylase. While the previous editions were written
by three authors and rewritten by Bastien Gomperts, so that it appeared
as written by one mind, one hand, this edition also differs in that it has
been written by one hand only (or, less poetically, typed by two hands on
a keyboard). The two “greybeards” have pulled out after publication of
the second edition and, very sadly, Bastien Gomperts has passed away
in October 2013. If, from the previous editions, you appreciate the writ-
ing style, the wit, and the anecdotes, bearing from some unusual sources,
much of the credit goes to him. He was an inspiring mentor indeed.
With a few exceptions, for instance the chapter on protein phosphatases,
each chapter now has a theme of its own, around which specific aspects
of signal transduction pathways are developed. For teaching purposes,
Table 1-1 attempts to give a short overview of each chapter’s subjects and
highlights, so that, depending on the pathway to be explored, a relevant
(suitable) context can be selected. Although there still is a gradual build-
up of the subject, where later chapters make reference to earlier chapters,
each chapter could stand on its own. Naturally, the signaling aspects
highlighted are not necessarily unique to the context in which they are
developed, but it allows teachers (and students) to tell a story rather than
just listing a sequence of signaling events (Kramer and Thomas, 2006).
As a consequence, this edition contains more on cell biology, physiology,
pathology, and immunology. By providing precise examples, embedded
in precise contexts, the book offers the possibility to integrate signaling
xv
xvi PREFACE
FIGURE 1-1
xviii PREFACE
Of course, the authors of this paper would themselves never have recog-
nized the expression signal transduction, and it would be a further 100 years
before it made its appearance in the biological literature. The sensations
brought about by pituri, an alkaloid that Ringer and Murrell described as
sharing some of the pharmacological properties of atropine (courage, infu-
riation, frustration, and headaches), are not dissimilar to those experienced
in the writing of this book. Indeed, they will be familiar to many students
and investigators in this and other fields of research. However, we should
not take this too far. When Ringer (1879) tested the effects of the applica-
tion of pituri on four men, he noted that it also causes drowsiness, faint-
ness, pallor, giddiness, hurried and superficial breathing, dilates the pupil,
produces general weakness with convulsive twitchings, and antagonizes
the action of muscarin on the heart. Unlike atropine, it produces sickness
and increases the salivary secretion in large doses copiously, the breathing
becomes quick and shallow, and general weakness ensues. Reading all this,
it leads one to wonder who, among their students, colleagues, and servants,
may have offered themselves up as willing, or less than willing, guinea pigs
in the furtherance of scientific research. Ringer and his friends apparently
preferred to eschew membership of the very honorable brotherhood of self-
experimenters, of which the more famous members include Sir, Humphry
Davey, who breathed nitrous oxide as well as other more noxious gases,
John Scott Haldane, who too inhaled lethal gases; and more recently Barry
Marshall, who has swallowed a culture of Helicobacter pylori to show that it
caused stomach ulcers and who with Robin Warren was awarded the Nobel
Prize in Physiology or Medicine in 2005. Another member of this fraternity,
Charles Eduard Brown-Sequard, figures prominently in “prologue” chapter.
NOTES
References
We have tried to provide original text sources to nearly all the state-
ments, experiments, and discoveries discussed. The main reason for this
PREFACE xix
References
Kramer, I.M., Thomas, G., Spring 2006. Meeting report: teaching signal transduction. CBE
Life Sci. Educ. 5, 19–26.
Ringer, S., Murrell, W., 1878. On pituri. J. Physiol. 377–383.
Ringer, S., 1879. On the action of pituri on man. Lancet 290–291.
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N.,
Bourne, P.E., 2000. The protein data bank. Nucleic Acids Res. 28, 235–242. http://www.
rcsb.org/pdb/.
TABLE 1-1 Contexts, pathways, subjects, and proteins/molecules elaborated in different chapters
xx
Highlights on molecules, proteins,
Title/context/main pathway Subjects and personalities
1. Prologue: Signal transduction from An account of how the term “signal transduction” • A lfred Gilman
an historical perspective entered biomedical research and how stimulus– • M artin Rodbell
response coupling, hormones, neurotransmitters, • T homas Henry Huxley
growth factors, and their receptors were brought to • S teve Grand
light • C harles Edouard Brown-Séquard
• H enry Hallett Dale
• O tto Loewi
• G eorge Oliver
• E dward Scharpey-Schäfer
• E rnest Henry Starling
• W illam Maddock Baylis
• C ONRO, a self-reconfigurable robot
• P aul Ehrlich
• J ohn Newport Langley
• F rancis Peyton Rous
• R ita Levi-Montalcini
• S tanley Cohen
• A lexis Carrel
• H oward Temin
• R enato Dulbecco
xxi
Continued
Highlights on molecules, proteins, and
Title/context/main pathway Subjects personalities
• P
hospho-amino acids, most occurring phosphate
xxii
acceptors in proteins, stability of phospho-ester,
phospho-ramidate, and phospho-anhydride
bond
• P
hosphoryl transferase, phosphorylation,
protein kinase, catalytic mechanism, role of
conserved residues
• P
RKACA, protein kinase A, catalytic subunit,
serine/threonine kinase, structural composition,
conserved residues, N-lobe, C-lobe, signature
sequences, αC-helix, catalytic mechanism
• P
rotein kinases, classification, serine/threonine,
tyrosine and dual-specificity protein kinases,
their mode of regulation
• P
rotein phosphatases, classification, serine/
threonine, tyrosine and dual-specificity
phosphatases, structural composition, catalytic
mechanisms
• P
YGM, glycogen phosphorylase muscle form,
structural composition, dimer, hydrolysis of
glycogen and phosphorylation of glucose (glucose-
1-phosphate), allosteric regulation of enzyme,
phosphorylation by glycogen phosphorylase
kinase on serine-14, change in configuration, tense
to relaxed state
• R
ASA1, RAS GTPase-activating protein, RAS–
GAP domain, molecular structure, catalyzes
hydrolysis of GTP
• R
eceptors, classification, ligands, overview of
different types
• S
OS1, RAS-nucleotide exchange factor, GEF, Cdc25
domain, molecular structure, αH helix, mechanism
of removal of GDP from nucleotide pocket
• T
wo-component signaling and environmental
sensors in bacteria
3. Regulation of muscle contraction • C
atecholamines (adrenaline, noradrenaline, • A DCY, adenylyl cyclase, structure, catalytic
by adrenoceptors dopamine), molecular composition mechanism, production of cAMP, family
Contexts: • C
entral and autonomic–peripheral nervous members, mode of activation, and inhibition
a. Cardiac muscle contraction system, anatomy, and neurotransmitters involved • A DRA, ADRB, adrenoceptor, adrenergic
b. Smooth muscle contraction • A
drenoceptors, adrenergic receptors, history, receptor, ligand-binding site, conformational
Pathways: classification changes, energy landscape, coupling to
a. Action potential, voltage • A
gonist, inverse agonist, biased agonist, and heterotrimeric G-proteins or G protein-receptor
sensitive Ca2+ channels, Ca2+- antagonist, mode of action, examples kinases (GRK)
induced-Ca2+ release (ryanodine • M
uscle contraction, cardiac and smooth muscle, • a drenalin, composition, its agonists, inverse
receptor), intracellular free Ca2+ anatomy, myosin–actin cross-bridge cycle agonists, biased agonist, and neutral antagonists
release, troponin, myosin–actin • G
-protein effectors, adenylyl cyclase and • A RRB, arrestin proteins, structure, family
cross-bridge cycle phospholipase C, second messengers cAMP, and members
b. Adrenoceptor β1, heterotrimeric diacyglycerol/IP3 • G RK6, G protein-receptor kinase, structure,
G-proteins (Gαs), adenylyl • N
oradrenaline-mediated control of cardiac- function, family members, mechanism of
cyclase, cAMP, and protein muscle contraction: ADRB1 (β1AR), GNAS (Gαs), attachment to GPCR
kinase A ACDY5, cAMP, PRKACA (PKA), CACNA1C • H eterotrimeric G-proteins, mechanism of
c. Heterotrimeric G-proteins (Gαs), (voltage-sensitive Ca2+ channel), RYR2, TNNC1, nucleotide exchange, guanine-exchange function
beta-adrenergic receptor kinase, TTNI3 (troponin), myosin–actin cross-bridge (GEF) of seven-membrane-spanning receptors
arrestin, switch to MAP-kinase cycle, PLN (phospholamban), ATP2A2 (SERCA2, (GPCR)
pathway, non-receptor tyrosine Ca2+ pump), KCNQ1 (K+ channel), ATP2B2 (Ca2+ • I TPR1, IP3 receptor, cryo-electromicroscopy-
kinases, and protein kinase B pump) determined structure, molecular detail of the
(AKT) • G
protein-receptor kinases (GRK), among which IP3-binding site
ADRBK1 and GRK6 • P LC, phospholipase C, domain architecture,
• A
rrestins and arrestin-dependent signaling structural composition, TIM barrel, X/Y-
(among others, SRC, RAF–MAPK, AKT1, NFKB) linker, catalytic mechanism, production of
diacylglycerol and inositol-1,4,5-trisphosphate
(IP3), family members, family tree, control of
PLCB3 by GNAQ (Gαq)
• F
eedback mechanisms, modeling of
noradrenaline-mediated molecular events
xxiii
Continued
xxiv
Highlights on molecules, proteins, and
Title/context/main pathway Subjects personalities
xxv
cycle
Continued
xxvi
Highlights on molecules, proteins, and
Title/context/main pathway Subjects personalities
• O
dorant receptors, GPCR, Gαolf (GNAL),
adenylyl cyclase (ACDY3), cyclic nucleotide-
gated channel (CNG), Ca2+/calmodulin-gated
chloride channel (ANO2)
• E
xcursion on G protein-coupled receptors
6. Intracellular calcium alcium-storing organelles and Ca2+ transporter
• C • C a2+-binding domains or motifs, molecular
Contexts: a2+-coordination geometry, Ca2+-binding
• C structure of EF-hand, C2-domain, Calx-β motif
a. Muscle contraction proteins and Ca2+ chelators (EDTA, EGTA) and gelsolin repeat
b. Neurotransmitter release a2+-binding domains (EF-hand, C2-domain, P-
• C • C a2+-permeable channels, members, membrane
c. Cell migration and C-domain, Calx-β-motif, gelsolin-repeat) topology
Pathway: • C
almodulin-binding proteins as effectors • C ALM, calmodulin, structural composition,
a. Phospholipase C, inositol-1,4,5- a2+ indicators (from aquorin to genetically
• C change in conformation upon binding of four
trisphosphate, diacylglycerol, encoded indicators) Ca2+ ions, interaction with Camk2a, Mylk2, and
IP3-receptor, Ca2+-induced a2+-permeable channels (ITPR, RYR, TPCN,
• C Kcnn2
Ca2+-release (ryanodine receptor), KNCA, TRP, THEM16A, CACNA1, ORAI1) • C AMK, Ca2+/calmodulin protein kinase,
intracellular free Ca2+ • S
tore replenishment through ORAI1 (calcium molecular structure of hub, linker and kinase
- Ca2+/calmodulin sensitive release-operated calcium channel), the Ca2+- domain, schematic representation of the
smooth muscle myosin light sensor STIM1 and the Ca2+-ATPase (ATP2A1) assembly into a multiprotein complex, control of
chain kinase, myosin–actin a2+ blips, puffs, spikes and waves
• C kinase activity by Ca2+ oscillations
cross-bridge cycle smooth • V
esicle fusion with membrane, SNARE complex, • G CaMP3, genetically encoded Ca2+ indicator,
muscle synaptotagmin, voltage-gated Ca2+ channel EGFP bound to Ca2+/calmodulin, molecular
- Synaptotagmin, membrane (CACNA1C) structure
fusion, voltage-gated Ca2+ • C
ell migration, protrusion, retraction, actin • I TPR, IP3-receptor, cryo-microscopy-derived
channel neurotransmitter cytoskeleton (arcs and stress fibers) structure, control of Ca2+ conductivity, molecular
release hemokine receptor-mediated localized Ca2+
• C structure of IP3-binding site
b. Protein kinase C, oscillations, activation of smooth-muscle myosin • M etal coordination geometry, Ca2+-binding
phosphorylation of Rho- light-chain kinase (MYLK) and activation of proteins and metal chelators (EDTA, EGTA)
dissociation inhibitor WAVE/SCAR/WASP-mediated actin-filament • M ichel Abercrombie, a pioneer in cell migration
- Guanine nucleotide exchange nucleation • R YR, ryanodine receptor, cryo-microscopy-
(ARHGEF1), monomeric • M
ichel Abercrombie, a pioneer in cell migration derived structure, molecular composition of
GTPase (RHOA), Rho- cytoplasmic vestibule, and control of Ca2+
kinase, phosphatase inhibitor conductivity
(MYPT), smooth muscle
myosin activation, myosin–
actin cross-bridge cycle
- Guanine Nucleotide exchange
(TIAM1), monomeric GTPase
xxvii
(RAC1), activation of actin
nucleation (WASP/ARP),
membrane protrusion
Continued
Highlights on molecules, proteins, and
xxviii
Title/context/main pathway Subjects personalities
7. Bringing the signal into the • E stimated number of human genes and the • A
KAP79, schematic representation of scaffolding
nucleus: Regulation of gene central dogma of molecular biology role in signaling complex assembly (ADCY8,
expression • S tarvation and the processes that control PPP3CB, PPP3CA, PRKACA, PRKARIIA, DLG1),
Context: gluconeogenesis, role of glucagon and role in control of phosphorylation of the AMPA-
a. Gluconeogenesis glucocorticoid type glutamate receptor (GRIA1)
Pathway: • S ignaling by the glucagon receptor, adenylyl • b
ZIP, basic leucine-zipper protein, list of
a. G protein-coupled receptors, cyclase, cAMP, and regulation of activity of members of the protein family
heterotrimeric G-protein, Gαs, protein kinase A • C
REB1, cAMP response-element binding
adenylyl cyclase, cAMP, protein • A KAP, anchoring of protein kinase A to protein, structural composition of bZIP domain
kinase A, cyclic AMP-response subcellular compartments and scaffolding of bound to cAMP-response element (CRE),
element-binding protein (CREB), signaling complexes, example of AMPA receptor, phosphorylation sites in KID domain and
induction of the gluconeogenic DLG1, and AKAP79 interaction with CREBBP
program • C REB, transcription factor, is a nuclear target of • G
CGR, glucagon receptor, bound to glucagon,
protein kinase A predicted structure
• G ene transcription and transcription factors, from • H
istone-3, methylation and acetylation
Jacob and Monod until today, histone acetylation signatures of a repressed and activated enhancer,
and methylation, pre-initiation transcription promotor and coding region
complex • P
IC, transcription pre-initiation complex,
• C REB recruits co-activators, CREBBP, PE300 and schematic representation of proteins
CRTC2 • P
RKACA, catalytic subunit of protein kinase
• C REB1, FOXO1, PPAR and the glucocorticoid A, domain architecture, structural composition,
receptor NR4A1 drive the gluconeogenic program conserved residues, position of N-tail with
• I nsulin disables the gluconeogenic program myristate and of C-tail, co- and posttranslational
(cytoplasmic sequestration of CRTC2 and FOXO1, phosphorylation and phosphosite sequence logo
phosphorylation and dissociation of CREBBP) of substrates
• P
RKARIA, regulatory subunit of protein kinase
A, domain architecture, molecular structure with
or without cAMP, function of pseudo-substrate
(RRGAI), dimerization through dimerization
domain and CNBA interactions
8. Nuclear receptors • S
teroid hormones, everything from domestic • E
SR1, estrogen receptor, molecular structure
Contexts: animals, the Chinese Pharmacopoeia of 725 AD, of ligand binding with agonist (DES), detail
a. Sperm motility and capacitation to nineteenth and twentieth century personalities of coordinating amino acids of the ligand-
b. Mammary gland development in the discovery of steroids binding pocket, position of NCOA2 co-activator,
c. Consolidating memory (and • S
teroids accumulate in the nucleus, nuclear molecular structure of dimer of DNA-binding
dealing with pregnancy) receptors domain, comprising two C4-type Zn2+ fingers
Pathways: • R
egulation of transcription discovered in giant • L
udwig Fraenkel and the search for
Nuclear receptor-mediated chromosomes of insect salivary glands progesterone
regulation of gene transcription • S
uperfamily of nuclear receptors and recognition • N
uclear receptors, domain architecture,
of specific promoter enhancer sites (inverted or classification, ligands, molecular composition of
direct repeat DNA sequences) ligands
• L
igand-mediated activation or repression of gene • R
ARA and ESR1, conformational changes of the
transcription, histone acetylation or de-acetylation ligand-binding domains and interaction with
• C
haperone (or heat-shock) proteins and the NCOR1 or NCOA1, in the presence of an inverse
loading of receptors with their ligand agonist (BMS493), agonists (AM580, DES) or
• C
ooperation with other transcription factors antagonists (BMS614, tamoxifen)
(transrepression or transactivation) • V
DR/RXRA, molecular structure of dimer
• N
on-genomic action of nuclear receptors bound to DNA, cryo-electron microscopy-
(activation of SRC, interfering with integrin derived structure, crystal structure modeled
binding, gating of the AMPA-type glutamate to cryo-EM, associated ligands 1,25-dihyroxy
receptor) vitamin D3 and 9-cis retinoic acid
• P
aracrine signaling between estrogen and
progesterone receptor-bearing epithelial cells and
mammary-gland stem cells
• S
perm capacitance and motility induced by
progesterone in a non-genomic fashion (effect on
the CATSPER Ca2+ channel)
• G
lucocorticoid-mediated synapse strengthening
• E
ndocrine disruption in a plastic world
(bisphenol A)
xxix
Continued
Highlights on molecules, proteins, and
Title/context/main pathway Subjects personalities
xxx
transformation and cell polarity inflammation JUN and FOS bound to DNA and linked through
Contexts: • P
rotein kinase C family, member of AGC kinases, leucine zipper, different protein combinations
a. Oncogenic transformation domain architecture (JUN/JUNB, JUN/ATF7, FOS/JUN, FOS/ATP7,
b. Cell polarity (spindle orientation lassical protein kinase C, role of Ca2+ and
• C and so on), different response elements (TRE, CRE,
in development, migration diacyglycerol (or phorbol ester) in activation of MARE1, MAREII and ARE)
of astrocytes, and axonal the kinase, displacement of pseudo-substrate • B P1 domain, molecular structure of type-I,
outgrowth) sequence by C1 and C2 domains type-II, and type I/II domains, OPCA motif,
Pathways: • A
typical protein kinase C, role of AC1 and PB1 lysine, heterodimer assembly, and formation of
a. Classical protein kinase C: domain plus substrate in rendering atypical homotypic array
- RAF kinase inhibitor, RAF, protein kinases catalytically competent • C 1A, C1B, and C2 domains, Ca2+ binding,
MAP-kinase pathway, FOS • P
rotein kinase C anchoring proteins, RACKs, membrane binding, role in protein kinase
transcription factor, precancer STICKs, and PICKs activation
stem-cell program • P
rotein kinase C as a potential oncogene, history, • P olarity complexes, composition, membrane
- Jun-kinase-1, JUN phorbol ester and signaling to AP-1 transcription anchors (GNAI or CDC42), signaling complex
transcription factor, precancer complexes (PARD3, PARD6, atypical PKC), adaptors
stem-cell program • R
ole of classical protein kinase C (PRKCA) in (GPMS2, NUMA or INSC,GPMS2, DLG1), motor
b. Atypical protein kinase C: facilitating the cancer stem-cell program, role of proteins (dynein complex or kinesin complex),
Monomeric GTPase (CDC42), JNK1 and JUN, and RAF and FOS and microtubules
polarity complex (PARD3, • A
typical protein kinase C, different types of • P horbol ester, phorbol-12-myristate-13-acetate,
PARD6), cell polarity substrates polarity cues and the localization of PARD- PMA, TPA, molecular composition
NUMB, LGL, CRB3 polarity complexes • P RKCI, atypical protein kinase iota, molecular
• D
iscovery of PAR proteins in Caenorhabditis structure of kinase domain and PB1 domain,
elegans (zygote) potion of AGC tail, and model of activation
• P
olarity complexes in flies and mice (CDC42, mechanism (removal of AC1, pseudo-substrate,
PRKCI or PRKCZ, PARD3, PARD6, GNAI3, and PB1, role of substrate in rendering kinase
GPSM2, INSC, NUMA, and DLG1) fully competent
• P rotein kinase C, PKC, classical and novel,
family members, molecular structure of
domains, priming of the protein kinase through
phosphorylation of the AGC tail by mTORC2
(co-translational), and through phosphorylation
of the activation segment by PDK1, comparison
of conserved phosphorylation sites and
phosphosite sequence logo of PRKCA substrates
10. Regulation of cell proliferation by • R
eceptor tyrosine protein kinases, classification, AKT1, serine/threonine protein kinase, structural
receptor tyrosine protein kinases family composition, conserved residues, substrate-binding
Context: • E
GF/ERBB receptor, family members, ligands, site (penetrates into catalytic cleft, comparison with
EGF-mediated activation of gene dimer combinations, intracellular adaptors and INSR)
expression, cell division effectors • B RAF, domains, structural composition,
Pathway • A
daptors and effector proteins of receptor conserved residues, activation mechanism, side-
EGFR, recruitment of nucleotide tyrosine kinases, their discovery, SH2 and PTB to-side dimerization, oncogenic mutants
exchange factor (SOS/GRB2), domains • E GFR, extracellular and transmembrane
activation of monomeric GTPase • S
H2 and PTB-containing proteins, enzymes, segment, domain architecture, structural
(RAS), activation of kinase transcription factors, adaptors, docking proteins composition, ligand-mediated conformational
cascade RAF, MEK, MAPK, • D
rosophila compound eye, C. elegans vulval changes, CR domain-mediated dimerization
translocation into the nucleus, induction, and the elucidation of the Ras–MAP- • E GFR, intracellular segment, role of LLRRL
regulation of transcription factors kinase pathway helix in juxta-membrane segment in membrane
• E
GFR, SOS, RAS, BRAF, MEK1, ERK1 pathway, binding of receptor monomer and in
detail of BRAF dimer stabilization of kinase domain in receptor dimer,
• R
AS and RAF oncogenes, detail of multiple allosteric regulation through asymmetric dimer
regulation mechanisms that control RAF formation of two kinase domains
• M
AP-kinase (ERK) docking sites • E GFR, kinase domain, detail of regulation of
• M
AP-kinase-activated kinases, family tree (MNK, kinase activity through removal of leucine
RPS6K, MAPKAPK) wedge (L858, L861), illustration of how
• M
APK-mediated phosphorylation of transcription oncogenic L858R mutation removes the
factors, example ELK4 inhibitory constraint (increase in kinase activity
• M
NK1-mediated regulation of protein synthesis, without need of receptor dimerization)
phosphorylation of components of the ribosome • E LK4 and SRF, DNA-binding domain, SRE
translation initiation complex enhancer element
• S
caffold for the RAS–MAPK pathway, yeast STE5, • I NSR, insulin receptor kinase domain, tyrosine
mammalian KSR2 protein kinase, structural composition,
• W
hy are signaling pathways so complicated? conserved residues and substrate-binding site
• M
AP-kinase-related proteins, subfamilies, ERK, (surface-oriented, long tyrosine required to reach
JNK, and p38 pathways, family tree catalytic residue, comparison with AKT1)
• O
ther branches of EGFR signaling pathways, • M APK1 (ERK2), structural composition,
Ca2+/calmodulin, PI-3-kinase, STAT proteins conserved residues, activation mechanism,
xxxi
• T
ransactivation, from GPCR to EGFR activation segment phosphorylation
Continued
Highlights on molecules, proteins, and
Title/context/main pathway Subjects personalities
xxxii
• M
AP-kinase-related proteins, scheme of three-
tier cascades of ERK, p38, and JNK pathways,
family tree of MAPK members, activation
segment signature
• R
eceptor tyrosine protein kinases, RTK,
classification, domain architecture
• S
H2 domain, selectivity, contextual peptide, and
selectivity of phosphotyrosine recognition
• S
OS1, domain architecture, structural
composition, function, tandem-binding sites for
RAS.GTP
xxxiii
Continued
Highlights on molecules, proteins, and
xxxiv
Title/context/main pathway Subjects personalities
• W
nt signaling disables the AXIN/APC • D
omain architecture and domain interactions
destruction complex (role of FZD, LRP, DVL, of components of Wnt pathway (LRP6, DVL1,
CSNK1G1, casein kinase) AXIN, APC, GSK3B, CSNK2A2 (casein kinase),
• W
nt signaling, induction of expression of SNAI1, CTNN1B, CDH1)
SNAI2 (slug), TWIST1, ZEP1 and suppression of • D
omain architecture and domain interactions
expression of CDH1 (E-cadherin) of TCF7 and TCF7L1 and their association
• W
nt signaling (WNT3 and FDZ7/LPR6) and stem with transcriptional repressor and activator
cell self-renewal, stem cell niche of crypts in small complexes
intestine, role of R-spondins and LGR5 receptor in • E
pithelium small intestine, villus, crypt of
boosting Wnt response Lieberkühn, enterocyte, Paneth cell, goblet cells,
• W
nt expression and ephrin-B receptors (EphB) crypt base columnar cell (Lgr5+ stem cell)
• W
nt and planar cell polarity in Drosophila and • F
zd8, Frizzled-8, receptor extracellular segment
mammalian cells (RHO, ROCK, myosin light bound to wnt-8 (xWnt8), structural composition
chain, actin filament nucleation and organization) • L
EF1, lymphoid enhancer factor, C-terminal
• A
denomatous polyposis coli, colon cancer, segment (HMG-BT) bound to DNA
mutations in CTNNB1, AXIN, and APC • T
CF family members, gene structure and
domain architecture
14. Chemokines and traffic of white • F irst evidence of extravasation in the tongue of a • C
hemokine receptors, downstream enzymes,
blood cells frog, the account of Augustus Waller (1864) their products and biological effects
Context: • B acterial infection (S erysipelas) in treatment • C
hemokines, classification, topology of cysteine
Immunity and recruitment from “new growth” and the discovery of tumor bonds
of leukocytes to sites of necrosis factors • C
XCL8, interleukin-8, bound to fragment of
xxxv
inflammation • I nflammatory mediators and their sources CXCR1, receptor, structural composition
Continued
Highlights on molecules, proteins, and
xxxvi
Title/context/main pathway Subjects personalities
Pathways: • T
NF receptor (TNFRSF1A), trimerization, • E
xtravasation, a three-step process, circulation,
a. TNF, TNF-receptor, assembly of signaling complex through death attachment/rolling and arrest/diapedesis
ubiquitinylation-mediated domains (DD), binding of TRADD, TRAF2, RIPK1 • L
UBAC, role of linear ubiquitin chains, M1, in
signaling-complex assembly • K
63–ubiquitin chain attachment to RIPK1 by stabilization of signaling complexes, complex of
(TRADD, TRAF2, RIPK1 the E3–ubiquitin ligase complex BIRC2/UB2D3, RNF31 (HOIP), RBCK1 (HOIL), SHARPIN
and the E3–ubiquitin ligase binding of IKBKG (Nemo) and TAB2 associated • P
rotrusion and retraction, mode of cell
BIRC2), recruitment of TAB2/ with MAP3K7 (TAK1), IKBKB (IKKβ) and CHUK migration, proteins involved, domain
MAP3K7 (TAK1) and IKBKG/ (IKKα) architecture, and domain interactions (PI
IKBKB/CHUK (IKKα/β), hosphorylation of NFKBIA (inhibitor κB),
• P 3-kinase-γ, TIAM, RAC1, GNA13, ARHGEF1,
activation of transcription recognition by CSFBTRC followed by its RHOA, ROCK1)
factor NFKB, transcription of destruction, translocation of NFKB to the nucleus • T
AB2, adaptor, binding to K63–ubiquitin dimer,
inflammatory mediators and • L
UBAC, linear ubiquitin-chain assembly, by structural aspect
enhanced expression of adhesion E3–ubiquitin ligase RNF31, reenforces signaling • R
NF31 (HOIP), domain architecture, linear
molecules (among which ICAM1 complex ubiquitin chain formation (M1–G76), RING-
and VCAM1) • R
ole of E3–ubiquitin ligase PELI3 in preventing between-RING segment of E3–ubiquitin ligase,
b. Chemokine CXCL1 (Gro), apoptotic pathway schematic representation of association with
CXCR2 receptor, phospholipase- • C
hemokine receptor-mediated activation of SHARPIN, RBCK1 (Hoil), OTULIN, CYLD, and
Cβ, phosphatidylinositol-4,5- phospholipase A2 (PLA2G6), phospholipase C ubiquitin chains
bisphosphate, inositol-1,4,5- (PLCB2 or PLCG1), phospholipase C (PKD1) and • T
NFRSF, members of the tumor necrosis factor
trisphosphate, diacylglycerol, PI3-kinase (PIK3CA), enzyme products and their receptor superfamily, domain architecture and
guanine exchange factor biological effects ligands
RASGRP2, monomeric GTPase • C
XCL1 (Gro), CXCR2 and activation of PLCB2, • T
NFRSF1A, TNF-receptor-1, domain
RAP1A, activation of intergrins, formation of diacylglycerol, activation of architecture, structural composition, schematic
arresting leukocytes RASGRP2 (guanine nucleotide exchange factor), representation of receptor associated adaptors
loading of GTP on RAP1A, leading to membrane and effectors (TRADD, TRAF2, BIRC2, RIPK1) or
recruitment of RASSF5, APBB1IP, and talin- the inhibitor (BAG4)
mediated activation of integrins, binding to
ICAM1, and arresting the cell on the surface of
vascular endothelium
• C
hemokine-mediated migration of leukocytes,
role of RHOA and RAC1
15. Activating the adaptive immune • O verview of members of non-receptor protein • B CL10, adaptor protein with CARD domain,
system: role of non-receptor tyrosine kinases cryo-electromicroscopy-derived evidence of
tyrosine kinases • T -cell receptor, antigen-presenting dendritic cell, filamentous assembly, formation of a large
Context: MHC class II, CD4, CD28, CD80 adaptor structure that recruits numerous MALT1
T-cell activation, T-cell receptor • A ctivation of ZAP70 by LCK, phosphorylation proteins (caspase-like protease) and these, in
engaged by antigen bound to of LAT, recruitment of various effectors, among turn, recruit TRAF6 proteins (E3–ubiquitin
MHCII which phospholipase Cγ (PLCG1) ligase), assembly of a big signaling complex
Pathways: • P roduction of diacylglycerol and IP3, liberation of • C ARD11 (CARM1), schematic representation
a. Phospholipase Cγ, Ca2+ from intracellular stores, activation of Ca2+/ of protein unfolding, nucleation site of BCL10
phosphatidylinositol- calmodulin-sensitive calcineurin (phosphatase), assembly through CARD–CARD interaction
4,5,bisphosphate, diacylglycerol dephosphorylation of NFAT, nuclear • C SK, non-receptor tyrosine kinase, activator
and inositol-1,4,5-trisphosphate, translocation, DNA binding, and gene expression kinase of SRC, domain architecture, structural
IP3, intracellular free Ca2+, • A ctivation of atypical protein kinase-θ (PRKCQ), composition, membrane recruitment. and
serine/threonine phosphatases phosphorylation of CARD11 (Carma1), activation through phosphorylated PAG1 (CBP)
(calcineurin), dephosphorylation filamentous assembly of BCL10 (CARD • I FN, interferons, classification
of transcription factor (NFAT), domains), binding of MALT1 and TRAF6 leading • I FNAR1, IFNAR2, interferon receptors bound
nuclear translocation to ubiquitin-mediated assembly of a large to interferon-α (IFNA), molecular structure
b. Protein kinase Cθ, CARD11, signaling complex, comprising TAB2/MAP3K7, combined with schematic representation
adaptor protein BCL10, IKBKG (Nemo)/IKBKB (IKKβ)/CHUK(IKKα), • M HCII, major histocompatibility complex class-
recruitment of E3–ubiquitin phosphorylation of inhibitor kappa B, nuclear II, schematic representation, binding of CD4
ligase TRAF6, caspase-like translocation of transcription factor NFKB/RELA, • N on-receptor tyrosine protein kinases (NRTK),
protease (MALT1), ubiquitin DNA binding and gene expression classification, domain architecture, members
chain, recruitment TAB2/ • I nterferon-mediated dimerization of IFNAR1 acting as oncogenes
MAP3K7, IKBKG (Nemo)/ and -2, activation of the non-receptor protein • S RC, non-receptor tyrosine kinase, domain
IKBKB (IKKβ)/CHUK(IKKα), tyrosine kinases TYK2 and JAK1, JAK1-mediated architecture, structural composition,
phosphorylation of inhibitor phosphorylation of STAT1 and -2, dimerization, activation mechanisms, role of the membrane
kappa B, nuclear translocation of binding of IRF9, nuclear translocation, DNA recruitment protein PAG1 (CBP), the upstream
transcription factor (NFKB) binding, gene expression protein tyrosine kinase CSK and the tyrosine
• D own-regulation of interferon pathway phosphatase PTPRC (CD45)
xxxvii
Continued
xxxviii
Highlights on molecules, proteins, and
Title/context/main pathway Subjects personalities
• E
xcursion on non-receptor tyrosine protein • S
TAT, signal transducer and activator of
kinases transcription, schematic representation of
phosphorylation, dimerization, association
of IRF9, DNA binding and induction of gene
expression
• T
CR, T-cell receptor, schematic and realistic
representation, proximity of CD4
• T
CR-mediated activation of NFAT, domain
architecture and domain interactions of proteins
involved in the signaling pathway
16. Signaling through the insulin • A brief history of the discovery of insulin • A GC kinases, members, their domain
receptor: Phosphoinositide • I nsulin receptor dimer, change in relative architecture, and common priming and
3-kinase and AKT positions of kinase domain (mechanism activation mechanism
Context: unknown), activation of kinases through • A KT2, domain architecture, family members,
Anabolic action of insulin transphosphorylation of activation segment structural composition, hydrophobic motif,
Pathways: • r ecruitment of scaffold protein IRS1 and adaptor activation segment, conserved residues,
Insulin receptor protein SH2B2 via an phosphotyrosine PTB and activation mechanism, role of mTORC2
- Phosphorylation insulin- SH2 domain respectively (priming) and of PDK1 (activation), phosphosite
receptor substrate • R ecruitment of phosphatidylinositol 3-kinases sequence logo of substrates
(IRS1), recruitment and production of phosphatidylinositol-3,4,5- • G SK3B, surface representation of kinase
phosphatidylinositol phosphate domain, inhibition through phosphorylation of
3-kinase, phosphatidyl-3,4,5- • R ecruitment of PDK1 and AKT2 through their the N-terminal (pseudo-substrate), processive
trisphosphate, recruitment of PH domain, formation of a transient kinase dimer phosphorylation, role in glycogen metabolism
kinases PDK1, AKT2 followed by transphosphorylation (in activation • I NSR, insulin receptor, extracellular segment,
segment) and activation of AKT2 structural composition, α- and β-chains, domain
architecture, cleavage sites, and disulphide
bonds
- GTPase-activating protein • P hosphorylation and inhibition of GSK3B, • M
TORC1, kinase complex, domain architecture,
TSC2, monomeric GTPases activation of glycogen synthase (GYS) and complex composition, MTOR (kinase), RAPTOR
(RHEB), activation kinase phosphorylation and inhibition of TSC2 (interacting with RRAGA/B), DEPTOR
complex (mTORC1), protein (GTPase-activating protein), accumulation of the (inhibitor), MLST8 and interaction with FKB12/
kinase (RPS6KB1) and mRNA monomeric GTPase RHEB in its GTP bound state rapamycin
capping protein (4EBP1), at the lysosomal membrane, activation of the • M
TORC2, kinase complex, domain architecture,
pathway to protein synthesis mTORC1 complex in the presence of RAGA/B complex composition, MTOR (kinase), RICTOR
- GTPase-activating protein bound to GTP and RAGD/D bound to GDP (interacting with PROTOR), DEPTOR (inhibitor),
(TBC1D4), monomeric GTPase (permissive condition, only occurs in the presence MLST8
(RAP10), pathway of vesicle of sufficient amino acids in the lysosome) • P
hosphoinositide metabolism (PI), kinases,
transport (glucose transporter • m TORC1 phosphorylation and activation of phosphatases, and interacting protein domains
supply) RPS6KB1 and phosphorylation and inhibition of (ENTH, FYVE, PH, PX, WD-repeat)
- Protein kinase GSK3B, 4EBP1 (removed from EIF4E, bound to the mRNA • P
IK3C, PI 3-kinase, phosphatidylinositol
pathway to glycogen 5′cap, stimulation of protein synthesis) 3-kinase, classification, regulatory subunits,
synthesis • 5 ′-AMP-mediated activation or PRKAA2 (AMPK), upstream receptors (TRK, GPCR/ARRB1/
- Recruitment of SH2B2 and with the help of STK11, phosphorylation and RALGDS, GPCR/Gβγ) and interacting proteins
guanine nucleotide exchange activation of TSC2, accumulation of RHEB in • P
IK3CG, PI3-kinase-γ, structural composition,
factor (RAPGEF1), monomeric GDP-bound state, enhanced autophagy and binding to phospholilpid membrane and
GTPases (RHOQ), pathway reduced protein synthesis phosphatidyl-4,5-bisphosphate, interaction with
to vesicle docking and fusion inhibitors (LY and wortmannin)
proteins (TRIP10, EXOC7) • R
ibosome, translation initiation complex,
schematic representation, of components and
phosphorylation processes (mRNA, EIF3,
EIF4G, EIF4E, IEF2G, EIF4A/4B, tRNAmet, RPS6,
RPS6KB1, MTORC1
• T
SC1, domain architecture, phosphorylation
sites
• T
SC2, domain architecture, phosphorylation
sites
xxxix
Continued
Highlights on molecules, proteins, and
Title/context/main pathway Subjects personalities
17. TGFβ and signaling through • T GFβ, a matrix-associated cytokine, precursor form • S
MAD, transcription factor, structural
xl
receptor serine/threonine • A family or receptors, accessory and pseudo- composition, MH1 and MH2 domain,
protein kinases receptors, ligands and traps DNA binding, schematic representation of
Contexts: • c ontribution of Drosophila and C. elegans in the phosphorylation and ubiquitinylation sites,
a. Cell cycle regulation discovery of signaling pathway composition of trimeric complex
b. Cell fate decision during • T ype-1 and -2 receptor, phosphorylation of GS • T
GFβ, ligand, dimer, cysteine knot, precursor
development domain, removal of inhibitory wedge, kinase protein LAP-TGFβ
c. Epithelial–mesenchymal activation, role or ZFYVE9 (SARA) in bringing • T
GFBR, TGFβ receptor type-1 and -2,
transition SMAD to the receptor extracellular segment, domain architecture,
Pathways: • S MAD types, receptor regulated, common mediator structural composition, ligand binding,
Canonical, SMAD-mediated, and inhibitory, phosphorylation of regulated SMAD dimerization
pathway protein by type-1 receptor, association with common • T
GFBR, overview of receptor types, pseudo-
Noncanonical pathway: receptor mediator SMAD4, translocation to the nucleus, receptors and accessory receptors, their ligands
adaptor protein (PARD6), binding to SMAD-binding element and traps
E3–ubiquitin ligase (SMURF1), • A ssociation of co-activators (PIN1, YAP1, EP300, • T
GFBR1, kinase domain, structural composition,
ubiquitinylation of RHOA, loss of CREBP, mediator complex, elongation complex, GS domain, L45 loop, conserved residues,
tight junction disassembly SWI/SNF activation mechanism
• R ole of master transcription factors, SPI, POU5F1, • T
RIM33, bromo- and PHD domain, interaction
MYOD1, in making DNA accessible for SMAD with acetylated and methylated Histone-3.3
proteins, cell-lineage dependent, cooperative
action with other transcription factors (FOXO1,
E2F4, STAT3, ATF3, JUN, RBL1) which are
controlled by other cytokines (signal integration)
• P hosphorylation of linker region determines
duration of transcriptional activity, role of kinases
CDK8, CDK9 and phosphatase PPM1A and the
RNA polymerase-associated phosphatases CTDSP1,
CTDSP2 and CTDSPL, regulation of protein half-life
by phosphorylation through kinase GSK3B
• M ono-ubiquitinylation dissociates SMAD
complexes, role of TRIM33/UBE2D3, poly-
ubiquitinylation (K48) causes destruction, role of
NEDD4L and SMURF1
• P hosphorylation of linker region in cytoplasm
prevents nuclear translocation, role of MAP-kinase,
and promotes destruction, role of SMURF1
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Barfota, sotig, ful ‒ ‒ i ett palats?
Nej, blif i askan du, det är din plats.
Perander sanoi: »Die Sterne begehrt man nicht, man freut sich nur
ihrer Pracht.» [Tähtiä emme halua omistaa, me iloitsemme niiden
loistosta.] Kuitenkin hän halusi omistaa Suomalaisen teatterin
nuoren tähden eikä tyytynyt häntä vain kaukaa ihailemaan. Frithiof
Perander oli lähes kaksikymmentä vuotta vanhempi kuin Ida
Aalberg.
»Hyvä Ida!
Sinun kirjeesi oli niin rikas sisällyksestä, etten tällä kertaa ennätä
vastata, niinkuin tulisi. Kun asuu bolag'issa saapi niin vähän
rauhaista hetkeä yksinololle. Iloista oli lukea sinun kirjettäsi. Siitä
näin, että olet paljon mietiskellyt. Nuo muutamat
valtiopäivämiesvaalit, joihin viittaat» (j.n.e. politiikkaa y.m.).
»Luullakseni matka on vaikuttanut edullisesti terveyteeni. Varsinkin
Norjan tunturi-ilma oli hyvää lääkettä hermoilleni. Saa nähdä koska
minä saan tavata sinua. Oietkoon jo Tampereella? Missä Elokuun
kuutamo viehättää sinua? Sinä olet, kuten näen, ollut altis sen
kauneuden vaikutuksille. Näyttää kuin olisit ruvennut luontoa ja sen
ihanuutta entistä enemmän rakastamaan ja mielesi syvyyteen
painamaan. Kaunis on kuvauksesi syksyisen eli syksyyn kallistuvan
luonnon laadusta. Se on todellakin äiti, joka on monta muretta
nähnyt, vaan ei kuitenkaan vielä ole huolista riutunut. Hän vaan
ajattelee ja pitää huolta kuinka elämä muille kävisi turvalliseksi.
Nyt hyvästi, Ida raiska! Voi hyvin eläkä liioin rasita voimiasi
näyttämön puuhissa.
Frithiof»
Hyvä Neiti,
*****
Mariasi.»
Kun Ida Aalberg 1880 oli Saksassa ja Unkarissa, oli Maria Grape,
kuten sanottu, hänen pankkiirinaan. Siihen aikaan ei vielä tiedetty,
että Grapen ennen niin hyvä liike oli Turkin sodan jälkeen
luisumassa alaspäin, ja Maria Grapen kirjoittamista kirjeistä voidaan
päättää, että hänellä oli vaikeuksia lähettäessään rahamääriä niistä
varoista, jotka Ida Aalberg olin hänen haltuunsa uskonut. 1881 Maria
Grape kävi Norjassa Winterhjelmien luona, ja hänen läsnäollessaan
Ida Aalberg ja Hedvig Winterhjelm suunnittelivat yhteistä kiertuetta
Suomeen ja sopivat, että sellainen tehtäisiin. Heti Maria Grapen
Suomeen palattua hän saa Ida Aalbergilta kirjeen, jossa tämä moitti
häntä huhujen levittämisestä ja toisten asioihin sekaantumisesta.
»Olen vain puhunut totuutta, kertonut, että lääkäri on käskenyt sinua
vaikenemaan, en ole puhunut mitään pahaa», vastaa Maria Grape ja
vetoaa vanhaan palvelusintoonsa. Juuri näihin aikoihin Maria
Grapen liike teki vararikon. Hänellä oli vielä hallussaan Ida Aalbergin
rahoja 700 markkaa, ja Ida Aalberg, ihmeissään siitä, ettei Maria
Grape, vaikka he vastikään olivat tavanneet, ollut mitään puhunut
odotettavasta surkeudesta, tiedusteli rahojensa kohtaloa erään
yhteisen tuttavan välityksellä. Tästä toimenpiteestä Maria Grape oli
hyvin pahastunut, hän selitti Ida Aalbergin rahojen kyllä olevan
turvassa ja sanoi maksavansa ne milloin tahansa. Välit menivät
lopullisesti rikki Ida Aalbergin palattua Suomeen. Rouva Winterhjelm
oli tiedustellut Maria Grapen tilaa Ida Aalbergilta, ja tämä oli antanut
epäedullisia selostuksia. Tosiasia olikin, että Maria Grape näihin
aikoihin etsi pikarista lohdutusta intohimoiselle mielelleen.
»Ida kulta!
Hedvig Winter-Hjelm.»
»Suurenmoinen Taiteilija!