1. Protein Kinases, the Most Important
Biochemical Regulatory System in
Animal Cells
• Big Picture
• Definition, History, and Gene Number
• Classifications
– Serine/Threonine Kinases
– Tyrosine Kinases
• MAP protein kinase networks and pathways
3. Protein Kinases in Animal Cells
• Cell division
• Apoptosis
The first messenger
interacts with a receptor
and a second messenger is formed
4. History and Importance I
• About 518 genes in humans encode protein
kinases; there are an estimated 30,000 genes in
humans, so that about 1.7% of the human genome
encodes protein kinases
• Protein kinases are the fourth largest gene family
in humans
– C2H2 zinc finger proteins (3%)
– G-protein coupled receptors (2.8%)
– Major histocompatibility (MHC) complex
protein family (2.8%)
5. How Many Protein Kinases Are
There? (518)
• The kinome refers to all protein kinases in the genome
• There are 478 conventional eukaryotic protein kinases
(ePKs) plus 106 pseudogenes
– 388 Protein-serine/threonine kinases
– 90 Protein-tyrosine kinases
• 58 receptor PTKs
• 32 Non-receptor PTKs
• There are 40 atypical protein kinases (e.g. EF2K/alpha
kinases)
• 478 + 40 = 518
• The exact numbers aren’t important; understand the
classification
6. General Classes I
• ACG Group
• Protein kinase A; cyclic AMP-dependent
protein kinase
• Protein kinase C
• Protein kinase G
• Basic amino acid-directed enzymes that
phosphorylate serine/threonine (you don’t
have to memorize any sequences)
7. General Classes II
• CaMK
• Calcium-calmodulin-dependent protein kinases
– I
– II
– III
– IV
• Type II is a broad specificity kinase
• The others are dedicated kinases with a limited
substrate specificity
8. General Classes III
• CMGC
• Cyclin-dependent protein kinases
– These are important regulators of the cell cycle
• MAP (Mitogen activated protein/microtubule
associated protein) kinases
– Many of these promote cell division
• GSK3 (glycogen synthase kinase-3)
• Clk (Cyclin-dependent like kinase)
9. General Classes IV
• PTK (Protein-tyrosine kinases)
– Receptor, e.g., epidermal growth factor
receptor, insulin receptor
– Non-receptor, e.g., Src, Abl protein kinases
• Specifically phosphorylate protein-tyrosine
(note they are not tyrosine kinases but
protein-tyrosine kinases)
10. Protein Kinase Classifications
• Protein-Serine/threonine
• Protein-Tyrosine
– Receptor: ligand binding domain and catalytic site on the
same polypeptide
– Non-receptor: catalytic domain separate from the
receptor
• Dual Specificity (both serine/threonine and tyrosine)
also occur
• Broad Specificity: have several substrates, e.g., PKA
• Narrow Specificity: have one or a few substrates,
e.g., pyruvate dehydrogenase kinase with one
substrate
• Classified by activator: PKA, PKG, PKC
15. Activation of Protein Kinases
• Know PKA activation
mechanism
– It is the only one where there
is a dissociation of regulatory
subunits from catalytic
subunits
– This was the first activation
mechanism to be described,
but it turns out to be atypical
or unique
• PKG, allosteric
• PKC, allosteric
17. Protein Kinase A Structure
• Bilobed
– N-lobe (upper)
mostly beta sheet
– C-lobe (lower)
mostly alpha helix
• Active site between
the two lobes
• ATP is bound in the
active site
20. Selected Protein Kinase A Substrates
• Phosphorylase kinase alpha and beta subunits
• Pyruvate kinase (Liver type)
• 6-Phosphofructo-2-kinase/phosphatase
• Hormone sensitive lipase
• Protein phosphatase inhibitor 1
• CREB (a transcription factor)
• Aromatic amino acid hydroxylases
– Tyrosine hydroxylase
– Tryptophan hydroxylase
– Phenylalanine hydroxylase
– What else is special about these three enzymes?
• Raf
• Grandmother
21. Earl W. Sutherland, Jr (cAMP)
Edwin Krebs (PKA) Albert G. Gilman (G-protein)
Edmund Fischer (PKA) Martin Rodbell G-protein)
22. Enzyme Cascades and
Phosphorylase and Synthase
• Hormonal regulation
• Hormones (glucagon, epinephrine) activate adenylyl cyclase
– Glucagon, liver
– Epinephrine in muscle
• cAMP activates kinases and phosphatases that control the
phosphorylation of phosphorylase and glycogen synthase
• GTP-binding proteins (G proteins) mediate the
communication between hormone receptor and adenylyl
cyclase
• Learn the regulation of the PKA-phosphorylase cascade!!!
24. Regulation of Glycogen
Metabolism
PKA phosphorylase kinase phosphorylase
A kinase acting on a kinase that phosphorylates a protein is a cascade
Steps 3 and 4 make up the first cascade to be described
25. Protein Kinase G
• Activated by cGMP
• Second second messenger protein kinase (after
cAMP)
• Little known about physiological protein
substrates despite extensive investigation
• Two types of guanylyl cyclase
– Second messenger generated by atrial naturetic factor
as an integral membrane guanylyl cyclase
– Second messenger generated by NO action on the
soluble guanylyl cyclase reaction
30. Selected Protein Kinase G Substrates
• G substrate (cerebellum)
• Vasodilator-stimulated phosphoprotein
• Most substrates and their functions are
unknown
31. Calcium-Dependent Protein Kinases
• Protein Kinase C
– Requires calcium, diacylglycerol, and phospholipid for
activity
– Diacylglycerol generated by the action of
phospholipase C
– Activated by phorbol esters (tumor promoters)
– Many isozymes
• Calcium-calmodulin-Dependent Protein Kinases
– CAM Kinases I, II, III, IV
– Several other protein kinases activated by calmodulin
including myosin-light chain kinase, phosphorylase
kinase, some isoforms of adenylyl cyclase and some
isoforms of phosphodiesterase
34. Hydrolysis of PIP2
• Two second messengers
are generated
– DAG activates PKC
– IP3 leads to a rise in
cytosolic Ca2+
– This activates PKC and
CaM Kinases
• Fig. 12-6
35. Protein Kinase C
Family
• PKC
– C refers to calcium
– DAG and phospholipid
were also described as
necessary for the
activation of this enzyme
– There are many isozymes
that are products of
different genes
• It is paradoxical to have
PKCs that are
independent of Ca2+ and
DAG
36. Selected Protein Kinase C Substrates
• Glycogen synthase (at least two sites,
inactivates)
• PDGF receptor
• EGF receptor
• Insulin receptor
• Transferrin receptor
• Ribosomal protein S6
• Raf
• No need to memorize any of these
37. Calcium-calmodulin Dependent
Protein Kinases
• CAM Kinase I: synapsin I and II
• CAM Kinase II
– CAM Kinase II (autophosphorylation)
– Tyrosine hydroxylase (rate-limiting for catecholamine
biosynthesis)
– CREB transcription factor
– Many others
• CAM Kinase III: Elongation factor II of protein
synthesis (This is a dedicated protein kinase)
• CAM Kinase IV
– Found in the nucleus
– Also phosphorylates the CREB transcription factor
– Many others
38. Receptor Protein-Ser/Thr Ligands
Transforming Growth Factor-β Ligands
• This family has diverse functions (that you don’t need to
remember)
– BMP2 subfamily: BMP2 and BMP4, chondrogenesis and other
developmental functions
– BMP5 subfamily: BMP5,6,7,and 8, development of nearly all organs
– BMP3/osteogenin subfamily: bone formation
– Activin subfamily: erythroid cell differentiation
– TGF-β1, 2, and 3: control of proliferation and differentiation; production
of the extracellular matrix
• There are about 15 BMPs
– They are synthesized as integral membrane proteins and the
BMP is cleaved extracellularly in a regulated fashion
– Proteins contain about 450 aa; BMPs are about 110 residues
– BMP-2 and BMP-4 are expressed by human adult pulp tissue
– BMP 1 is a C-terminal procollagen protease
39. Smads
• Transforming growth factor beta ligands including
the BMPs activate receptor protein Ser/Thr kinases
– Smad transcription factors are phosphorylated and
activated
– Smads enter the nucleus to bring about a response
• These human proteins are homologous to
Drosophila proteins called Sma or Mad, thus smad
• Smads play a role in normal cell growth, cell
division, and apoptosis (programmed cell death)
41. Protein-Tyrosine Kinases
• Receptor
– Insulin
– Epidermal Growth Factor
– Platelet Derived Growth Factor
• Non-receptor
– Src protein kinase
– Abl and Bcr-Abl
– Jak (Janus kinase [two catalytic regions]) or whimsically, just
another kinase
42. Human Protein-Tyrosine Kinases
from the Human Genome Project
• The protein-tyrosine kinases are a large multigene family
with particular relevance to many human diseases, including
cance
• A search of the human genome for tyrosine kinase coding
elements identified several novel genes and enabled the
creation of a nonredundant catalog of tyrosine kinase genes
• Ninety unique kinase genes can be identified in the human
genome, along with five pseudogenes
– Of the 90 tyrosine kinases, 58 are receptor type, distributed into 20
subfamilies
– The 32 nonreceptor tyrosine kinases can be placed in 10
subfamilies
43. Epidermal Growth Factor Receptor Family
• In the 1950s-60s Stanley Cohen discovered a factor present
in crude submaxillary preparations that induced precocious
tooth development in newborn mice that he called epidermal
growth factor
• He purified EGF, determined its sequence, studied its
binding to the EGF receptor, showed that a single molecule
contained EGF binding and protein kinase activity
• He demonstrated that the EGF receptor was a protein-
tyrosine kinase, the first to be described (1980)
• He also showed that EGF and receptor are taken up by cells
and are degraded in lysosomes (many receptors undergo this
fate)
45. ErbB and Malignancies
• Head and neck squamous cell carcinomas (>90% associated
with ErbB overexpression)
– 27,000 new cases in the US per year
• Bladder
• Breast
• Kidney
• Non-small cell lung
• Prostate cancers
• Many other solid tumors
46. CA of the
Tongue
• Early squamous cell carcinoma of the tongue
• Malignant neoplasms of the oral cavity account for 3-5% of all malignancies
– 50% involve the tongue (lateral border and ventral surface most common)
– Then floor of the mouth > gingiva > alveolar mucosa > buccal mucosa > palate
• Squamous cell carcinomas account for >90% of all malignancies of the oral cavity
• Men/woman = 2/1
• Usually more than 40 years of age
• Under diagnosed; more than 50% have metastasized at the time of Dx
47. Receptor Activation
• Ligand binds, dimers form,
transphosphorylation occurs, and the
receptor is activated
– Homodimers: ErbB1/ErbB1, etc.
– Heterodimers: ERbB1/ErbB2 (common in
breast cancer)
– One of the dimers phosphorylates the other, and
the other dimer phosphorylates the one
48. How Does the Growth Factor
Activate the Receptor?
49. Monoclonal Abs in the Rx of Cancer
• Mabs are directed toward the ectodomain of the
ErbB2/HER2 receptor
• Herceptin
– 20-30% of all human breast cancers overexpress
ErbB2, or HER2 (Human Epidermal growth factor
Receptor)
– These tumors can be treated with Herceptin
• It targets domain IV of ErbB2
• Erbitux
– Treatment of colorectal cancer that has spread
– In combination with irenotecan (a DNA topoisomerase
I inhibitor)
– From ImClone (The Martha Stewart case)
– Approved by US FDA in February 2004
50. Structure of the EGF Receptor
Protein-Tyrosine Kinase Domain
• Open activation loop is
active (blue or green)
• Compact activation loop is
inactive (magenta)
• This is an important
regulatory concept
• Blue: EGF
unphosphorylated
• Green: IRK phosphorylated
• Magenta: IRK
unphosphorylated
51. ErbB1 Protein-
Tyrosine Kinase
Inhibitors
• Irressa is approved for the
Rx of non-small cell lung
cancers
• Tarceva is near approval
• ATP-competitive inhibitors
• Aromatic ring systems of
OSI make a 42 degree
angle when bound to
ErbB1 kinase domain
53. The Philadelphia
Chromosome
• It results from the reciprocal
translocation involving
chromosomes 9 and 22
• This fuses the Abl gene from
chromosome 9 to the Bcr gene on
chromosome 22
– This results in the transcription
of an mRNA corresponding to a
Bcr-Abl oncoprotein with
protein-tyrosine kinase activity
– The oncoprotein produces
chronic myelogenous leukemia
• Ph1 is usually the paternally
derived chromosome 9 that is
translocated to the maternal
chromosome 22; it is a shortened
chromosome 22
54. Bcr-Abl Protein Kinase
• The Philadelphia chromosome occurs in the granulocytes in
patients with chronic myelogenous leukemia (CML)
• The resulting Bcr-Abl protein-tyrosine kinase is
constituitively activated (it is active all of the time)
• Gleevec is a specific inhibitor of the Bcr-Abl protein-
tyrosine kinase, and Gleevec is used therapeutically for
chronic myelogenous leukemia
• This malignancy is unusual because it results from a single
genetic alteration; most cancers result from multiple somatic
genetic alterations
56. Gleevec
• This drug is useful in the
treatment of chronic
myelogenous leukemia
• It is an inhibitor of the Bcr-
Abl protein-tyrosine kinase
• It is competitive with respect
to the ATP substrate
• Many oncogenes are protein
kinases, and there is a major
effort underway to develop
therapeutic agents that inhibit
these enzymes
• Protein kinase C, src, and the
EGF receptor are also drug
targets for cancer therapy
58. The Activation Loop
• A, blue loop in compact, inactive conformation
• B, red loop in open, active conformation
59. Regulation of Normal Abl Kinase
• The latch, Sh2, and Sh3
domains lock Abl into an
inactive conformation
• Sh2, ordinarily binds
phosphotyrosine
• Sh3, binds to proline
residues
• The fusion oncoprotein
lacks the normal N-
terminus and the latch;
the protein assumes an
active conformation
60. Leukemia
• The oral changes that occur in leukemia are related to local
leukemic infiltrations, thrombocytopenia, neutropenia, and
anemia
• Left: leukemic gingivitis due to infiltration of leukemic
cells, also gingival hemorrhage
• Right: pale (anemia) with petechial hemorrhages
(thromocytopenia)
61. Chronic
Myelogenous
Leukemia
• This shows marked gingival enlargement; it is more
common in lymphocytic than myelocytic leukemias
• Chronic leukemias
– Middle aged persons; men > women
– Onset and course insidious and it is often diagnosed
accidentally during a routine blood check
63. MAP Kinase Nomenclature
Mitogen Activated Protein Kinase
• Kinase: MAPK is ERK
• Kinase kinase: MAPKK is MEK
• Kinase kinase kinase: MAPKKK is Raf
64. Initiation of a Signal
• Ligand binding produces receptor dimerization,
trans phosphorylation, and the resulting p-Tyr
attracts proteins via SH2 domains
• Proteins that (may) dock with P-Tyr via SH2
domains: PLC, PI3 kinase, Shc, Grb-2, and many
others
– Not all RPTKs associate with all SH2-containing
proteins
• There may not be phosphorylation of other
substrates by the receptor protein-tyrosine kinase
65. Src, A Non-Receptor Protein Tyrosine Kinase
• v-Src was discovered as an oncogene of Rous sarcoma virus, a
chicken virus, and this was the first oncogene to be described as such
• c-Src, the normal homolog, is activated by PDGF and CSF receptors,
which are in turn activated by their ligands and protein-
phosphorylated
• Src may be activated by transmembrane receptors that lack protein-
tyrosine kinase activity
• c-Src is also phosphorylated and activated during mitosis
• Myristoylation of the N-terminus is required for attachment to the
plasma membrane and for activity (Src lacks a signal peptide and is
found initially in the cytosol)
• The physiological substrates for c-Src are unknown despite exhaustive
experimentation
• High activity in brain, a non-dividing tissue
• The protein contains SH2 domains that bind to protein tyrosine
phosphates and SH3 domains that bind to proline-containing regions
as we saw in Abl
67. Protein Phosphatases (P’ases) Fig. 4-8
• These catalyze the hydrolytic removal of
phosphate from proteins; these are unidirectional
reactions
68. How Many Protein Phosphatases
Are There?
• Studies from the human genome indicate that
there are the following number of P’ases
– 32 serine/threonine phosphatases
– 42 protein-tyrosine phosphatases
– 46 dual specificity phosphatases
• It is surprising that there are so many protein-
tyrosine and dual specificity P’ases
69. Protein-Serine/threonine Phosphatases
Catalytic subunit Regulatory
Elements
Regulated
Functions
PPP Family
PP1 >15 that target and regulate
the catalytic subunit
Glycogen metabolism, muscle
contraction, cell cycle, mRNA
splicing
PP2A B subunits target and regulate
core enzyme
MAP kinase pathway,
metabolism, cell cycle
PP2B Ca/CAM activates T-lymphocyte activation,
brain NMDA receptor
signaling
PPM Family
PP2C Integral N or C-terminal
peptides
Antagonism of stress
activated kinases
70. PPP Family of P’ases
• Contain Zn2+ and Fe2+ in the active site
• M subunits target the 38-kDa catalytic subunit of PP1 to
myosin
• G subunits target PP1 to glycogen
• PP2B, or calcineurin
– Regulated by Ca2+
– It couples Ca2+ to protein dephosphorylation
– Two subunits
• A forms the P’ase active site with Zn2+ and Fe2+
• B subunit binds Ca2+
• Ca/CAM is the true activator
• PPM
– Unrelated to PPP by sequence, but both use Zn2+ and Fe2+
– Evolutionary convergence
71. Protein-Tyrosine Phosphatases
Catalytic Subunit Regulatory
Elements
Regulated
Functions
PTP Family
Cytosolic (PTP1B, SHP1, SHP2) SH2 and other domains
target to substrates
Various
Transmembrane PTPs (cd45,
RPTPμ, RPTPα
Homodimerization inhibits Lymphocyte activation
Dual Specificity
Cdc25 Family Polo kinase, Chk1 kinase,
phosphatases
Cell cycle
Low Molecular weight (Acid
phosphatases)
Located in lysosomes ?
72. Protein-Tyrosine P’ase
• All four families bind phosphate to a sulfur in a sequence
Cys-x-x-x-x-x-Arg
• Forms a covalent P-S bond
• Evolutionary convergence
• PTP family
– 230 residue catalytic domain
– Cytoplasmic and transmembrane members
– CD45
• 10% of the plasma membrane protein of white blood cells
• Required for antigens to activate B and T cells
• May activate one or more of the Src-family tyrosine kinases associated
with the T-cell receptor by dephosphorylating inhibitory phosphotyrosine
residues
73. Protein-Tyrosine P’ase
• Dual specificity
– Inactivate the MAP kinases
– Substrate binding site is shallow and can attack pY, pT,
and pS
• Cdc25 Subfamily
– Remove inhibitory pY and pT from CDK1 and CDK2
– This dephosphorylation promotes cell cycle progression
– These dephosphorylations thus have a positive effect
• Cooperation between kinases and P’ases
– PP2A is bound to Ca/CAM kinase IV
– MPK-3 (MAP kinase P’ase 3) is bound to ERK 2, one of
the MAP kinases
75. Cyclic Nucleotide Metabolism
• First and second messengers
• G-proteins
• Adenylyl cyclases
– 9 forms of membrane bound enzyme
– 1 soluble form
• Guanylyl cyclases
– 3 major forms
• ANF (Atrial naturetic factor) receptor in membrane
• Soluble form activated by NO
• Cyclic nucleotide phosphodiesterases
– 11 forms with varying substrate specificity and
regulatory properties
77. Functions of the Isoforms
• ACI is important in behavior and memory
as shown in knock-out mice
• ACVIII knock-outs do not exhibit increased
anxiety in response to stress
• ACV is important in cardiac function
• Much more remains to be done
78. GC and AC
• Adenylyl cyclases and guanylyl cyclases show high specificity for
their respective substrates
• This is essential for the coexistence and fidelity of signaling
pathways, since virtually all cells contain both enzymes.
• Guanylyl cyclases exist as both soluble and membrane-bound
species. Both types of the enzyme contain cytoplasmic domains
similar to those of the adenylyl cyclases
• Membrane-bound guanylyl cyclases are homodimers, whereas the
soluble enzymes contain and alpha and beta subunits, both of which
are required for catalysis
• Each subunit contains a carboxyl-terminal domain that is
homologous to the C1 and C2 domains of adenylyl cyclase;
alpha most closely resembles C1 while beta more closely resembles
C2.
79. Phosphodiesterases
• PDEs are clinical targets for a range of biological disorders
such as retinal degeneration, congestive heart failure,
depression, asthma, erectile dysfunction, and inflammation
• cAMP or cGMP + H2O 5’AMP or 5’GMP
• There are 11 families of enzymes and 21 genes
– Families differ in substrate specificity
• cAMP: 4, 7, 8
• cGMP: 5, 6, 9
• Both: 1, 2, 3, 10, 11
– Families differ in regulation
– Families differ in tissue distribution
– PDE1, 3, 4, 6, 7, and 8 are multigene families
– PDE6 is expressed only in photoreceptors
80. Cyclic Nucleotide Phosphodiesterases
• PDE3 is a target for CV drugs
• PDE4 (cAMP) for depression and inflammation
– PDE4 is the chief PDE in inflammatory cells
– Targeted diseases include atopic dermatitis, chronic obstructive
pulmonary disease (COPD, emphysema), and asthma
– Side effects are common with PDE4 inhibitors such as rolipram
because of nausea and vomiting
• PDE5 for erectile dysfunction
– Sildenafil (ViagraTM) was the first FDA approved PDE inhibitor
• A recent clinical trial indicates that Viagra is effective in the
treatment of pulmonary hypertension
– cGMP relaxes smooth muscle
– Smooth muscle relaxation in arteries/arterioles decreased BP
– Lungs have the highest activity of protein kinase G of any tissue
81. PDE5 inhibitors in the market
• Forty million American men have some degree of erectile
dysfunction.
• As many as 10 million have tried impotency drugs, but only about 3
million have stayed on the treatments.
• The drugs don’t save lives, but there’re big business.
– Pfizer’s Viagra generated $894 million in sales, up 11% from the
prior year.
– It is expected that the three approved PDE inhibitory drugs (next
slide) will generate $6 billion by 2009.
– Cost $10-15 per pill
• There is some cross inhibition of PDE5 and PDE6 (rod cell) by Viagra
which causes patients to see blue aberrations
• Patients taking nitroglycerin for ischemic coronary artery disease
should not take PDE5 inhibitors because the combined effects of these
agents might lower blood pressure to a lethal level
– Nitroglycerin generates NO and activates soluble guanylyl cyclase
83. PDE5 Inhibitors for Erectile Dysfunction
Pfizer/Viagra
Blue pill
Bayer/Glaxo Levitra,
Orange pill
Lilly/ICOS Cialis
Yellow pill
Generic name Sildenafil Vardenafil Tadalafil
Status Sold worldwide Sold worldwide Sold worldwide
Launch date 2000 2003 2003
Rate of successful
intercourse (dose)
66% (20 mg) 75% (20 mg) 63% (20 mg)
Improved erections in
nondiabetics
63% (25 mg) 85% (20 mg) 81% (20 mg)
Drug’s time to onset One hour before sex Within 15 min Within 30 min
Duration of
effectiveness
Within four hours of
taking the drug
Within 6 hours Up to 24 or more
hours (TV ad says
36 h)
Food interaction Absorption reduced by
a fatty meal
Absorption not
affected by food
Absorption not
affected by food
84. Nobel Prize in Medicine 1998
for their discoveries concerning nitric oxide as a signaling
molecule in the cardiovascular system
http://www.nobel.se
Robert Louis Ferid
Furchgott Ignarro Murad
EDRF; endothelium derived relaxation factor
