5. G Protein
Ø Guanylate binding protein 鸟苷酸结合蛋白
Ø Includes heterotrimeric G proteins and small GTPases
Alfred G. Gilman
(1941-2015),
Univ. of Texas
Southwestern Medical
Center at Dallas, USA
Martin Rodbell
(1925-1998)
Univ. of Texas
Southwestern Medical
Center at Dallas, USA
The Nobel Prize in Physiology or
Medicine 1994 was awarded
jointly to Alfred G. Gilman and
Martin Rodbell “for their
discovery of G-proteins and the
role of these proteins in signal
transduction in cells”.
7. Heterotrimeric G proteins
• Gα, which carries the binding
site for the nucleotide. 21
different kinds of Gα molecules
are found in mammalian cells.
– Gα
.GTP, active form
– Gα
.GDP, inactive form
• Gβγ
• In mammals, 21 Gα, 5 Gβ , 12 Gγ
doi:10.1038/nrm2299
8. Human and Mouse Gα Subunits
Syrovatkina et al. J Mol Biol. 2016, 428(19):3850-3868.
13. Resonance energy transfer (RET)
Förster resonance energy transfer (FRET)
Bioluminescence resonance energy transfer (BRET)
Resonance energy transfer (RET) assays: a proximity assay that reports a
qualitative assessment of distance and orientation of energy donor and
acceptor moieties. Intramolecular RET assays involve donor and acceptor
moieties on different domains of the same molecule (e.g., receptor or β-arrestin,
heterotrimeric G proteins), therefore, indicate the relative domain movement as
a readout of conformational change.
19. Ø a nucleotide-binding domain (the Ras-like domain)
Ø a helical domain (the α-H domain, AHD)
20. Structural comparison of nucleotide-free Gαs (red) coupled to β2AR (gray,
PDB 3SN6) and GTPγS-bound Gαs (orange, PDB 1AZT).
Guanosine gamma thio-phosphate (GTPγS), a non-hydrolyzable GTP analog
21. Science, 2020, 31;369(6503):eaba3373
Activation of Class A GPCRs
One hallmark of GPCR activation is the outward movement of the
cytoplasmic end of transmembrane domain 6 (TM6) that opens up an
intracellular cavity to accommodate the Gα subunit, leading to nucleotide
exchange and activation of the G protein.
22. Activation of Class B GPCRs
Science, 2020, 31;369(6503):eaba3373
In family B GPCRs, TM6 shows a disruption of the helical fold and the
formation of a sharp kink.
This differs from the gradual bending in TM6 observed in family A GPCRs.
23. Class C GPCRs
mGlu5 GABABR
Nature. 2019;566(7742):79-84. Cell Res. 2020;30(7):564-573.
24. Class C GPCR activation - the case of mGlu5
Nature. 2019;566(7742):79-84.
25. Class C GPCR acivation - the case of GABAB receptor
Nature. 2021. doi: 10.1038/s41586-021-03507-1
There is no outside movement in GB2 TM6.
26. Class C GPCR acivation - the case of GABAB receptor
Nature. 2021. doi: 10.1038/s41586-021-03507-1
A distinct mode of G-protein activation: the Gα C-terminal end interacts with a
shallow groove that involves TM3 and the ICLs of GB2 rather than with a central
pocket that results from TM6 movement (as observed with other GPCRs).
The activated G protein retained all of the expected conformational changes.
27. Asymmetric activation of GPCR dimmer - the case of mGlu2
Nature. 2021. doi: 10.1038/s41586-021-03495-2
28. Asymmetric activation of GPCR dimmer - the case of mGlu2-7
Nature. 2021. doi: 10.1038/s41586-021-03641-w
29. Knowledge points summary
Ø GPCR pathway
Ø G protein classification
Ø GPCR activation
Ø Asymmetric activation of GPCR dimer
30. Signal transduction in GPCRs
G protein-
independent pathway
or
β-arrestin-dependent
pathway
31. Domain Structure of β-arrestins
• The arrestin family consists of four members.
– Visual arrestins (arrestin 1 and arrestin 4) are expressed almost exclusively
in the retina.
– β-arrestin 1 and β-arrestin 2 (non-visual arrestins, also known as arrestin 2
and arrestin 3), however, are ubiquitously expressed in most tissues and
play an important role in regulating signal transduction by numerous
GPCRs.
Lan Ma and Gang Pei (2007) J Cell Sci. 120:213-218
33. Structural Snapshots of GPCR-βarrestin1 Complexes
Cell,2020,180(6), 1041-1043
neurotensin receptor type 1 (NTSR1)
34. GPCR mediated β-arrestin pathway
b-arrestins sterically hinder further G protein coupling to the receptor
and in turn lead to receptor desensitization.
GRK: GPCR kinase
Current Opinion in Structural Biology 2017, 45:160–169
35. Front. Pharmacol., 2015, https://doi.org/10.3389/fphar.2015.00040
β-Arrestin Mediated Internalization of GPCRs
37. β-Arrestin Dependent Signaling
Srivastava et al. (2015) Trends Endocrinol Metab. 26(11):628-642
b-Arrestins can scaffold various
components of multiple signaling
kinases and phosphatases to trigger
a G protein-independent signaling
pathway in the cells.
b-Arrestins can also scaffold
multiple ubiquitin E3 ligases
(E3L) and bring them into close
proximity of GPCRs and thereby
promote ubiquitination of the
target proteins
38. β-arrestins in the activation and targeting of
mitogen-activated protein kinase (MAPK)
40. Sustained signaling through the formation of endosomal class
B GPCR–G protein–β-arrestin megacomplexes
Nature Structural & Molecular Biology 26, 1123–1131 (2019)
45. G protein and β-arrestin-mediated signalling
Ø In the classical model for GPCR activation, signalling is mediated by G
proteins and desensitization is mediated by β-arrestins.
Ø In the current model for GPCR activation, binding of a ligand results in
activation of signalling by G proteins and β-arrestins, as well as
desensitization and internalization by β-arrestins.
Ø In a system with biased agonism (β-arrestin-biased in this example),
signalling only proceeds through one pathway.
Nat Rev Drug Discov. 2010;9(5):373-86.
46. Ø Biased agonism: the phenomenon of a ligand being an
agonist for one pathway downstream of a receptor while
being either a neutral antagonist or an inverse agonist for
the other downstream signaling pathway(s).
Ø Biased ligand: a ligand capable of selectively engaging one
signaling pathway downstream of a receptor over the other
downstream of the same receptor. A complete β-arrestin-
biased ligand does not promote G protein coupling but
induces robust β-arrestin recruitment. Similarly, a G protein-
biased ligand leads to robust coupling and activation of G
proteins but not of β-arrestins.
Ø Unbiased ligand: also referred to as a ‘full agonist’ or
‘balanced agonist,’ it displays efficacies for all downstream
effectors. Often, the endogenous agonist of GPCRs is
considered an unbiased ligand and used as a reference
ligand for comparing the bias of synthetic ligands.
Trends Biochem Sci. 2014;39(12):594-602
55. Emax is the maximal effect.
EC50 is the concentration of a drug that gives half-maximal response.
Potency and efficacy
56. Binding affinity is the strength of the binding interaction between a single
biomolecule (e.g. protein or DNA) to its ligand/binding partner (e.g. drug or
inhibitor). Binding affinity is typically measured and reported by the equilibrium
dissociation constant (KD), which is used to evaluate and rank order strengths
of bimolecular interactions. The smaller the KD value, the greater the binding
affinity of the ligand for its target. The larger the KD value, the more weakly the
target molecule and ligand are attracted to and bind to one another.
58. Ø Selectivity is the preference of the drug to one receptor or its
subtype (as compared to other receptors or other subtypes).
Ø Specificity is the ability of the drug to bind to only one
receptor.
Ø Synergism: When the action of a drug is increased when
given in the presence of another drug, it is called synergism.
59. The full agonists achieve their maximal effect without occupying all of the
relevant receptors of a cell. This is because extra receptors are present. This
phenomenon is called the spare receptor concept or receptor reserve.
60. Ø Agonist: A ligand that binds to a receptor and alters the receptor state
resulting in a biological response
Ø A full agonist reaches the maximal response capability of the system
Ø A partial agonist does not reach the maximal response capability of the
system even at full receptor occupancy.
Compound types
61. ØAntagonists can be competitive (by binding reversibly to the receptor) or non-
competitive (bind irreversibly to the receptor or by allosterically changing the
conformation of the protein). The action of a competitive inhibitor can be reversed by
increasing the concentration of the agonist.
Compound types
62. Ø Constitutive, spontaneous, or basal activity. Physiological response
that occurs in the absence of any receptor-activating ligand due to a
fraction of the receptor being in an activating conformation.
Ø Inverse agonist: ligands that suppress the basal activity of the
receptors (i.e., constitutive activity in the absence of activating
ligands) are referred to as inverse agonists. Inverse agonists
stabilize inactive conformation of the receptors and, in most cases,
occupy the orthosteric ligand-binding pocket of the receptor.
63. Ø An allosteric modulator increases (or decreases) the actions of a primary
agonist while having no effect on its own.
Different binding site from orthosteric ligand;
Modulation (positive or negative)
Ø Synergism: When the action of a drug is increased when given in the
presence of another drug, it is called synergism.
75. Cell Signaling Process
ü Extracellular signals are
registered by membrane
receptors and conducted into
the cell via cascades of
coupled reactions.
ü The first steps of signal
transmission often take place
in close association with the
membrane, before the signal
is conducted into the cell
interior.
ü The cell uses mainly two
mechanisms for
transmission of signals at
the cytosolic side of the
membrane and in the cell
interior.
- Protein-protein interaction
- Second messenger
76. Second messengers
- Low-molecular-weight messenger
substances
- Diffusible signal molecules
- Hydrophobic character: diacylglycerol or
phosphatidylinositol phosphates (二酰基甘油或
磷脂酰肌醇磷酸酯)
- hydrophilic,
cytosolic:
cAMP, cGMP,
inositol
phosphates (磷
酸肌醇), Ca2+
Question: What is second messenger?
What is the special characters?
77. The intracellular “second messengers” are characterized by a
series of properties that make them particularly suitable as
elements of signal transduction:
- Intracellular messenger substances can be formed and
degraded again in specific enzyme reactions. Via enzymatic
pathways, large amounts of messenger substances can be
rapidly created and inactivated again.
- Messenger substances such as Ca2+ may be stored in special
storage organelles, from which they can be rapidly released by a
signal.
- Messenger substances may be produced in a location-specific
manner, and they may also be removed or inactivated according
to their location. It is therefore possible for the cell to create
signals that are spatially and temporally limited.
Definition: Spatio-temporal
Second messengers
78. cAMP production
cAMP signaling pathway
- Gs-coupled GPCRs;
- Gi/o-coupled GPCRs
PKA
AC
cAMP-PDE
Phosphodiesterase: 磷酸二酯酶
81. Main path for Ca2+ release
– G-protein-mediated signaling pathways
– signaling pathways involving receptor tyrosine kinases
– influx of Ca2+ via voltage- or ligand-gated Ca2+ channels
82. Functional assays
An ideal assay for GPCR ligand screening should be simple,
nonradioactive, robust, homogenous, and easily adapted to
a microtiter plate format (96-, 384-, or 1536-well) for robotic
automation.
84. Advantage of HTRF: You don’t have
a big Rluc or YFP inside your target
protein and the expression would
be OK.
Disadvantage of HTRF: You could
see a distance change between two
proteins but not just conformational
change. Meanwhile, you can’t know
the kinetics by this assay.
85. cAMP detection: TR-FRET assay
Time-Resolved Fluorescence Resonance Energy Transfer
(TR-FRET) assay
To counteract the degradation of cAMP to AMP by the action of phosphodiesterase
(PDE) enzymes, a PDE pan-inhibitor (IBMX) is recommended to ensure proper
cAMP accumulation and its subsequent measurement.
93. G Protein
Ø Guanylate binding protein
Ø Includes heterotrimeric G proteins and small GTPases
Not only for GPCRs
94. Small GTPases
• A family of hydrolase enzymes, cytosolic monomers, 21 to 30
kDa.
• Homologous to the alpha subunit of heterotrimeric G-proteins,
but unlike the alpha subunit of G proteins, a small GTPase can
function independently as a hydrolase (水解酶) enzyme to
bind to and hydrolyze GTP to form GDP.
– GTP binding form: active
– GDP binding form: inactive
• Function as molecular switches that control many eukaryotic
cell functions including cell proliferation, cellular trafficking,
and dynamics.
• All small GTPases belong to a superfamily, often named the
Ras superfamily because the founding members are encoded
by human Ras genes initially discovered as cellular homologs
of the viral ras oncogene.
95. Ras Superfamily
Subfamily Function
Ras Cell proliferation (MAPK signaling)
Rho Cellular dynamics, cell morphology
Rab Vesicular trafficking
Rap Vesicular trafficking
Arf Vesicular trafficking
Ran Nuclear transport
Rheb mTOR signaling
Rad
Rit
Miro Mitochondrial transport
>100 members,divided into 10 subfamilies based on the
amino acid sequence, structure and function.
97. Discovery of Ras
• Ras: rat sarcoma, first identified as the transforming oncogene.
• 1960s, Jennifer Harvey and Werner Kirsten discovered viruses
in rat sarcoma.
• Edward M. Scolnick and colleagues at the National Institutes of
Health (NIH) found cancer-causing activities of the Harvey
(HRAS) and Kirsten (KRAS) sarcoma viruses.
• In 1982, activated and transforming human RAS genes were
discovered in human cancer cells by Geoffrey M. Cooper at
Harvard, Mariano Barbacid and Stuart A. Aaronson at the NIH
and by Robert Weinberg of MIT.
• Subsequent studies identified a third human RAS gene,
designated NRAS, for its initial identification in human
neuroblastoma (神经母细胞瘤) cells.
98. Robert A. Weinberg
Founding member of MIT Whitehead Institute for biomedical research.
A pioneer in cancer research mostly known for its discoveries of the first human
oncogene – the ras oncogene that causes normal cells to form tumors, and the
isolation of the first known tumor suppressor gene - the Rb gene (Retinoblastoma
gene,视网膜母细胞瘤).
1. "The Biology of Cancer" , by Robert A. Weinberg, June 2006, (Garland Science
Textbooks), 864pp.
2. "One Renegade Cell" (Science Masters) by Robert A. Weinberg, October 01, 1999,
170pp.
3. "Racing to the Beginning of the Road: The Search for the Origin of Cancer" , by:
Robert A. Weinberg, May 01, 1996 (Harmony Books) 270pp.
4. "Genes and the Biology of Cancer" (Scientific American Library) by: Harold
Varmus, Robert A. Weinberg, October 01, 1992, 215pp.
5. "Oncogenes and the Molecular Origins of Cancer" (Monograph Ser No. 18), March
01, 1990, Cold Spring Harbor (R.A.Weinberg, Editor) 270pp.
99. The Hallmarks of Cancer
血管生成 浸润和转移
Cell. 2000 Jan 7;100(1):57-70
104. Common Structural Features of Ras
Superfamily
• Members of this superfamily share
several common structural features,
including four guanine nucleotide
binding domains and an effector
binding domain.
G-domains
Prenylation
异戊二烯基化
Effector binding domain
C terminal membrane targeting region is lipid-modified by farnesyl
transferase (法尼基转移酶/脂肪酸转移酶)
105. Lipid anchor of the Ras protein.
Membrane association of the Ras
protein is mediated via a
palmitoyl and a farnesyl anchor.
106. Lipid Modifications of Ras Superfamily
The Rab prenylation motifs consist of two C-terminal cysteine residues, found
in one of the following combinations: XXXCC, XXCCX, XCCXX, CCXXX
or XXCXC.
107. Regulatory Proteins of Small GTPases
• GEF (guanine nucleotide exchange factors)鸟嘌呤核苷酸交换因子
• GDI (Guanosine nucleotide dissociation inhibitors)鸟苷核苷酸解离
抑制剂
• GAP (GTPase activating protein) GTP酶活化蛋白
Active
Inactive
108. Ø Guanine nucleotide exchange factors, GEFs
The transition from inactive GDP state to active GTP state may be
accelerated by proteins that cause the bound GDP to dissociate.
The guanine nucleotide exchange factors (GEFs) play an essential
role in the function of the Ras superfamily members.
Ø Inhibitors of guanine nucleotide dissociation, GDIs
For the Rab and Rho/Rac families, proteins have been described
that bind the GDP form of GTPase and prevent dissociation of
GDP. Proteins with these characteristics are known as guanine
nucleotide dissociation inhibitors (GDIs).
The GDIs are localized in the cytosol and bind to Rab and Rho/Rac
proteins modified with a prenyl residue. Their function is thought to
be to extract the Rab and Rho/Rac proteins from the membrane
and to prepare a cytosolic pool of these proteins.
In this way, GDIs may prevent early dissociation of the bound GDP
and premature nucleotide exchange during intracellular
translocation of GTPases.
109. Ø GTPase-activating proteins, GAPs
The lifetime of the active GTP-bound state may be reduced by
GTPase-activating proteins. The primary function of the
GTPase activating proteins (GAP) is to negatively regulate
signal transmission.
Ø Activation of GTPase
Under the influence of Ras-specific GTPase-activating proteins,
the rate of GTP hydrolysis of the Ras protein may be increased
up to 105-fold. The GTPase-activating proteins control the
activity state of Ras protein by drastically reducing the lifetime
of the active GTP state. Because of this property, they function
as negative regulators of the Ras protein.
110. • Question 1:Which factor can transform the G protein
to active state?
(A) GEF
(B) GAP
(C) GDI
(D) Gβγ
• Question 2:The GPCR acts as a __of heterotrimeric
G proteins.
(A) GEF
(B) GAP
(C) GDI
(D) Gβγ
111. Ras Superfamily
Subfamily Function
Ras Cell proliferation (MAPK signaling)
Rho Cellular dynamics, cell morphology
Rab Vesicular trafficking
Rap Vesicular trafficking
Arf Vesicular trafficking
Ran Nuclear transport
Rheb mTOR signaling
Rad
Rit
Miro Mitochondrial transport
>100 members,divided into 10 subfamilies based on the
amino acid sequence, structure and function.
112. Ras
• Mammals have at least three different Ras genes: H(arvey)-ras,
K(irsten)-ras or K-ras, and the N(euroblastoma)-ras gene, with the K-
ras gene producing a major (K-Ras 4B) and a minor (K-Ras 4A) splice
variant.
• The general importance of Ras proteins in growth regulation was
recognized at the beginning of the 1980s, when it was demonstrated
that close to 30% of all solid tumors in humans show a mutation in the
Ras gene coding for a 21 kDa product, named the Ras protein or p21ras.
H-Ras
113. Ras mutation in Cancer
– Constitutive active mutations:
• G12V mutation, renders the GTPase domain of Ras
insensitive to inactivation by GAP and thus stuck in the
"on state".
• Q61K mutation, reduces the rate of intrinsic Ras GTP
hydrolysis to physiologically meaningless levels
– Dominant negative mutations:
• S17N
• D119N
• Ras inhibitor trans-farnesylthiosalicylic acid (反式法尼基硫代水杨
酸) exhibits profound anti-oncogenic effects in many cancer cell
lines.
V, Valine; Q, glutamine; K, Lysine; N, Asparagine; D, Aspartic acid
117. Ras Superfamily
Subfamily Function
Ras Cell proliferation (MAPK signaling)
Rho Cellular dynamics, cell morphology
Rab Vesicular trafficking
Rap Vesicular trafficking
Arf Vesicular trafficking
Ran Nuclear transport
Rheb mTOR signaling
Rad
Rit
Miro Mitochondrial transport
>100 members,divided into 10 subfamilies based on the
amino acid sequence, structure and function.
118. Identification of the Rho GTPases
• The first identified Rho member was RhoA, isolated serendipitously
in 1985 from a low stringency cDNA screening.
• Rac1 and Rac2 were next identified in 1989 followed by Cdc42 in
1990.
• Eight additional mammalian Rho members were identified from
biological screenings until the late 1990s, a turning point in biology
where availability of complete genome sequences allowed full
identification of gene families.
• As early as 1990, Paterson et al. began injecting active Rho protein
into Swiss 3T3 cells.
• In the 2006 review article released by Bement et al., the spatial
zones of Rho activation in fibroblasts were explained.
• Dr. Alan Hall, one of the front-runners in Rho protein research,
compiled evidence in his 1998 review, which showed that it is not
only fibroblasts that formed processes based on Rho activation, but
virtually all eukaryotic cells.
119. Adapted from Heasman SJ and Ridley AJ, Nat. Rev. Mol. Cell Biol. 2008
Rho GTPases
Family
8 subfamilies
20 members
120. The Functions of Rho GTPases
Cytoskeleton Transcription Trafficking
Cell polarity
Cell division
Motility
Survival/death
RhoGDP
RhoGTP
GDIs
GEFs
GAPs RhoGTP
Effector
GTP
GDP
P
126. Activation of Rho kinase by RhoA-GTP in endothelial cells
Retinal Physician, Volume: 17, Issue: September 2020, page(s): 24-26
127. Ras Superfamily
Subfamily Function
Ras Cell proliferation (MAPK signaling)
Rho Cellular dynamics, cell morphology
Rab Vesicular trafficking
Rap Vesicular trafficking
Arf Vesicular trafficking
Ran Nuclear transport
Rheb mTOR signaling
Rad
Rit
Miro Mitochondrial transport
>100 members,divided into 10 subfamilies based on the
amino acid sequence, structure and function.
128. Rab GTPases
• Ras-associated binding (Rab) proteins, the largest family in
most organisms
• Highly conserved from yeast to humans.
– Humans: ~ 70 members
– S. cerevisiae:11
– C. elegans:29
– D. melanogaster:26
• Important in regulating signal transduction and cellular
processes such as differentiation, proliferation, vesicle
transport, nuclear assembly, and cytoskeleton formation.
130. SNAREs Mediated Membrane Fusion
• v-SNARE is comprised of two proteins: synaptobrevin & VAMP (Vesicle Associated
Membrane Protein)
• t-SNARE is made up of the proteins: syntaxin and SNAP-25
• Conformational changes occur in the v-SNARE-t-SNARE association
• A fusion protein complex is formed with SNAP25 which binds to syntaxin and VAMP
• The fusion protein complex disrupts the lipid bilayers leading to biomembrane fusion
131. 2013 Nobel Prize in Physiology or
Medicine
"for their discoveries of machinery regulating vesicle
traffic, a major transport system in our cells"
James E. Rothman
(1950-)
Yale University, ,
New Haven, CT, USA
Randy W. Schekman
(1948-)
University of California,
Berkeley, CA, USA,
Howard Hughes Medical
Institute
Thomas C. Südhof
(1955-)
Stanford University,
Stanford, CA, USA,
Howard Hughes Medical
Institute
132. Ras Superfamily
Subfamily Function
Ras Cell proliferation (MAPK signaling)
Rho Cellular dynamics, cell morphology
Rab Vesicular trafficking
Rap Vesicular trafficking
Arf Vesicular trafficking
Ran Nuclear transport
Rheb mTOR signaling
Rad
Rit
Miro Mitochondrial transport
>100 members,divided into 10 subfamilies based on the
amino acid sequence, structure and function.