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ANAT458 > Dr. Van-Lamarche (Rho GTPases) lect21-24 > Flashcards

Dr. Van-Lamarche (Rho GTPases) lect21-24 Flashcards

1
Q

name the 4 main cellular responses to a signal

A

survive, divide, differentiate, die

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2
Q

what kind of ligands interact with cell surface vs intracellular receptors?

A

hydrophilic ligands with cell-surface; hydrophobic ligands with intracellular

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3
Q

name and briefly describe the 4 types of extracellular signalling

A
  1. contact dependent: cells touch. ex eph/ephrins
  2. paracrine: secreted ligands over short distance
  3. synaptic: long distance signalling with neurotransmitters
  4. endocrine: long distance signalling via hormones travelling in blood
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4
Q

name the 3 classes of cell-surface receptors

A
  1. ion-channel-linked
  2. GPCRs
  3. enzyme-linked receptors
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5
Q

what process are ion-channel linked receptors involved in?

A

synaptic connections: they change ion permeability of the PM changing escitability of the postsynaptic cell

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6
Q

how many TM domain do enzyme-linked receptors have?

A

1 short TM domain

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7
Q

how do enzyme-linked receptors work?

A

2 options:
1. ligand binds in form of a dimer to a dimerized receptor: receptor has catalytic activities itself
2. single signal molecule binds: receptor activates an enzyme which has catalytic acitivty

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8
Q

what are relay proteins? give examples

A

enzymes, kinases/phosphatases, mediates signaling via phosphor/dephosphorylation

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9
Q

what are scaffold proteins?

A

no enzymatic activities, multiple signaling domains to mediate interactions, induce large cluster of protein complexes

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10
Q

what are amplifiers?

A

GTPases, Kinases, phosphatases: enzymes on/off, small GTPases, interact with intracellular mediators that have their downstream effect

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11
Q

what do intracellular mediators can amplifiers interact with?

A

integrators! (substrates or effectors of amplifiers)

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12
Q

kinases required what to act?

A

ATP

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13
Q

how can a signaling complex get assembled? (2 ways)

A
  1. via scaffolding protein
  2. via the activated receptor itself that binds multiple proteins
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14
Q

name the most common amplifier

A

GTPase!

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15
Q

name 2 differences between kinases/phosphatases and GTPases

A
  • Kinases use ATP, GTPases use GTP
  • the phosphate released does not go to phosphorylate another protein with a kinase
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16
Q

what is the role of integrators?

A

modulate the interaction between signaling pathways

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17
Q

how many families of RTKs are there?

A

7

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18
Q

what are characteristics of RTKs structure?

A
  • long intracellular domain containing the tyrosine kinase domain
  • short TM domain
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19
Q

most RTKs are what kind of receptors?

A

growth factor and hormone receptors

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20
Q

what are the major cellular roles in which growth factor and hormone receptors are involved in?

A

cell proliferation, cell survival, cell motility, cell differentiation

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21
Q

dysregulation of RTKs are involved in what type of diseases?

A

cancer

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22
Q

the addition of a negative charge (phosphate) to a protein can lead to what?

A

change in conformation, stimulation/inhibition of proteins, protein interactions

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23
Q

what aa get phoosphorylated?

A

tyrosine, serine, threonine

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24
Q

briefly describe the general mechanism of activation of RTKs

A
  1. ligand binds
  2. oligomerization of the receptor
  3. trans-phosphorylation
  4. tyrosine kinase activation
  5. binding of substrates
  6. activation of intracellular signaling proteins
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25
Q
A
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26
Q

what type of proteins can RTKs bind to induce oligomerization?

A

proteoglycans

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27
Q

what type of proteins can RTKs bind on a different cell?

A

ephrins

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28
Q

how is the FULL kinase activity of RTKs unlocked?

A

phosphorylation of a critical tyrosine residue

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29
Q

the phosphprylation of tyrosine residues on the RTKs triggers what?

A

high affinity binding of proteins to the phosphorylated tyrosines

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30
Q

what kind of domain do phosphotyrosine of RTKs interact with?

A

SH2 domain (Src homology domain)

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31
Q

via what does the phosphotyrosine of RTKs interact with the SH2 domain?

A

via a small amino acid side chain

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32
Q

name some domain found in protein signaling modules

A

SH2, PTB, PDZ, SH3, WW, 14-3-3

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33
Q

what are protein signaling modules used for?

A

to build up complex networks of interacting proteins;
involved in signaling from cell surface to nucleus, protein trafficking, subcellular localisation, cell shape, cell motility, cell interactions

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34
Q

what does SH2 bind?

A

specific phosphotyrosine residues

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35
Q

more specifically describe how SH2 interacts with RTK

A

SH2 has a + charged conserved binding pocket that interacts with pY;
and a + charged specificity binding pocket that interacts with the side chain

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36
Q

what dpes 14-3-3 interact with? where does it go after?

A

it interacts with phosphoserine/ phosphothreonine and goes to the nucleus to induce transcription

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37
Q

what does the PH domain bind to? why?

A

binds PIP2 to localize protein at the plasma membrane

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38
Q

what is the scaffolding protein for the insulin receptor B subunit?

A

IRS-1 (insulin receptor substrate)

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39
Q

name the 2 methods mentionned for detection of protein-protein interactions via specific signaling modules

A
  • ip
  • GST pulldown
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40
Q

explain a GST pulldown assay

A
  1. use recombinant DNA to fuse protein with GST
  2. incubate your sample with GST-tagged protein
  3. immobilize on glutathione sepharose beads
  4. wash
  5. SDS-PAGE
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41
Q

explain how immunoprecipitation works

A
  1. tag your protein & introduce it in host cell
  2. whole cell extract
  3. incubate with antibody againt the tag
  4. incubate with a-sephrose beads
  5. centrifuge to collect beads. discard supernatant
  6. wash pellet
  7. separate protein by SDS-PAGE
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42
Q

what are the 5 subfamilies of the Ras small GTPases superfamily? name their function

A
  • Ras: cell prolifration & diffferentiation
  • Rho: cell morphology and movement
  • Ran: nuclear import
  • Rab / Arf: vesicular trafficking & secretion
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43
Q

name the prenyltransferases that can modify Ras-related proteins and what domain they each modify in what GTPases

A

1) farnesyltransferase: modifies CAAX domain of Ras proteins
2) type 1 geranylgeranyltransferase: CAAX domain of Rho annd Rap proteins
3) type 2 geranylgeranyltransferase: CXC or CC in Rab proteins

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44
Q

what is X in the CAAX domain of Ras vs Rho/Rap proteins that is modified by a prenyltransferase?

A

Ras: X = Met or Ser
Rho/Rap: x = Leu

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45
Q

how long is the farnesyl group added to Ras protein by farnesyltransferase?

A

15 carbons

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46
Q

via what bond is farnesyl bound to Ras proteins?

A

thioether/covalent bond between the carbon and sulfate at the terminal cysteine of Ras protein

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47
Q

what would be a target to inhibit Ras activity?

A

prenyltransferase!

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48
Q

what has a higher concentration in the cell, GTP of GDP?

A

GTP has a concentration that is 10x higher

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49
Q

name an important GEF for Ras

A

SOS protein

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50
Q

what is the structure of a Ras protein composed of?

A
  • 6 beta sheets, 5 alpha helices
  • switch helix (effector binding region)
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51
Q

what happens to the switch helix of Ras proteins when it is GTP vs GDP bound?

A

GTP-bound = switch helix is exposed
GFP-bound = hidden

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52
Q

Ras mutations are found in 30% of what diseases?

A

cancers

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53
Q

what mutation keeps Ras GTPase activated (inhibits GAP)

A

G12V-Ras

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54
Q

what mutation keeps Ras GTPase inhibited (inhibits GEF)?

A

S17N-Ras

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55
Q

you can say that Ras is what type of gene?

A

oncogene

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56
Q

name a GAP for Ras

A

neurofibronin

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57
Q

what proteins are involved in Ras activation by RTK?

A
  1. RTK binds Shc via Yp-SH2 interaction
  2. Shc binds GRB2 via Yp-SH2 interaction
  3. GRB2 binds SOS via SH3-PXXP interaction
  4. SOS (GEF) activates Ras
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58
Q

appart form the GEF domain and proline rich motif, what other domain does SOS have?

A

PH domain to bind lipids

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59
Q

what is the MAPK pathway require for?

A

cell division and proliferation

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60
Q

what are the main players of the MAPK pathways (name them)

A
  • MAPKKK (Raf)
  • MAPKK (Mec)
  • MAPK (ERK)
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61
Q

MAPKs are what type of kinases?

A

serine threonine kinases

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62
Q

what are the outputs of the MAPK pathway?

A

MAPK phosphorylates protein to regulate their activity and/or goes to nucleus and affects gene expression

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63
Q

name ras effectors involved in cell growth and remodeling of the actin cytoskeleton

A
  • Raf (MAPKKK)
  • PI3K
  • RAL-GDS
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64
Q

what are PI3K’s downstream effectors and their function

A
  1. AKT/PKB: cell survival
  2. Rac: cell migration
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65
Q

like Ras, what kinase is also often mutated in cancers

A

PI3K

66
Q

what is PI3K involved in?

A

cytoskeleton regulation, cell migration.
its effector Ras involved in actin reorganization

67
Q

different Ras mutations affects different what?

A

downstream effectors (ex Raf or PI3K)

68
Q
A
69
Q

what kind of transformation are induced by oncogenes like mutated Ras?

A
  • Increase cell proliferation/division
  • Loss of inhibition of cell-cell contacts
  • Loss of adhesion
  • Increased cell migration
70
Q

how did they test Ras mutant activity?

A

transfected cells with one Ras mutation or both or none. Culture for 10 days. count the numbers of colonies.

71
Q

what did they find about Ras mutant activity?

A

each mutation alone was enough to cause oncogenic activity, but the oncogenic activity wwas most when the 2 mutations were present

72
Q

remember: name the 5 subfamilies in the Ras superfamily of small GTPases and their function

A

Ras: growth and differentiation
Rho: cell morphology and movement
Rab & Arf: vesicular transport
Ran: nuclear import

73
Q

name the main members of the Rho subfamily

A

Rho, Rac, Cdc42

74
Q

which prenyltransferase post-translationally modifies Rho GTPases again? at what motif?

A

type 1 geranylgeranyltranserase: CAAX motif where X = Leu

75
Q

what are the specific CAAX motifs of RhoA, Rac1, and Cdc42?

A

RhoA = CLVL
Rac1 = CLLL
Cdc42 = CVLL

76
Q

how long is the geranylgeranyl group?

A

20 carbons

77
Q

what is a GDI?

A

Guanine nucleotide dissociation inhibitor: inhibits GEF

78
Q

GDI has the same effect at what Rac/Rho mutations? meaning it keeps GTPase in what?

A

N17Rac/N19Rho
keeps the GTPase inactive (GDP-bound)

79
Q

what kind of proteins GEFs?

A

oncogenic

80
Q

what are the 2 families of GEFs

A

TRIO (Ddl family) and DOCK

81
Q

what are the domains the TRIO Dbl GEFs family

A

DH-PH-SH3-DH-PH-SH3-kinase

82
Q

what does the DH domain do?

A

interacts with GTPase

83
Q

DH domain is specific to what?

A

the Dbl family (its a Dbl homology domain)

84
Q

what does the PH domain do in GEFs?

A

localizes the GEF close to PM

85
Q

what are called the domains specific to Rac1/RhoG and RhoA?

A

GEFD1 is specific to Rac1 and RhoG
GEFD2 is specific to RhoA

86
Q

the GEFD1/2 are made up of what smaller domains?

A

DH + PH

87
Q

what are the domains that make the DOCK-A Gefs?

A

SH3-DHR1-DHR2-PXXP

88
Q

what are the DHR1 / DHR2 domains

A

DHR1 = PH
DHR2 = DH

89
Q

what domain is specific to GAPs?

A

rhoGAP

90
Q

what domains make up GAPs

A

SH2, SH3, PH, GAP, PXXP

91
Q

name a few cellular processes controlled by rho proteins (Rho, Rac, Cdc42)

A
  • cytoskeletal dynamics
  • cell motility / adhesion
  • phagocytosis
  • cytokinesis
  • apoptosis
  • cell proliferation
  • cell cycle
92
Q

what is the cytoskeleton involved in?

A

organelle transport, chromosome segregation at mitosis

93
Q

what processes is actin-based motility involved in? in what way?

A
  • embryogenesis: important morphogenic processes
  • inflammatory response: leucocyte migration
  • wound healing: fibroblast andvascular endothelial cells migration
  • metastasis: tumor cells migration
94
Q

give an example of how actin polymerization allows for cells to move?

A

unicellular bacteria Listeria moves via its actin tail

95
Q

cell motility involves the coordination of what activities?

A

cytoskeleton, membrane, and adhesion systems

96
Q

what is the basic engine for gliding and crawling locomotion?

A

actin cytoskeleton

97
Q

where is actin found in the cell?

A

monomeric actin filaments are found beneath the PM

98
Q

how microtubules are organized in the cell?

A

tubulin: rigid structure with one end attached to a centrosome

99
Q

microtubules provide what to the cell?

A

cell division and cell polarity

100
Q

what do intermediate filaments provide to the cell?

A

mechanical strenght

101
Q

what is the name of the rope-like fibers made of intermediate filaments?

A

vimentin and laminin

102
Q

what are the 2 types of actin? describe briefly

A
  • G-actin = monomeric actin bound to ATP
  • F-actin: filamentous actin bound to ADP
103
Q

what is special about G-actin’s activity?

A

its an ATPase

104
Q

which type of actin is polymerized?

A

F-actin!

105
Q

what is the Cc?

A

when the Koff/Kon = 1 (because filaments maintains a certain length due to equal poly and depolymerization)

106
Q

at which end of the actin filament does polymerization happen?

A

polymerization is favored at the + barbed end.
depolymerization at the - pointed end

107
Q

elongation of actin filaments only happens when what?

A

they form and oligomer

108
Q

what molecules are required from actin polymerization?

A

ATP, Mg2+, K+

109
Q

actin filaments grow in what direction?

A

toward the barbed + end which points towards the PM

110
Q

what makes that there is more polymerization happening at the pointed + end?

A

there is more monomeric actin at that end

111
Q

give 2 examples of how actin-binding proteins can act

A

block actin polymerization by:
- binding to the actin-binding site
- keeping actin ADP-bound

112
Q

name 2 main actin-binding proteins and what they each do

A
  • thymosin: inhibits polymerisation
  • profilin: promotes polymerisation
113
Q

what is vinculin/ERM?

A

actin binding protein that couples actin filament to PM

114
Q

what is Gelsolin?

A

actin binding protein that breaks the existing F-actin

115
Q

what are filamin and fimbrin?

A

actin binding proteins thaat link actin filaments

116
Q

what is the Arp2/3 complex?

A

actin binding protein involved in actin assembly

117
Q

basically name the actin binding proteins that increase actin polymerization

A

profilin, ARP2/3

118
Q

name the actin binding proteins involved inthe actin filament structure (no dynamic role)

A

actinin, fimbrin, filamin

119
Q

name the motor proteins that are actin binding proteins

A

myosins

120
Q

name the motor proteins that are for microtubules

A

kinesins/dyneins

121
Q

describe the structure of myosin

A

helical tail that assembles in a dimer with 4 light chains at the neck

122
Q

what are the light chains in myosins?

A

regulatory subunits

123
Q

myosin II provides what?

A

contraction and movements of actin filaments

124
Q

how does myosin assemble into filaments? what triggers its activation?

A

phosphorylation of myosin light chains activates it, releasing its tail causing a spontaneous self-assembly

125
Q

name the 3 types of actin structures and what Rho protein is associated with each

A
  • filopodia: Cdc42
  • lamellipodia: Rac
  • Stress fibers: Rho
126
Q

what do stress fibers do to the cell? where are they found in the cell

A

stretch the cell (promote contractility); found everywhere in the cell

127
Q

where are lamellipodia mostly found in the cell and what do they do?

A

dense mesh of filaments; enriched at the periphery of the cell;
they are involved in cell MIGRATION

128
Q

where are filopodia found in the cell

A

at the periphery; they extend the membrane

129
Q

what is useful to study actin dynamics in vivo?

A

toxins!

130
Q

name 3 toxins used to study actin dynamics and how each works

A
  • cytochalisin: prevent actin polymerization by binding to the neg barbed end, allowing depolymerization at pointed end
  • phalloidin: binds the side of actin filament and stabilizes them, allowing for visualisation
  • latrunculin: stabilizes actin MONOMERS to block their incorporation
131
Q

what method can be used to visualize actin filaments?

A

indirect immunofluorescence

132
Q

what are the 4 steps of indirect immunofluorescence?

A

1) fix cells with paraformaldehyde 4%
2) permeabilize with mild detergent
3) incubate with primary antibody and secondary antibody coupled to FLUOROPHORE
4) visualize cell with fluorescent miscroscope with excitation/emission filter

133
Q

how do cells attach to the extracellular matrix?

A

actin binds to intergin via adhesion complexes / focal adhesion proteins

134
Q

name the focal adhesion proteins

A

talin, paxillin, vinculin

135
Q

what do integrin bind to on the extracellular side?

A

fibronectin

136
Q

what activated Cdc42, Rac, and Rho in the context of actin filaments / cell migration?

A

Cdc42 and Rac = growth factors
Rho = GPCRs

137
Q

what is p160ROCK?

A

rho-kinase: GTP-Rho binding protein

138
Q

what kind of kinase domain does p160ROCK have?

A

Ser/Thr kinase domain

139
Q

what domains is p160rock made of?

A

Kinase domain, Rho-binding domain, PH domain

140
Q

what is p160ROCK involved in?

A

regulation of smooth muscle contraction, the formation of stress fibers and focal adhesions, neurite retraction, and cytokinesis, etc

141
Q

what domains make up myosin phosphatase?

A

MBS (myosin binding subunit), catalytic domain, regulatory domain

142
Q

what are the effect of myosin phosphatase?

A

dephosphorylatesmyosin, deactivating it and causing the disassembly of actin

143
Q

p160ROCK and MBS are therefore believed to regulate what?

A

the level of MLC phosphorylation cooperatively

144
Q

explain the 3 ways how p160ROCK and Rho-GTP modulates MLC phosphorylation

A

1) p160ROCK directly phosphorylates MLC
2) p160ROCK phosphorylates MLC phosphatase, inhibiting it
3) RhoGTP directly inhibit MLC phosphate

145
Q

what is WAS?

A

Wiskott-Aldrich syndrome protein: x-linked immunodeficiency

146
Q

what are the symptoms of WAS?

A

recurrent infections, hematopoietic malignancies, eczema, thrombocytopenia

147
Q

what is WASP?

A

arp2/3 activator proteins (no catalytic action, but it is a crosslinker scaffold protein)

148
Q

what does WASP bind to?

A

Cdc42 GTPase, Arp2/3, F- and G-actin, PIP2, SH3

149
Q

what is the role of the Arp2/3 complex in Listeria?

A

it activates actin polimerization and bacterial propulsion, and generates new actin filaments

150
Q

how does WASP-N protein get activated and what does it bind to do that?

A

1) binds PIP2 and Cdc42 -> unfolds and gets activated
2) then binds G-actin and Arp2/3

151
Q

name the 3 rho GTPases, what actin filament structure they form via which adaptor proteins

A
  • Rho -> p160ROCK -> MLC phosphorylation -> STRESS FIBERS
  • Cdc42 -> WASP -> Arp2/3 -> FILOPODIA
  • Rac -> WAVE -> Arp2/3 -> LAMELLIPODIA
152
Q

in what part of the cell movement are each rho gtpase involved in?

A
  • Rho = stress fibers = back of the cell
  • Cdc42 = filopodia = cell direction/middle
  • Rac = lamellipodia = forward/cell adhesion
153
Q

in what order do the rhogtpases act in cell movement?

A

1) Cdc42 (cell direction movement)
2) Rac (protrusions)
3) Rho (contraction)

154
Q

how did they do the 2D migration assay?

A
  • stain F-actin
  • stimulate cells with growth factor (rac), GPCR (RhoA), bradykinin (Cdc42)
  • express a GAP in the cells and see which cells stop moving
155
Q

what did they find when using dominant negative GTPases as a tool to determine their functions in signaling pathways?

A

Dominant negative RacN17 but not Cdc42N17 blocks
The ability of the receptor to induce lamellipodia formation

156
Q

explain the GST-pulldown Rho GTPase Activation Assay

A
  • added a GTPase specific effector bound to GST
  • gluthatione beads pulldown
  • western blot with Cdc42 and UNC5 (receptor) antibodies
157
Q

when they added the ligand netrin (UNC5 ligand) what did they find?

A

increase in Cdc42 -> UNC5 activation can modulate Cdc42

158
Q

what is ICY?

A

FRET: intermolecular CFP/YFP reporters

159
Q

using FRET/CFP, they found that UNC5 does what?

A

activate RhoA in cells with neurites

160
Q

basically what are UNC5 receptor activation’s effects on neurite, and it acts via what protein?

A

UNC5 activates Rac1 -> induces neurite formation and extension.
UNC5 activates RhoA -> induces neurite stability

ANAT458 (10 decks)

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