Lecture 12 Flashcards

1
Q

Explain how nAChR’s form and what their role is

A

ACh is secreted by vertebrate pre-synaptic motor neurons which lead to the activation of ion channels called nAChR in post-synaptic muscle cells. nAChR are able to conduct Na which causes depolarization of the cell, leads to an action potential, leads to Ca channels activation/opening, causes an influx of Ca ions, which causes muscle contraction. This is an example of an EPSP.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Discuss the post-synaptic potentials mediated by Cl- channels

A

Kakuza et al discovered a shift in post-synaptic responses in mouse superior olive neurons to the neurotransmitter glycine.
Glycine activates post-synaptic Cl- channels which are also known as glycine receptors.
A developmental shift in the concentration of Cl out vs Cl in causes GABA and Glycine receptors to change from excitatory to inhibitory

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Who is in the Cys-loop family? What are some characteristics of this family?

A

nACh, Glycine, and GABA are all part of the ligand-gated ion channels known as the cys-loop channels.
These channels are pentameric (meaning that they contain 5 protein subunits to make up a channel)
Each subunit contains an extracellular poor loop bearing 2 cysteine amino acids. The cysteine is present so that it can stabilize the loop, hence the name cys-loop channel.
Cys-loop channels can be anionic (GABA, Glycine for Cl-) or they can be cationic (nACh for Na+ and K+)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is biochemical isolation? Give an example?

A

Biochemical isolation is the extraction of desired channel proteins or subunits.
nAChR’s were first isolated from the electric organs of the torpedo ray. The torpedo ray contained modified muscle cells in the electric organs that are packed with cholinergic synapses and nAChR’s. Alpha snake bungarotoxin is a peptide toxin that is known to bind very strongly to nAChR’s. So the used that toxin as bait to fish out all of the nAChR’s from the protein extracts of the electric organs of the torpedo ray. They found that the nAChR’s were composed of 5 proteins: 2 alpha, 1 beta, 1 gamma, and 1 delta.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is sequencing? Give an example

A

Sequencing is the next step for studying ion channel structures. In this step the purified channel proteins/subunits are sequenced, the corresponding mRNA’s are found and then those are also sequenced (very laborious research). They found that the 4 nAChR subunits were very similar in that they each contained 4 TMH’s dubbed M1 to M4, a large extracellular N-terminal loop containing 2 cysteines, an extended intracellular loop between M3 and M4 helices, and lastly an extracellular C-terminus.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Digression on ion channel protein sequencing

A

Ion channel properties arise from the amino acids that are associated with them. Amino acids can be arranged in different sequences to create different secondary structures such as alpha helices, beta sheets, or disordered loops. Amino acids have polar side groups that contribute to either hydrophobicity or hydrophilicity. Lastly, some amino acids have charges, for example glutamic and aspartic acid are negatively charged and histidine, lysine, arginine are positively charged.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What kind of amino acids to TMH’s have?

A

TMH’s contain mostly hydrophobic amino acids.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Digression on ion channel protein sequencing pt 2

A

The secondary structures come together and form tertiary structures, this is the final form of the folded protein/subunit. The tertiary structures come together and form the quaternary structure and this is what the ion channel is. nAChR channel is an example of quaternary structure made up of 5 subunits.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Remember the voltage sensor TMH’s on Nav, Kv, and Cav channels?

A

S4 helices contain hydrophobic amino acids. Positively charged lysine and arginine are crucial for voltage sensing.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Remember the voltage sensor TMH’s on Nav, Kv, and Cav channels?

A

S2-S3 helices contain hydrophobic amino acids. They also contain negatively charged glutamate and aspartate residues that act as counterions to the S4 charges

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

More on sequencing (step 2)

A

Using the deciphered protein sequences, researchers were able to sequence the corresponding mRNA’s. This is a crucial step because it allows you to find out what gene was responsible for coding the ion channel/receptor in question.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Further sequencing and cloning discovered a whole super family of cys-loop channels
(step 2)

A

GABA receptors, glycine receptors, seratonin receptors, invertebrate MOD-1 receptor, glutamate gated receptor, and EXP-1 (GABA) receptor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

GABA Receptor (step 2)

A

anionic (conducts Cl-), found at inhibitory synapse, vertebrates and invertebrates.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Glycine receptor (step 2)

A

anionic, inhibitory synapse, (vertebrates/chordates)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Seratonin receptors (step 2)

A

cationic (Na, Ca), excitatory synapse, vertebrates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

invertebrate MOD-1 receptor (step 2)

A

anionic, invertebrate

17
Q

Glutamate gated receptor (step 2)

A

anionic, invertebrates

18
Q

EXP-1 (GABA) receptor (step 2)

A

cationic, invertebrates

19
Q

How are HEK-293T cells commonly used for ion channel research (step 2)?

A

Human embryonic kidney cells are all one common system.
Gene cDNA is cloned into a DNA plasmid vector bearing a strong mammalian promotor. This vector is then introduced to the HEK-293T cell nuclei (via transfection) which leads to transcription, translation, and channel membrane expression. It is very easy to record HEK-293T cells.

20
Q

How are frog oocytes commonly used for ion channel research (step 2)?

A

Gene cDNA is cloned into a DNA plasmid vector which permits the synthesis of synthetic mRNA (in-vitro). The mRNA is then injected into the isolated frog oocytes, this will express your channel protein. Then, perform patch clamp electrophysiology.

21
Q

Step 4
Mutate coding sequences and the test hypothesis on how amino acids and channel structure affect channel function

A

Mutation studies are mutating/altering amino acid so that you can study:
- channel structure, function, folding, ion selectivity
- channel gating (voltage-gated, ligand-binding, channel inactivation)
- mutations associated with diseases
- binding of drugs to alter/correct channel function (pharmacology)

22
Q

Step 5
What are the different methods that can be use to determine or predict channel structures?

A

x-ray crystallography, high-resolution electron microscopy, cryo-electron microscopy, predict structures with homology modelling, lastly, predict structures de-novo with alpha fold.

23
Q

X-ray crystallography

A

-make a crystal with the protein of choice (can be hard)
-shine an x-ray at the crystal
-using the diffraction pattern predict the structure of the channel
-can produce high resolution images provided that the crystal is of good quality

Problems:
- difficult to make crystals from membrane-spanning proteins that have hydrophobic TMH’s
- can use tricks to crystallize membrane proteins (ex. using antibodies) but these can create artifacts in the structure

24
Q

High-resolution electron microscopy

A
  1. embed proteins of interest in the isolated membrane preparations
  2. take transmission electron microscope images
  3. average single protein images into a consensus structure

Problems:
- more representative of channel structure but it requires fixation
- lower resolution than x-ray crystallography

25
Q

Cryo-electron microscopy

A

-newer iteration of high resolution electron microscopy
-cryogenically freeze the sample before imaging with an electron beam (this helps reduce damage and create a higher quality image)
-structural analysis is similar to that of x-ray crystallography due to lack of chemical fixation
-recent advances have permitted these images to be the same resolution to that of x-ray crystallography
-leading technique because it is able to determine the structure of ion channels and large protein complexes that were not amenable to x-ray crystallography

26
Q

Homology modelling

A

Ex. Phyre2
Use the known structure of a protein to predict the structure of another protein by checking for similarities in amino acid sequences

27
Q

Predict structure de-novo using AlphaFold

A

-Developed by DeepMind (AlphaGo)
-Uses A.I. to accurately predict protein structure directly from user inputted protein sequences

28
Q

Summary of all the steps

A

-These 5 general methods were used to uncover cys-loop receptor structure and function

-Each receptor is made up of 5 subunits, each have a large extracellular domain and 4 TMH’s
-The extracellular loop contains 2 cysteine amino acids linked with a disulfide bond, hence the name cys-loop

29
Q

Describe ion-selectivity in cys-loops receptors

A

-M2 helices line the aqueous pore and interact with permeating ions
-Different M2 sequences create cation or anion selectivity (ex. cationic ACh receptors and anionic Glycine receptors)

30
Q

Describe ligand-binding and channel activation in cys-loop receptors

A

-The outside domain consists of two sets of beta strands arranged in sheets
-Ligand-binding causes a conformational change in these sheets
-Upon ligand-binding, the conformational change are transmitted to the pore-region
-Pore-forming M2 helices move outward, opening the ion-conduction pathway

31
Q

What are gap junctions?

A

-Gap junctions are aqueous conduits between juxtaposed cells
-When enough gap junctions are clustered together, they form electrical synapses
-Electrical synapses allow for graded and action potentials to pass through them
-Gap junctions are formed when two hemi-channels of adjacent cells are brought together

32
Q

What are the three types of hemi-channel genes/subunits?

A

-vertebrates have 20 connexins and 3 pannexins
-invertebrates have >25 innexins
-pannexins and innexins are evolutionarily related
connexins and pannexins/innexins have similar structure but there is no evidence for shared ancestry (could this be because of independent evolution or extreme divergence in protein sequence)

33
Q

Protein complexing and nomenclature

A

6 connexin proteins = 1 connexon hemi-channel
6 pannexin proteins = 1 pannexon hemi-channel
6 innexin proteins = 1 innexon hemi-channel

34
Q

What is the role of connexons?

A

connexons can couple to form gap-junctions in vertebrates

35
Q

What is the role of innexons?

A

innexons can couple to form gap-junctions in invertebrates

36
Q

What is the role of pannexons?

A

pannexons do not form gap junctions
pannexons contain extracellular glycosylation moieties that prevent gap junction formation

37
Q

What are general features of hemi-channels?

A

-Outwardly permeable to ATP (leaks ATP out of the cell)
-Inwardly permeable to dyes such as lucifer yellow and 6-carboxyfluorescin (cells can readily take up external dyes)
-Pore opening can be induced by membrane depolarization
-Pore opening can also be induced by ischemia (low blood supply), mechanical stress, osmotic shock, and cytokines
-Pore closing can be induced by drugs, low cytoplasmic pH, and cytoplasmic kinases

38
Q

Describe the general functions of connexins, pannexins, and innexins as gap junctions?

A

-mediate electrical coupling between cells
-permit the sharing of resources (soluble, membrane impermeable molecules)

39
Q

Describe the general functions of connexins, pannexins, and innexins as hemi-channels

A

-Mediate the release of signaling molecules such as ATP and Glutamate
-Activate ATP-gated cation channels (Purinergic receptors) for cell to cell (paracrine) and self (autocrine) signaling