L4- Ion channel structure and function

What toxin do pufferfish release and what does it block

Tetrodotoxin→ blocks sodium channel

What toxin do deathstalker scorpions release and what does it block

Charybdotoxin (CTX) → is a potassium channel blocker

What toxin do funnel web spiders release and what does it block

W-agatoxin → is a calcium channel blocker

What can the different toxins show

Substrate selectivity → ther are separate pathways for the flux of different ions

Types of gating (3)

• control ion channel opening/closing

• Dynamic control

• Voltage/signal/ligand/ stretch gated

What is gating

Ion channels opening/ closing in response to stimuli

Leak channels

Class of channels that are open all the time at rest

What is the state of channels influenced by

Cell behaviour

Features of voltage gated channels (2)

• if you change the amount of ions at the surface the position of the channel will be altered

• The protein itself has a charged, flexible region that takes different shapes depending on its electric field across the membrane

Features of ligand binding channels (2)

• occurs when ligand binding changes the shape of the protein

• Can distort the protein causing part of the component of the receptor to form a space through which ions can pass through

Features of mechanically gated channels (2)

• occurs when something stresses the cell eg physical movement against receptor, tensing of the cell, osmotic challenge etc

• Forces apart the channel causing stress along the membrane pulling the channel open

What can mutations do

Provide key insights into channel function

Example of mutation that was used to demonstrate channel function

Shaker Sh gene in drosophila → when anaesthetised the leg shakes, when unanaesthetised there is aberrant movements

How can ion channel structure be student (3)

• experimentally

• Computational predictions

• AI

• amino acid sequence

How can looking at the amino acid sequence be beneficial in investigating ion channel structure

Can tell you about specific amino acid side chains which allow you to make predictions about protein structure

What are experimental methods for investigating ion channel structure

• x ray crystallography (standard)

• Electron microscopy (emerging)

Steps of x ray crystallography (6)

• protein

• Crystallised

• X rayed

• Get diffraction patter m

• Get electors denisty map

• Make atomic model

Why are ion channels hard to crystallise (6)

• transmembrane

• Larger proteins

• Multiple conformations

• Multiple subunits

• Dynamic and disordered

• Not very soluble

Which proteins lend themselves to crystallography (2)

• insulin

• Albumin

What does Cryo Em utilise

Many thousands or views of randomly oreintated particles → can create an average of all pictures taken to analyse by using clustering techniques

What is considered the future of protein biology

Alphafold → using protein structure databanks to predict structures using AI

How does alpha fold work (2)

• computer can see thousands of variants of proteins and certain patterns

• Train the computer and then give a specific sequence of amino acids for it to predict the structure of

BK channel

Big potassium channel, a high conductance k+ channel

Ion channel structure

Composed of multiple alpha subunit eg typical K+ channel has 4 homologue domains→> each with 1 voltage sensing and one pore forming domain

What is the main divisions of cell activity determine by CHECK

Charge of residues → an ionic channels are lined with amino acids that are positively charge to encourage negatively charged ions to cross and visa versa

What can single mutations do

Abolish selectivity of ion channels

N type inactivation of channels

• amino acids at the n terminus occlude the intercellular side of the channel pore leading to rapid inactivation

C type channel inactivation (3)

• hinged lid

• Conformational change at the selectivity filter or at the extracellular entrance to the channel pore leading

• Is slow in activation

How can channels influence drug design

Is possible to design different drug to different aged channels/. Proteins