Protein Folding Flashcards
Central dogma of biology
DNA > RNA by transcription using RNA polymerase > protein by translation using ribosomes
what are proteins and what do they do?
muscle contraction
fight infection
control glucose levels
they are nanomachines that do everything in and out of our cells
when can disease result?
disease can result from absent, abundant, inactive, overactive, mis-located or malfunctioning proteins
ATP synthase
made of protein molecular motor found in the mitochondria responsible for making ATP rotation of a turbine synthesises ATP 2 motors
making functional proteins
all stages need to be error free
DNA - no mutations
RNA - transcription without error
Protein - need to be translated, folded and located in the correct part of the cell or outside
protein synthesis at ribosome
ribosomes read mRNA and assemble a chain of amino acids, joined by peptide bonds .
A specific tRNA binds each triplet of RNA bases, leaving behind the amino acids for which they code
what is protein folding
formation of tertiary structure
primary structure of protein
string of amino acid
secondary structure of proteins
alpha helices and beta pleated sheets
tertiary structure of proteins
functional domains, protein folding
what bonds forming during secondary protein structure
hydrogen bonds between carbonyl and amino groups of the amino acids
what bonds forming during tertiary protein structure
basic and acidic R groups polarise and become attracted to each other forming ionic bonds
hydrogen bons
covalent bonds between certain R groups
polar forces between hydrophilic and hydrophobic R groups
how many different amino acids are there?
20
what are the categories of amino acids?
nonpolar, aliphatic R groups polar uncharged R groups \+ charged R groups - charged R groups nonpolar aromatic R groups
what determines protein folding/ its 3D protein structure?
amino acid sequence
charged side chains
hydrophobic side chains
hydrogen bonding between side chains\chaperone proteins help the protein fold by holding nascent/ developing chains
how can the 3D structure of a protein be determined?
using computer simulations
it can help identify the function of new genes and design drugs
membrane proteins
carry out most membrane functions
examples of membrane proteins
enzymes - adenyl cyclase
receptors - EGFR
anchors - integrins
transporters - CFTR -
CFTR
a chloride transporter membrane protein
making membrane proteins
they enter the membrane at their site of synthesis - endoplasmic reticulum and fold in the membrane because their transmembrane domains are lipid soluble
CFTR synthesis
transcription translation and protein folding post-translational modification protein trafficking surface expression
Quality control of CFTR synthesis
cells have inbuilt quality control mechanism to deal with misfolded and aggregated proteins
for membrane proteins like CFTR this control process happens in the ER
if a protein is misfolded but salvageable then it will be refolded by chaperones in the ER
if a protein is terminally misfolded it is passed back through the ER membrane into the cytoplasm where it is degraded by protease enzymes
how are membrane proteins made?
nascent chain - new chain
first few amino acids are signal sequence which is recognised by signal recognition particle which takes the new chain and ribosome to the membrane of the ER. It finds a signal recognition receptor which the particle binds to. This is next to a translocon.
Translation
inserted through membrane of ER and winds its way in and out of the membrane
Translocon helps the protein stay in the membrane domain
what is a translocon?
protein pore in ER membrane through which proteins are synthesised.
Ribosome sits on top of it and the new protein chain is inserted
CFTR
1480 amino acids and 12 alpha helices that cross the membrane. It has globular domains on the inside of the membrane
protein trafficking
from ER through ER golgi complex to golgi to plasma membrane
back from membrane through endosome and degraded by lysosome
class 1 CFTR mutations
no functional CFTR protein
class 2 CFTR mutations
CFTR trafficking defect
class 3 CFTR mutations
defective channel regulation
class 4 CFTR mutations
decreased channel conductance
class 5 CFTR mutations
reduced synthesis of CFTR
class 6 CFTR mutations
decreased CFTR stability
p.Phe508del CFTR mutation
most common cause of CF
deletion of 3 DNA bases which results in a missing phenylalanine amino acid at position 508 in the protein
just one missing F results in a protein that cannot fold correctly
the misfolded CFTR is recognised by the cell’s quality control machinery and help in the ER and is then degraded
membrane protein quality control
chaperone proteins like Bip and calnexin are in the ER to hold back misfolded proteins
CF treatment
bronchodilators antibiotics corticosteroids pulmozyme insulin biphosponates vaccinations/ flu jab nutrition physio airway clearance lung transplantation only treats the symptoms
fixing the defective CFTR protein
for treating type 3 or 4 mutations where there is a reduction in protein function potentiators can be given
when there is a reduction in the amount of the protein - type 1,2,5,6 correctors and production correctors can be given
what do potentiators do?
increase the function of CFTR channels on the cell surface
what do correctors do?
improve the processing and delivery of functional CFTR protein to the cell surface. Increases the amount of CFTR protein at the cell surface and increases ion transport
what do production correctors do?
AKA read through agents
they promote the read-through of premature termination codons in CFTR mRNA
Ivacaftor
Kaleydeco
VX-770
a potentiator
Clinical effects of Ivacaftor
(10%) increase in FEV1 weight gain decreased pulmonary exacerbations decreased sweat chloride concentration decreased endobronchial colonisation with P.aeruginosa
who can ivacaftor be used on
patients with at least 1 class 3 CFTR mutation
who is kaleydeco available for?
people in the UK with CF over the age of 6 months with 1 of 9 gating mutations and to over 18s with another mutation
targeting the p.Phe508del mutation
lumicaftor
lumicaftor
corrector
targets p.Phe508del CFTR proteins
what does lumicaftor do?
increases the number of CFTR proteins that are trafficked to the cell surface
clinical effects of lumicaftor
excellent results in vitro
improved function of sweat duct but no improvement in lung function
ivacaftor and lumicaftor
Orkambi
suggested that CFTR needed a combination of lumicaftor and ivacaftor to get the CFTR to the cell surface and to facilitate channel opening and closing.
Orkambi
was clinically effective
reduced pulmonary exacerbations
increased BMI
increased FEV1
other diseases caused by protein misfolding
alzheimer’s
parkinsons
alzheimer’s
results from a build up of protein aggregates in the brain
treating alzheimer’s
there is no cure
treatment with acetylcholinesterase inhibitors reduces symptoms
prevents acetylcholinesterase from breaking down acetylcholine in the brain increasing the concentration of acetylcholine leading to increased communication between nerve cells
this temporarily alleviates ir stabilises symptoms of alzheimer’s
Mad cow disease
variant CJD
caused by build up of protein aggregates. There is an infectious prion protein which are indestructible and so can be passed on through eating infected meat despite being cooked
prion proteins
infection causes other prion proteins to fold in the same way, causing aggregates
