Protein interaction and quaternary structure Flashcards
insulin biosynthesis process begin
single chain formed - pre-proinsulin
insulin biosynthesis in ER
A and B peptide form disulphide bonds forming proinsulin
proinsulin kept linkage between A, B, C peptide due to joining chains
insulin biosynthesis in Golgi
joined chains are removed = only A and B linkage using disulphide bond = insulin
Denature experiment
A and B - form wrong linkage
linkage between A-A or B-B
B with 2 A linked on both sides
protein-protein interaction
transient / stable
system biology V Reductionism - including location and time
genome - DNA
transcriptome - RNA
proteome - protein
metabolome - metabolites
metabolites
sugar nucleotide amino acid lipid all go to phenotype or function
reversible protein modification
addition of:
small chemical groups - e.g. phosphorylation
complex molecules - e.g. sugar - Paul Skipp
polypeptide - e.g. Ub
small molecules like lysine-acetylation (methylation)
for gene expression - able to access DNA
acetylation
opens up DNA allowing transcription factors to access strands
lysine side chain - protein on protein
used to make isopeptide bonds with carboxyl terminus of Ub
proteins can have prosthetic groups
other non-protein molecules can be also conjugated
example of protein having prosthetic groups
glycoprotein with prosthetic group of saccharide
example - immunoglobulin - for antibodies
irreversible modification of amino acid
e.g. deamidation of Asn/Gln
proteolytic cleavage
partially unfolded intermediates
breaking peptide bond
can only be broken by hydrolysis by boiling in 6M acid or alkali
protease can be
indiscriminate or sequence specific
trypsin function
cuts C-terminals to arginine and lysine - useful in proteomics for mass spectroscopy
protein-protein interaction and quaternary structure
proteins form networks and form larger complexes
examples of protein forming networks
monomers, dimer, trimer……oligomer, polymer
homomeric/heteromeric
apoptosis
caspases cleave after Da.aD (aspartic residue)
homomeric
all same subunit
heteromeric
different subunits
example of protein-protein interaction
Haemoglobin
Haemoglobin structure
2 a-globin + 2 b-globin + 4 haem
- heterotetramer or dimer of 2 heterodimers
zymogens
precursors of enzymes - activated in proteolytic cascade after - releases as granules into duodenum
microtubule
heterodimer - a and b tubulin = MT subunit
actin filament formation
turning G-actin into F-actin
G-actin
globular protein
F-actin
fibrous protein
actin (and friends)
central binding molecules for many things
e.g. myosin, cell division etc
proteins interact via
motif or domain
motif
short, usually primary sequence
domain
larger, usually structural
forces/attraction/bonds used for protein-protein interaction
same as observed in tertiary structure
example of interaction
- conformational changes to allow a new site of interaction
- some proteins act as ‘scaffold’ for other to bind onto
- protein can compete for binding sites
- protein can have prosthetic groups
protein examples of interaction
shown how they work and interact
use that knowledge to apply to other interaction
conformational changes to allow new site of interaction example
PKR
PKR
kinase - activated when double stranded RNA is present in cell - usually sign of viral infection
dsRNA
double stranded RNA
dsRNA binding to PKR at inhibitory domain
changes conformation and allows dimerisation and activation of kinase
autophosphorylation of PKR
phosphorylates substrate - switch of general translation
inhibits ability of virus replication
some protein act as ‘scaffold’ for others to bind onto
spatial organisation
colocalisation
scaffold-mediated complex assembly
spatial organisation
compartmentalisation such as mitochondria
colocalisation
bind close to membrane
scaffold-mediated complex assembly
gathering protein - increase efficiency
input - protein phosphorylates/triggers next protein until output
protein compete for binding site example
regulation of elF2E availability for binding ‘scaffold’
when making protein - scaffold protein
type of ‘molecular mimicry’
4E binds to another (scaffolding) protein ( in this example, the elF4G)
inhibitory protein - similar sequence at binding site to scaffolding protein
to stop protein 4E from binding to inhibitory protein
has signalling pathway
kinase phosphorylates inhibitory protein - changes charge and stops el4E from binding to inhibitory and binds to elF4G
unwanted protein-protein interaction
motif/domain recognition is ‘blind’ to rest of protein
not able to recognise some antigens
antibodies - in unwanted protein-protein interaction
antibodies coded to recognise foreign antigens can instead cause autoimmune disease
example of autoimmune disease caused by unwanted protein-protein interaction
multiple sclerosis, Crohn’s, Lupus, Type 1 diabetes
example of excessive protein aggregation - genes containing polyglutamine
Huntington’s disease
genes contains polyglutamine track expansion
translation forms gene contain glutamine track expansion = misfolded protein
forming aggregated protein - gain of function
example of excessive protein aggregation - genes encode wild type protein sequence
Creutzfeldt-Jakob disease
genes encode wild type protein sequence
form protein conformation 1 protein conformation 2
protein conformation 2 cause aggregated protein - gain of function
