Chapter 6: protein structure pt. 2 and 3 Flashcards
Protein can be denatured by…
- heating
- Chaotropic agents
proteasome
proteolyzed or refolds misfolded proteins
*only some proteins can be refolded or renatured
chaotropic agents
disrupt interactions that stabilizes tertiary structure
Christian Anfinsen
- Used the correct folded state of RNase A
- denatured RNase A by using urea and beta-mercaptoethanol (reduced disulfide bonds)
- dialyzed out urea and most beta-mercaptoethanol to catalyze formation of correct disulfide bonds
- the RNase regained activity
-showed that primary structures determines tertiary structure
*-delta G=when its in its native state
Energetics of protein folding
the net delta G is negative=slightly favored
-delta G fold = -0.4 KJ/mol AA
-100 AA = -40 KJ/mol
*net energy of stabilization is small
Levinthal’s paradox
-proteins DONT sample all possible folding conformations
-fold by specific pathway
*most proteins fold in less than 10 secs
model of protein folding
- the polypeptide collapses in upon itself due to the hydrophobic effect
- secondary structure forms
*molten globule state: lot of secondary structure and little tertiary structure - tertiary structure begins to form
- then final native state forms
*takes less than 10 secs
Folding Funnel
energy landscape guides protein towards native structure
Folding in Vitro
-easy to fold
-folding by dilution in buffer
Folding in vivo
-difficult to fold
-the cellular environment is crowded so there is a high potential for misfolding and precipitation (aggregation)
Chaperons
-proteins that help other proteins fold in vivo
-also called Heat shock proteins (HSPs) bc they were discovered during HS
*most proteins can fold without chaperons
DnaJ and DnaK
-prevents precipitation/aggregation
-assists folding
-coats the unfolded protein and preventing denaturing/precipitation
GroEL and GroES: info
-also called Hsp60
-large chaperones called chaperonins
-actively fold proteins in prokaryotes, cytosol of eukaryotes, and mitochondria
-GroES: cap that seals unfolded protein from the outside
-GroEL: barrel
GroEL and GroES: mechanism
- protein in the barrel
- cap goes from one side to the other side of barrel?
- then it caps the end of the barrel that the protein went in
- completely folded protein comes out of the barrel
*requires energy from ATP hydrolysis
Protein disulfide isomerase
facilitates formation of correct disulfide bridges
peptidyl proline isomerase
catalyses cis-trans isomerisation of peptide bonds involving proline
How do protein folding diseases occur
-usually misfolded proteins get refolded immediately by a proteasome but sometimes they can accumulate as precipitates which can result in severe, chronic degenerative diseases that affect the brain and CNS
-Disease often occurs when protein with alpha-helix conformation misfolds into a precipitating beta-sheet conformation
*form a common cross-beta helical core filament structure
-leads to aggregation into amyloid fibrils masses which can form amyloid deposits (amyloid plaque) in brain
*can cause neuronal apoptosis
Precipitated proteins are associated with what diseases?
1.Prions related illnesses
- like Transmissible Spongiform
Encephalopathies (TSE’s)
-Bovine Spongiform
Encephalopathy (BSE)/ mad cow’s
disease
- Creutzfeldt-Jakob disease (CJD,
human BSE)
2. Amyloid related illnesses
- Alzheimer’s,
-Parkinson’s
-ALS
What is misfolding caused by
-genetics: through mutations
-transmission: Mad cow disease
protein folding mechanism
- native monomer
- misfolding
- beta-sheet oligomers
- amyloid fibrillar aggregates
prion def
proteinaceous Infectious particle
-infection involves a change of secondary structure and conformation in the protein
*converts from a alpha-helical to beta-sheet conformation
-PrP^C: protease-resistant protein, cellular = normal
-PrP^SC: protease-resistant protein, scrapie = bad prion
*can’t be broken down/ cant be destroyed by autoclave
Kuru
Fore tribe of Papua New Guinea
-prions PrP^SC transmitted by eating dead love ones brain
-kuru stopped dying when cannibalism was stopped
Stanley Pruiser
won nobel prize in medicine for discovering prions
-1st case of infectious agent being a protein ( was not a virus or bacteria)
Chronic Traumatic encephalopathy (CTE)
butting heads caused Tau misfolding (precipitation of beta-sheets)
-Alzheimer’s requires the Tau neuron
p53
tumor suppressor protein that sense damaged DNA sensor and stops them before they grow
-initiates apoptosis
what happens when there is a mutation in p53?
causes misfolding in p53 which leads to unregulated cell growth = cancer
LOOK AT CHAP 6 PT.3 SLIDES FOR STRUCTURES
OKAY
Domains
-independent folding regions within a protein often associated with a certain function
-25-100 AA residues
-connected to each other by loops
-bound by weak interactions between side chains
-fundamental unit of TERTIARY STRUC
*has hydrophobic core
-made of folds???
*in multifunctional enzymes each catalytic activity can be on one of several domains
Interfaces
btwn domains provide crevices, grooves, and pockets that make good binding or catalytic sites
what are the 3 domains of a polypeptide chain?
- regulatory domain
- substrate binding domain
- nucleotide binding domain
4 Protein Classes
- alpha
- beta
- alpha + beta
- alpha/beta: consists of 2 alpha+beta barrel
folds
-combination of secondary structure that form the core of a domain
-made of motifs (supersecondary structure)
EF-hand fold
-Structure: alpha helix; right hand like an L with fingers pointing towards you
*E helix = pointer finger
*F helix = thumb
-found in proteins that bind Ca^2+
Calmodulin
*know structure
- has 4 EF-Hand folds
Zinc Finger
-made with one alpha and one beta strand
-Zinc^2+ in the middle
-Zinc is bonded to cysteine and histidine
Jelly/ Swiss-Barrel Roll Fold
squished antiparallel beta barrel
TIM fold barrel
- alpha/beta barrel
-chicken muscle triose phosphate isomerase
Rossman Fold
-also known as dinucleotide binding fold
-alpha/beta barrel
-can bind NAD+ and ATP
Horseshoe Fold
-alpha/beta
-looks life a horseshoe
-Ribonuclease inhibitor
Quaternary Structure
rotational symmetry
-multisubunit protein display symmetry
-defined as Cn
*C: cyclical
*n: number of subunits
-higher order types: octahedral or tethrehedral etc..
Dihedral symmetry N-fold
it intersects a two-fold rotational symmetry at right angles
