Lecture 2: Protein folding Flashcards
Three basic types of protein transport mechanisms in eukaryotes
- transmembrane transport (co-translational and post-translations translocation)
- gated transport
- vesicular transport
Endoplasmic Reticulum
- the membrane of the ER is a network of tubes and sacs that is continuous with the nuclear envelope
–> interior is lumen
- Two distinct regions:
1. rough ER (ribosomes on surface)
2. smooth ER (lacks ribosomes)
Rough ER and Co-translational Translocation
- has bound ribosomes, synthesizing proteins into its lumen
–> each growing polypeptide chain conatinas a signal peptide directing it to the ER
–> SRP: this sequence binds to a signal recognition particle that then binds to the receptor of the ER membrane
–> in the RER lumen, proteins are folded and eventually further distributed via vesicular transport
Where does co-translational translocation occur?
Bacteria, Archaea, Eukaryotes?
- cytosol –> ER lumen
Where does post-translational translocation occur?
Eukaryotes? Bacteria?
Eukaryotes: Cytosol –> ER lumen (pulled into compartment of function)
Prokaryotes: cytosol –>extracellular space (pushed into compartment of function)
Structure of mitochondria
- smooth outer membranes
- inner membranes folded into cristae
two compartments of inner membrane:
- intermembrane space
- mitochondrial matrix
Protein transport complexes of outer mitochondrial membrane
- TOM complex
- SAM complex
Inner membrane mitochondrial protein transport complexes
- TIM 23
- TIM 22
- OXA
Translocation from cytosol into matrix space
TOM brings it in to intermembrane space
TIM 23 brings it in to matrix
Translocation from cytosol into outer membrane
TOM and SAM
TOM brings protein into intermembrane space then SAM needles it back into outer mebrane
Translocation from cytosol into inner membrane (without entering matrix)
TOM brings it in
TIM 22 needles it into inner mmebrane
Translocation from cytosol into inner membrane via matrix
TOM, TIM 23, OXA
Tom brings it in to inner membrane space
TIM 23 pulls it to matrix
OXA inserts it into matrix
Gated transport between nucleus and cytosol
- nucleus contains most of the DNA in a eukaryptic cell and is surrounded by a double membrane (nuclear enevelope) with tiny channels (nuclear pores)
- mRNAs and ribosomes are synthesized int he nucleus and exported into the cytoplasm, while materials needed in the nucleus are imported into the nucleus
–> transport of proteins and other large molecules into and out of the nucleus occurs through the nuclear pore complex
–> recognizes a “suitcase” carrying proteins and lets it in (nuclear localization signal)
Vesicular Transport from the ER via the golgi complex to the final destination
- as proteins are synthesized into the ER lumen, they fold into 3-dimensional strucutres and may be modified further
- protein transport is mediated by transport vesicles that bud off the ER and carry their cargo to the golgi complex, where the vesicles fuse and deposit the cargo
–> additional post translational modification steps may occur int he golgi complex
What is the key to ensuring that a cargo protein reaches its target destination?
- ability of membrane attached receprots to recognize certain features of the cargo protein (such as protein modifications)
Summary of vesicular transport from the ER via the Golgi complex to the final destination
- proteins are tagged
- proteins are sorted
- vesicles bud leaving lumen of Golgi (receptor type proteins on both sides of membrane)
- external proteins of vesicle interact with receptors on lysosome
- Fusion and Delivery
Protein Folding: general process
- driven by hydrophobic forces
- initially, regions of secindary structure or other marginally stable native-like mictorstructures (foldons) may form
- followed by folding into super secondary structures via foldon interactions
- folding intermediates are rapidly brought to molten globule states (based on hydrophobic collapse) abd then to a single native comformation (due to thermodynamic constraints)
Protein Folding model
- process can be pictured as a funnel of free energies
- rim at the rop represents many unfolded states
- polypeptides fall down the “wall” of the funnel to ever fewer possibilities and lower energies as they fold
- kind of “out of the blue” as they suddenly result in a functional protein
- lowest energy state is usually most functional
Proteins that facilitate protein folding
- molecular chaperones: heat shock proteins, function in preventing or reversing improper intramolecular or intermolecular protein aggregation
- protein disulfide isomerases: thioredoxins, form or break disulfide bridges of cysteine
- peptidyl propyl cis-trans isomerases: catalyze interconversions of X-pro peptide bonds between their cis and trans conformations. Whether or not proline in cis or trans
Protein aggregates that result from Intramolecular contacts
- folding intermediates
- native states
- partially folded states
Protein aggregates that result from intermolecular contacts
- amorphous aggregates
- oligomers
- amyloid fibrils
what do most human misfolding diseases result from?
- formation of highly ordered protein aggregates
- -> amyloid fibrils or amyloid plaques
Examples of amyloid related human disease
- alzheimers –> amyloid b or Ab peptide
- Parkinsons –> a synuclein
- spongiformencephalopathies –> prion protein
- amylotrophic lateral sclerosis–> superoxide dismutase I
- Huntington’s –> huntingtin with polyQ tracts
- Cataract –> y-crystallins
- Type II Diabetes –> Islet amyloid polypeptide (IAPP)
- Injection localized amyloidosis –> Insulin
Process of cotrasnalational translocation into ER
- translocon initially closed
- GTP on rna polymerase binds receptor on translocon
- translocon opens, RNA has affinity for translocon
- RNA injected
- signal peptidase cleaves signal sequence
TOM
- brings proteins from cytosol into inner membrane space
SAM
- needles proteins into outer membrane from inter membrane space
TIM 23
pulls proteins from inner membrane space into matrix
TIM 22
- needles proteins into inner membrane from intermembrane space
OXA
- needles proteins from matrix into inner membrane
Golgi apparatus
- cis face recieves from ER
- vesicles bud from trans
Molecular chaperones
- unfold misfolded proteins
- help protein get to its native state
Protein disulfide isomerases (PDI)
- interact with cysteine to facilitate formation of disulfide bridges
Peptidyl propyl cis-trans isomerases (PPI)
- interconversion of cis-trans isomers of pro peptide bonds
