Protein folding and misfolding Flashcards
what is a motif?
A motif is a cluster of conserved residues. Proteins with similar structure/function share similar motifs. Amino acids crucial for protein structure/function are highly conserved across species.
describe three secondary protein structures
α-helix - carbonyl oxygen of residue (i) forms a hydrogen bond with the amide of residue (i+4)
β-sheet - carbonyl oxygen and amide form hydrogen bonds; can be anti/parallel and planar/twisted
β-turn - carbonyl oxygen of residue (i) forms a hydrogen bond with the amide of residue (i+3)
how can disulphide bonds be broken?
using a reducing agent such as mercaptoethanol
what is a β-hairpin?
all-β motif -----> <----- often forms β-sheets if motif is repeated, forms an up-and-down sheet
what is a Greek-key turn?
all-β motif 2 4 four adjacent antiparallel strands 1, 2 and 3 are connected by hairpins 3 and 4 are connected by a longer loop
why is the Greek-key turn motif so common?
perhaps since it is an easily accessible extension of the β-hairpin
what is an EF-hand?
all-α motif
two helices joined together in a fixed conformation
found in calcium-binding proteins
calmodulin has 2 EF-hands, which it wraps around its substrate upon binding
what is a β-sandwich?
all-β motif
two β-sheets held together
found in some immunoglobin-like proteins such as antibodies
eg. Titin - giant muscular protein
give an example of a β-barrel protein
porins are transmembrane proteins with hollow centres through which small molecules can diffuse
how are parallel β-sheets connected to one another?
by a cross-over α-helix
only right-handed β-α-β motifs are observed
what is an intrinsically-disordered protein?
no defined structure
30% of proteins in the human genome are intrinsically disordered
many mediate protein-protein interactions
can gain structure when bound to a target eg. alpha synuclein
what is alpha synuclein?
intrinsically-disordered protein
forms a helical structure at the N-terminus when it interacts with calmodulin
binding to lipid membranes induces structure in the protein
aggregation of alpha synuclein in Parkinson’s disease
explain how GroEL/ES aids protein folding
GroEL/ES is a chaperonin; GroEL is comprised of two seven-membered rings that are stacked
a small, partially-folded protein enters the Gro-EL cage and binds to a hydrophobic surface near the rim
using ATP as an energy source, Gro-ES binds to form a lid, capturing the substrate protein
this causes Gro-EL to double in size and to become a hydrophilic environment, favouring the folding of the captured protein
when ATP is hydrolysed, Gro-ES dissociates and the protein is released
if complete folding was not achieved, the protein may re-enter Gro-EL for another round of folding assistance
what is a chaperonin?
molecular chaperone that can assist in protein folding and assembly
what is RNase A?
ribonuclease A; degrades RNA; held together by four disulphide bonds
what was Anfinsen’s experiment?
Anfinsen added urea and mercaptoethanol to RNase A
the resulting protein was unfolded and catalytically inactive; the disulphide bonds were reduced to cysteine residues
what are the three mechanisms for folding?
framework model, hydrophobic collapse, nucleation-condensation
what is the framework model?
local secondary structures form independently and are assembled
what is hydrophobic collapse?
the formation of a hydrophobic core prior to the formation of secondary and tertiary structures
what is nucleation-condensation?
a nucleus of the structure forms, providing a template on which the rest of the protein folds
what is a trigger factor?
first chaperone to interact with the nascent polypeptide chain
binds at the back of the ribosome exit
forms a protective cavity that allows the protein to fold
what diseases does the aggregation of amyloid fibrils cause?
Alzheimer's disease Parkinson's disease Huntington's disease Prion disease Amyotrophic Lateral Sclerosis (ALS) Systemic amyloidosis
what is an amyloid fibril?
made of different numbers of β-strand protofilaments
protofilaments are twisted around one another
carmelid antibodies (from camels; one domain) inhibit aggregation
what is a serpin?
serine-protease inhibitor
