Protein folding and misfolding

Question 1

what is a motif?

Answer 1

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.

Question 2

describe three secondary protein structures

Answer 2

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)

Question 3

how can disulphide bonds be broken?

Answer 3

using a reducing agent such as mercaptoethanol

Question 4

what is a β-hairpin?

Answer 4

all-β motif
----->
<-----
often forms β-sheets
if motif is repeated, forms an up-and-down sheet

Question 5

what is a Greek-key turn?

Answer 5

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

Question 6

why is the Greek-key turn motif so common?

Answer 6

perhaps since it is an easily accessible extension of the β-hairpin

Question 7

what is an EF-hand?

Answer 7

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

Question 8

what is a β-sandwich?

Answer 8

all-β motif
two β-sheets held together
found in some immunoglobin-like proteins such as antibodies
eg. Titin - giant muscular protein

Question 9

give an example of a β-barrel protein

Answer 9

porins are transmembrane proteins with hollow centres through which small molecules can diffuse

Question 10

how are parallel β-sheets connected to one another?

Answer 10

by a cross-over α-helix

only right-handed β-α-β motifs are observed

Question 11

what is an intrinsically-disordered protein?

Answer 11

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

Question 12

what is alpha synuclein?

Answer 12

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

Question 13

explain how GroEL/ES aids protein folding

Answer 13

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

Question 14

what is a chaperonin?

Answer 14

molecular chaperone that can assist in protein folding and assembly

Question 15

what is RNase A?

Answer 15

ribonuclease A; degrades RNA; held together by four disulphide bonds

Question 16

what was Anfinsen’s experiment?

Answer 16

Anfinsen added urea and mercaptoethanol to RNase A

the resulting protein was unfolded and catalytically inactive; the disulphide bonds were reduced to cysteine residues

Question 17

what are the three mechanisms for folding?

Answer 17

framework model, hydrophobic collapse, nucleation-condensation

Question 18

what is the framework model?

Answer 18

local secondary structures form independently and are assembled

Question 19

what is hydrophobic collapse?

Answer 19

the formation of a hydrophobic core prior to the formation of secondary and tertiary structures

Question 20

what is nucleation-condensation?

Answer 20

a nucleus of the structure forms, providing a template on which the rest of the protein folds

Question 21

what is a trigger factor?

Answer 21

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

Question 22

what diseases does the aggregation of amyloid fibrils cause?

Answer 22

Alzheimer's disease
Parkinson's disease
Huntington's disease
Prion disease
Amyotrophic Lateral Sclerosis (ALS)
Systemic amyloidosis

Question 23

what is an amyloid fibril?

Answer 23

made of different numbers of β-strand protofilaments
protofilaments are twisted around one another
carmelid antibodies (from camels; one domain) inhibit aggregation

Question 24

what is a serpin?

Answer 24

serine-protease inhibitor