Protein Folding Flashcards
How can an increased temperature lead pt protein aggregation?
population of unfolded proteins increases, hydrophobic side chains exposed.
These form one protein come into contact with those from another - high enough [] clumping becomes extensive & protein precipitates.
what is notable about unfolded conformations?
all energetically equivalent.
Give the number of possible conformations for a 100 residue protein?
3 conformations (lowest energy combos of phi and psi). 3e100 = 5 x 10e47
What does the lambda repressor domain show us about 2 state folding?
Gly destabilises alpha helices & replacement with Ala accelerates folding rate by factor of 10.
BUT
Glycine fits into major groove of DNA so optimised for function not speed of folding (interface is too small for larger chains,)
How do the diffusion collision and nucleation condensation models differ?
DC - SS elements form first & then collide with other SS elements forming native stucture. (alpha)
NC - general compaction of proteins leading to nucleation of native secondary and tertiary structure. (beta)
What is a cross beta spine and why does every protein have potential to form them?
B-strands packed so that long axis runs in plane of sheet while individual strands run perpendicular to axis.
B-strands are open structures which can be extended by adding additional strands to edges without limit.
Outline the mechanism of Hsp70.
When ATP bound affinity of peptide for substrate binding domain low.
Substrate binding stimulates ATP hydrolysis (ADP bound substrates trapped).
ADP dissociates & replaced by ATP, PBS opens & substrate can rapidly exchange again.
What is an example of an unfolded protein?
pKID domain of CREB unstructured when free in solution but forms helices when bound to KID - binding domain of CBP.
What is phi value analysis?
Measurement of relative contributions of different residues to free energy of TS.
Captures effects of mutation on F and U rates.
