Unwinding Mechanisms Flashcards
What mechanism do SF1 and SF2 helicases use to move along DNA/RNA?
Inchworm mechanism
What mechanism do SF3-6 helicases use to move along DNA/RNA?
Rotary hexomeric ring
What kind of folds do SF1 and SF2 contain?
tandem RecA folds
What kind of folds do SF3-6 helicases contain?
RecA/AAA+ folds
Can SF2-6 helicases move along dsDNA?
Yes
Do SF2-6 helicases move along and unwind dsDNA?
No they move but do not unwind
In the inchworm helicase mechanism which amino acid residues help to co-ordinate Mg2+?
T and D
In the inchworm helicase mechanism which amino acid residue cradles the phosphates of ATP?
K
In the inchworm helicase mechanism which amino acid residue activates water?
E
What is the function of the arginine finger in the inchworm helicase mechanism?
Senses the gamma phosphate and plays a role in controlling relative conformation of C and N core domains
What does Mg2+ co-ordinate in the helicase inchworm mechanism?
the beta and gamma phosphates via charge interaction
Once ATP has been hydrolysed why does the C core motif stretch forwards?
- Gamma phosphate no longer there
- Arg-ATP interaction lost
- Causes change in conformation
What happens to the C core domain once ADP+ Pi diffuse out of the active site?
- ATP can rebind
- C core domain returns to position
How does directionality come about in the helicase inchworm mechanism?
As a result of ATP controlling relative grip of domains on DNA
In the inchworm helicase mechanism in the ATP-free form which core domain has a tighter grip?
The tail domain
In the inchworm helicase mechanism what happens when ATP binds?
- Alters relative affinity of tail and head for DNA
- Tail loses some grip and the head has increased affinity
- Entire tail moves forwards relative to ssDNA
In the inchworm helicase mechanism what happens once ATP has been hydrolysed?
- Head has a loose grip and tail has strong grip
- Head skips forward
In the inchworm helicase mechanism how is the DNA unwound?
The head core domain has a pin attached which acts as a hydrophobic wedge
How does a helicase rotary motor unwind DNA?
One strand of DNA moves through the centre of the ring whilst the other strand is displaced
What is thought to be the benefit of the helicase rotary motor being hexameric?
It gives the helicase high processivity as the helicase is toplogically engaged with one of the strands so it is very difficult for it to fall off
Where does the hexameric helicase bind the DNA bases?
Each subunit binds one DNA base via a central loop
In hexameric helicases which loop has the tightest ATP binding pocket?
The highest loop
In hexameric helicases what is the step size?
1 base per ATP
In hexameric helicases what happens when ATP binds?
Causes DNA binding loop to flip to the top
In hexameric helicases which binding pocket will be the 1st to bind to a new ATP?
The most empty
In hexameric helicases why do DNA binding loops flip to the top of the subunit?
In order to anticipate binding at the next nucleobase
In hexameric helicases why when one subunit flips to the top of each subunit does every other subunit have to push down a little?
Because all loops are allosterically coupled
