DNA - proteins Flashcards
Outline the B form of DNA.
Narrower and more elongated than A
Minor groove hydration favours B form
Base pairs almost perpendicular to helical axis
10 base pairs per turn.!
What are nucleotide edges and why are they significant?
Edges of the grooves are accessible from outside (solvent accessible) which is basis of sequence specific DNA recognition.
Broadly speaking, why does the major groove provide better recognition?
4 stereo chemical groups at edges
Minor has only 3
Are histones completely non-specific?
How do we know restriction endonucleases are specific?
No - they bind flexible AT regions slightly better.
Changing the sequence of DNA by 1 base changes affinity 1 mn fold.
Why is a slower off rate beneficial for specific interactions?
Transcriptional regulators must stay bound long enough to recruit polymerase.
(Opposite for histones - fall off quickly ahead of replication fork rapidly).
What is the 2D diffusion model?
Proteins scan fires quince specific interactions - initially associating via weak electrostatic then ‘lock in’ to high affinity, stable once find target sequence.
What are the other models?
1d diffusion (sliding)
1d hopping (microscopic dissociation and rebinding)
Intersegmental transfer - move from one site to another via looped intermediate.
What is combinatorial screening?
Generate library of compounds by Binding ALA to resin
Vary AAs at defined positions
What did combi screening show regarding zinc fingers?
No linear code for binding site signature
Info such as Arg - guanine pair very frequently found
Outline the structure of TBP
B protein
C terminal is 180 AAs
2 identical symmetrical folds
Each 1/2 has 5 beta strands and two alpha helices.
Form saddle shaped sheet with pair of helices flanking either end and long helices spanning top of sheet.
How does it shape the DNA
Links it via two F residues between first and last base steps of binding site (residues in loops at either end of sheet).
Give an example of a conformational change.
LEF-1
Bonds minor groove - expands to accommodate it
Protein induces 90 bend towards major groove (collapses)
Protein tail positions Lys and Arg sequence - interacts with negative DNA.
