macromolecular interactions II

Question 1

what is the structure of a leucine zipper?

Answer 1

30-40 AAs with a leucine at every 7th residue. the zipper region forms an amphipathic a-helix with the leucines and hydrophobic residues arranged on one surface to form a basic region

Question 2

what is the leucine zipper characterised by?

Answer 2

a basic region responsible for contacting DNA but only after dimerisation via the leucine zipper

Question 3

which part of the DNA does the leucine zipper contact?

Answer 3

basic a-helices fit into major groove

Question 4

describe the structure of the homeodomain

Answer 4

globular, contains 3 a-helical regions. helix 3 contains one side with hydrohobic, which is packed against H1 + 2 to form a hydrophobic interior. the other face of H3 is hydrophilic and fits into the major groove of the DNA backbone

Question 5

which is the recognition helix in the homeodomain?

Answer 5

helix 3, which is aligned into the major groove by specific amino acids to allow base-specific interactions to occur

Question 6

what is structurally common amongst zinc finger proteins?

Answer 6

zinc is a flexible scaffold, stabilising the protein. they all achieve DNA recognition via an exposed a-helix that fits into the major groove

Question 7

why does oestrogen receptor contain zinc?

Answer 7

despite an abundance of cysteine residues, cannot form disulphide bonds due to reducing environment in the cell. the metal ion replaces the structural effect of the disulphide bonds

Question 8

what does the presence of water molecules on the surface of oestrogen receptor tell you?

Answer 8

binding is dominated by enthalpic contribution of interactions rather than increase in entropy via displacement of water

Question 9

what is the importance of recognition helix and inter-helix loop in the engrailed homeodomain?

Answer 9

rich in arginine and lysine, which form hydrogen bonds to the DNA backbone. the loop extends to allow interaction with arginine side chains in the minor groove. facilitating binding to major groove

Question 10

what is the purpose of tandem repeats in zinc-binding recognition motifs?

Answer 10

allow DNA interactions with more sequence

Question 11

why might side chains not always make ordered hydrogen bonds with the phosphate backbone?

Answer 11

the charge is spread across the whole DNA molecule

Question 12

how does the CAP activator bend DNA?

Answer 12

a base step - alternating purines and pyrimidines are easy to bend

Question 13

how does TBP cause a sharp bend in DNA?

Answer 13

distorts DNA by forcing 3 phenylalanines into the minor groove

Question 14

why must the nucleosome be basic?

Answer 14

must bind and distort DNA

Question 15

what dictates selectivity of nucleosome binding?

Answer 15

flexibility of the DNA sequence

Question 16

what is the advantage of a DNA binding protein e.g. zinc finger that is rigid?

Answer 16

slots into the DNA with less entropic cost compared to rigidifying

Question 17

describe the structure of the oestrogen receptor

Answer 17

2 zinc binding domains and many cysteine residues, it binds as a dimer, with the helices in the major groove.

Question 18

what is the advantage of oestrogen receptor containing zinc?

Answer 18

as the cell is a reducing environment, disulphide bonds cannot form between cysteine residues, the metal ion replaces this

Question 19

what does the presence of water molecules at the interface tell us about oestrogen receptor?

Answer 19

binding is dominated by enthalpic contribution of interactions

Question 20

describe the structure of the TAL effector

Answer 20

there is a central region of tandem 33-35 residue repeats, with each repeat encoding a single DNA base in the TALE binding site. within each repeat, residue 13 contacts the DNA base. other regions make contact with the DNA backbone, stabilising interactions

Question 21

what is meant by the ‘combinatory nature’ of transcription factors?

Answer 21

multiple cooperate to generate specificity

Question 22

what is inferred by the presence of water molecules on the surface?

Answer 22

there is no entropic gain by displacing them

Question 23

what does the absence of water molecules on the surface suggest?

Answer 23

the ligand forms tighter hydrogen bonds and electrostatic interactions