dna binding proteins

Question 1

Beta Sheet Saddle

Answer 1

TBP
2 5-stranded beta sheets and 2 helices joined by short loop
Saddle shape
Binds to major groove and bends DNA to 80º
Lys/Arg bind to backbone
Phe bind to bases and bend DNA
Asn/Thr H bond to nucleotides
Bind to TATA box (lots of A and T)
RNA polymerase assembly

Question 2

Helix-turn-Helix

Answer 2

ex. Homeobox
3 alpha helices connected by short loops
1 binds to Major groove
2 stabilize
Binds to 5’ ATTA 3’
Lys/Arg bind to adjacent minor groove phosphates
Transcription promoter

Question 3

Helix & Antiparallel Beta barrel

Answer 3

ex. P53
Forms a tetramer
Monomer has 5 domains
2 are function (TAD,CTD)
1 is tetramerization (OD)
1 Binds DNA
1 apoptosis (PRR)
9-stranded anti beta barrel with long loops ending in alpha helix
Alpha helix in major groove
Arg/lys bind nucleotides
Loops bind backbone
Arc mutations cause cancer
Oncogene
Prevents damaged DNA cells from dividing and triggers apoptosis if it is too damaged

Question 4

Zinc Fingers

Answer 4

Zinc ion coordinated by 2 his and 2 Cys
Alpha helix oriented by zinc coordination
Series of zinc fingers wrap around DNA
Alpha helix in major groove
Bound nucleotides depend on amino acid sequence
Can dimerize to bind
glucocorticoid receptors regulate transcription

Question 5

Leucine Zippers (bZIP)

Answer 5

ex. AP1
2 domains
coiled coil dimerizing domain
Dna binding helix
Choptsticks
Dimerize on either side of DNA
Bind into major groove
Lys/Arg backbone
Asn/Arg nucleotides
AP1 jun fos helices control differentiation,proliferation,apoptosis
oncogene

Question 6

Helix-Loop-Helix

Answer 6

Two helices separated by Loop
one binds to DNA
one dimerizes
Trainer chopsticks
Helices go into major groove
Bind to E-Boxes (CANNTG)
MyoD muscle cell differentiation