Protein DNA Interactions

Question 1

General modes of DNA recognition

Answer 1

-polarity/charge complementarity
a) hydrogen bonds and salt bridges to phosphate groups
b) most DNA-binding proteins have basic DNA binding face

-shape-specific interactions: complementary geometrically to double helix
a) helices in major groove
b) VDW interactions

Question 2

Efficiency in DNA binding

Answer 2

PROBLEM:
-number of residues in globular protein required to cover linear site on DNA is NOT linear

SOLUTION:
-INCREASE contact surface area by “wrapping” or bending DNA around protein surface
-Don’t use globular proteins
-multimerization: use protein dimers, trimers, and tetramers to increase site coverage

Question 3

Oligomers

Answer 3

HOMO(particularly dimers):
-two-fold dimer matches potential two-fold symmetry of DNA –> usually bind inverted repeats
-allows small monomer(less coding DNA) to recognize larger site for “free”
-allows cooperativity in binding and improves affinity

HETERO:
-assembled in different combinations, which allow fewer proteins to recognize a larger number of different DNA sites
-larger surface area on hetero-oligomer –>binds larger site on DNA with greater specificty

Question 4

Common protein-DNA binding molecules

Answer 4

-<100AA structural motifs
-helix-turn-helix
-zinc fingers

NOTE: All have…
-shape complementarity with DNA
-ionic phosphate-backbone binding with Lys/Arg/His
-specific interactions with bases in grooves, primarily with alpha helices in major groove

Question 5

Helix-turn-helix

Answer 5

-20 residues in 2 short alpha-helical segments, each 7-9 residues long separated by a beta-turn

-not stable by itself, usually part of a larger DNA-binding domain

-binds in the major groove

Question 6

Homeodomain

Answer 6

-60 highly-conserved amino acids and 3 alpha-helices within the domain

-common DNA-binding structural motif found in many regulatory proteins

-related to helix-turn-helix motif

Question 7

Zinc finger motif

Answer 7

-~30 residues form an elongated loop held together by Zn2+ ion

-coordinated by 4 residues(4 Cys or 2 Cys and 2 His) and doesn’t interact with DNA but stabilizes the structural motif

-interaction of a single zinc finger with DNA is typically weak

-can also function as RNA-binding motifs

Question 8

Leucine Zipper

Answer 8

-An amphipathic α-helix with a series of hydrophobic amino acid residues on one side forming the hydrophobic interface

-Leu occurs at every 7th position along the α-helices
-Helices form a coiled coil

• Often found in proteins with a separate DNA-binding domain containing a

-high concentration of basic residues that can interact with the DNA
backbone

Question 9

Basic Helix-Loop-Helix

Answer 9

• Conserved 50 amino acids that can form two short, amphipathic α helices
  linked by a loop of variable length
• 2 helix-loop-helix motifs can interact to form dimers

Question 11

RNA Recognition Motif (RMM)

Answer 11

• 90 to 100 amino acids arranged in a 4-strand antiparallel β-sheet
  sandwiched against two α helices (β1 -α1 -β2 -β3 -α2 -β4 )
• Found in some eukaryotic gene activators where they may bind DNA and
  RNA to induce transcription