4. The amino acid sequence of several leucine zipper proteins are indicated in the figure below The leucine zipper motif is comprised of a single a-helix. One portion of this ca-helix, termed the leucine zipper domain, homodimerizes with another identical protein and becomes active as a transcription factor. The other major domain is termed the DNA-binding domain, and as its name suggests, this is the part of the cu-helix that interacts with negatively charged DNA. Proteins with leucine zippers are often important transcription factors, or proteins that are involved in stimulating transcription of genetic material into mRNA. Highlighted residues in the figure below are conserved among different proteins and species. (a) Regulatory Source protein Amino acid sequence Connector DNA-binding region Leucine zipper (6 Amino acids) C/EBP DKNS NEY RVRR ERN NI A VRK SRD KA KQRN VET QQ K VLE TSDN DIR KRVE QLs RELDT RG ELT Mamma Jun SQERIKA ERKIRMRN RIAA, SKCRK RKLERI A RILE E KVKTLK AQN SELA STANMLTE QVAQLKQ Fos EERR RIRR IRR ERN KMA A AKCRN RRREL TDTL QAETDQLEDK SALQTE IAN LKEKEK EF Yeast GCN4 PES SDPA AL KRARNTEA AR RS IR ARK LQRMKQ LED K VE E LSKNYHLE NE VA RILK KLvGER Solution Answer: a) every 3rd-4th residue after Leucine is a hydrophobic amino acid i.e alanine, valine, isoleucine, phenylalanine, proline or glycine. other amino acids in this sequence are charged and polar. leucine occur every 7th position and hence followsa \'heptad\' kind of sequence. b) The hydrogen bond in and alpha helix is between the negatively charged amino acid where the N-H forms a hydrogen bond with a O=C at every 3-4 residues ahead in a protein sequence. Therefore evry 3-4 residues will be oppositely charged to facilitate H-Bonding. Amphiphatic helix is a type of helix having both hydrophobic and hydrophilic amino acids on two opposing faces of an alpha helix, an organisation best suited for dimerization. c) the leucine zipper actually works when two alpha helices form a coiled coil like structure dimerizing with the aminoacid back bone. The basic DNA binding elements however still flank from the helix and look like a partially opened zip. Something like this where ---- implies an alpha helix. \\-------- /-------- the side chains of the two helices pack in the holes provided by the hydrophobic amino acids at 3 position . the amino acids, arginine (N) and lysine (K) in the a.a chain have long side chains which help in creating salt bridges between the two helices. since the cytosol is hydrophilic the two alpha chains with hydrophobic side chains are drawn towards each other with nonpolar ends inside the dimerization zone and the polar ends towards the cytosol to faciluate the energetically favourable alignment and position. d) The yellow region has a lot of positively charged amino acids which help in binding to the negatively charged DNA sequence and hence help in DNA binding and sequence recognition and help leucine zippers to function as transcription factors. e) the z.

1. 4. The amino acid sequence of several leucine zipper proteins are indicated in the figure below
The leucine zipper motif is comprised of a single a-helix. One portion of this ca-helix, termed the
leucine zipper domain, homodimerizes with another identical protein and becomes active as a
transcription factor. The other major domain is termed the DNA-binding domain, and as its name
suggests, this is the part of the cu-helix that interacts with negatively charged DNA. Proteins
with leucine zippers are often important transcription factors, or proteins that are involved in
stimulating transcription of genetic material into mRNA. Highlighted residues in the figure
below are conserved among different proteins and species. (a) Regulatory Source protein Amino
acid sequence Connector DNA-binding region Leucine zipper (6 Amino acids) C/EBP DKNS
NEY RVRR ERN NI A VRK SRD KA KQRN VET QQ K VLE TSDN DIR KRVE QLs
RELDT RG ELT Mamma Jun SQERIKA ERKIRMRN RIAA, SKCRK RKLERI A RILE E
KVKTLK AQN SELA STANMLTE QVAQLKQ Fos EERR RIRR IRR ERN KMA A AKCRN
RRREL TDTL QAETDQLEDK SALQTE IAN LKEKEK EF Yeast GCN4 PES SDPA AL
KRARNTEA AR RS IR ARK LQRMKQ LED K VE E LSKNYHLE NE VA RILK KLvGER
Solution
Answer:
a) every 3rd-4th residue after Leucine is a hydrophobic amino acid i.e alanine, valine, isoleucine,
phenylalanine, proline or glycine. other amino acids in this sequence are charged and polar.
leucine occur every 7th position and hence followsa 'heptad' kind of sequence.
b) The hydrogen bond in and alpha helix is between the negatively charged amino acid where the
N-H forms a hydrogen bond with a O=C at every 3-4 residues ahead in a protein sequence.
Therefore evry 3-4 residues will be oppositely charged to facilitate H-Bonding. Amphiphatic
helix is a type of helix having both hydrophobic and hydrophilic amino acids on two opposing
faces of an alpha helix, an organisation best suited for dimerization.
c) the leucine zipper actually works when two alpha helices form a coiled coil like structure
dimerizing with the aminoacid back bone. The basic DNA binding elements however still flank
from the helix and look like a partially opened zip. Something like this where ---- implies an
alpha helix.
--------
/--------
the side chains of the two helices pack in the holes provided by the hydrophobic amino acids at 3
position . the amino acids, arginine (N) and lysine (K) in the a.a chain have long side chains
which help in creating salt bridges between the two helices. since the cytosol is hydrophilic the
two alpha chains with hydrophobic side chains are drawn towards each other with nonpolar ends

2. inside the dimerization zone and the polar ends towards the cytosol to faciluate the energetically
favourable alignment and position.
d) The yellow region has a lot of positively charged amino acids which help in binding to the
negatively charged DNA sequence and hence help in DNA binding and sequence recognition
and help leucine zippers to function as transcription factors.
e) the zipping process can be simplified and elaborated as:
leucine zipper is a motif that facilitates protein-protein interactions
the open flanking region of the zip i.e the basic region binds with the nucleic acid (DNA) while
another ZIP comes and is stabalized by the hydrophic interactions in the core.
this kind of a ZIP protein helps in the transcription of the nuclic acids and act as transcription
factor. facilitating oligomerization on the leucine rich part with other important protein to form a
complete complex.
e)