Model of Interaction of Zinc Finger Protein with DNA

1
Zinc Finger Proteins
Above Structure of the first zinc finger of
Zif268. Residues 13, 15, 16 and 19 are implicated
in DNA recognition, in this case the base triplet
GCG. The zinc ion is in the lower right portion
of the structure and is chelated by two cysteines
and two histidines.
Aparna Agarwal
2
What is a Zinc Finger ?

• In eukaryotes, often complex sets of regulatory
  elements control the initiation of transcription
  of structure genes. Upstream of the RNA
  polymerase II initiation site there are different
  combinations of specific DNA sequences, each of
  which is recognized by a corresponding
  site-specific DNA-binding protein. These protein
  are called transcription factor.
• Transcription factors have two functionally
  different domains, one that binds to specific DNA
  sequences and another that activates
  transcription. And now NMR methods recently have
  been used to determine the 3D structure of these
  motifs zinc fingers, leucine zippers, and
  helix-turn-helix motifs.
• Zinc Finger The zinc finger motif was first
  described in 1985 in the laboratory of Aaron Klug
  at the MRC laboratory of Molecular Biology in
  Cambridge, where it was inferred from an analysis
  of the amino acid sequence of the transcription
  factor TFIIIA from Xenopus laevis

3
Families of the Zinc finger

• 2-Cys-2-His family
• Nuclear hormone receptor DNA-binding domain
• Retroviral zinc finger
• Yeast transcription factor Gla4

4
Zinc Finger Proteins

• Protein(s) which contains at least one
  zinc-finger.
• A small, functional, independently folded domain
  that requires coordination of one or more zinc
  ions to stabilize its structure.
• These proteins use Zinc ions to fold properly
  into "Zn Fingers". Using a series of these
  Fingers, the transcription factor can recoginize
  a specific DNA sequence. So, folding of these
  zinc fingers is important
• Zinc-fingers vary widely in structure, as well as
  in function, which ranges from DNA or RNA binding
  to protein-protein interactions and membrane
  association.

5
Characteristics

• Structure One of the most abundant DNA-binding
  motifs. Proteins may contain more than one finger
  in a single chain each motif consists of 2
  anti-parallel beta-strands followed by an
  alpha-helix. A single zinc ion is tetrahedrally
  coordinated by conserved histidine and cysteine
  residues, stabilising the motif.
• Binding Fingers bind to 3 base-pair sub-sites
  and specific contacts are mediated by amino acids
  in positions -1, 2, 3 and 6 relative to the start
  of the alpha-helix. Contacts mainly involve one
  strand of the DNA. Where proteins contain
  multiple fingers, each finger binds to adjacent
  sub-sites within a larger DNA recognition site
  thus allowing a relatively simple motif to
  specifically bind to a wide range of DNA
  sequences.

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Model of Interaction of Zinc Finger Protein with
DNA
7
Zif268

• A zinc finger protein found in mice (also known
  as Krox-24).
• The crystal structure of a complex formed between
  the DNA and its binding region shows a modular
  pattern of DNA recognition.

8
Structure of Zif268

• The DNA binding portion of Zif268 is a small
  protein (only 90 residues) that contains three
  independent zinc finger domains of 24 residues
  each, connected by three to four amino acid
  linkers.
• Each finger consists of a single a helix joined
  to two strands of antiparallel sheet and held
  together via chelation of a zinc ion (see title
  slide).
• The three zinc fingers bind to three adjacent
  three base sequences on the DNA target.
• Two of the three fingers have highly homologous
  sequences and bind identical three base
  sequences.
• There are four critical residues on the fingers
  that appear to determine this specificity. Any
  time one desires a protein that must bind, in
  part, a GCG sequence, these four residue
  combination will produce a zinc finger domain
  capable of filling that function.

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Prospects

• The nature of protein-DNA interactions is very
  complex, involving subtle changes in the
  conformation and hydration of both molecules
  which make predictive efforts at determining
  specificity quite difficult
• Zinc fingers, especially Zif268, offer tremendous
  possibilities for rapidly developing design
  techniques for producing proteins that could bind
  any desired sequence of DNA.

10
References

• Å. Pavletich et al. (1991), Zinc finger-DNA
  recognition crystal structure of a Zif268-DNA
  complex at 2.1Science, 252, 809-817
• Keating, Amy http//web.mit.edu/biology/www/facul
  tyareas/facresearch/keating.shtmIntroductory talk
  on Protein-Protein interaction
• Shi, Yigong et alDNA unwinding induced by Zinc
  finger protein binding Biochemistry, 1996, 35,
  3845-3848http//biophysics.med.jhu.edu/berglab/pd
  f_files/yg96.pdf
• Web References
• http//us.expasy.org/cgi-bin/get-entries?KWZinc-f
  inger
• http//life.nthu.edu.tw/lablpc/old/ccc/zinc.html
• http//mcdb.colorado.edu/courses/3280/chime/tf3/ri
  ght-b.htm
• http//www.md.huji.ac.il/courses/biomol/Course_200
  2/exercise10.3.html