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Protein Nucleic Acid Interactions. September 28, 2006. Different types of recognition motifs. Helix turn helix Homeodomains Zinc finger Leucine zipper Winged helix Beta ribbon. 1. Helix turn helix HTH. Most common DNA binding motif Procaryotes Found in hundreds of DNA binding proteins

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different types of recognition motifs
Different types of recognition motifs
  • Helix turn helix
  • Homeodomains
  • Zinc finger
  • Leucine zipper
  • Winged helix
  • Beta ribbon
1 helix turn helix hth
1. Helix turn helixHTH
  • Most common DNA binding motif
  • Procaryotes
  • Found in hundreds of DNA binding proteins
  • Dimerization required for full activity
  • Sequences separated by approximately one turn of helix
  • Major groove contact to DNA
  • DNA sometimes bent
slide6
Cro
  • HTH 2nd and 3rd helix
  • 17bp operator
slide7
  • 2 fold symmetry
  • Recognition helices 34 A apart
  • DNA slightly distorted
slide8
434
  • 4 helix cluster, 2,3 HTH
  • 34 A between recognition helices
  • Slight distortion
comparison of 434 and
Comparison of 434 and 
  • Gln 33 H bonds to backbone
  • Gln 44 H bonds to adenine
  • Asn 52 H bonds to backbone
2 homeodomains
2. Homeodomains
  • HTH in eukaryotes
  • 60 amino acids
  • Helix-loop-helix-turn-helix
dna binding
DNA Binding
  • Helix 2 and 3 similar to HTH
  • Recognition helix (3) makes key contacts with major groove
  • Flexible arm in helix 1 contacts minor groove
3 zinc finger
3. Zinc Finger
  • 
  • Hormone receptor
  • Gal4
  • Loop sheet helix
slide14
a. 
  • Part of transcription regulatory proteins
  • 30 residue motif coordinating one zinc via 2 cysteines and 2 histidines
dna binding of zif268
DNA binding of Zif268
  • Monomer
  • Major groove
  • Finger bind to 3 base pair subsites
different zinc finger binding to dna
Different Zinc finger binding to DNA
  • Zn fingers all have similar structure
  • Different contacts to DNA
  • Arginine guanine contacts are common
b hormone receptor
b. Hormone receptor
  • Pseudosymmetric homo or heterodimer
  • 2 Zn coordinating modules
    • 1 Zn stabilizes DNA recognition helix, other Zn involved in dimer formation
  • Zn coordinated by 4 cysteines
  • Major groove contacts
c gal4
c. Gal4
  • Found in yeast transcriptional activators
  • 65 residue regions binds as dimer (C terminus)
  • 2 Zn coordinated by 6 cysteines (N terminus)
  • Major groove binder
d loop sheet helix
d. Loop sheet helix
  • P53-transcriptional activator involved in tumor suppression
  • Zn coordinated by 3 cysteines and a histidine
  • Tetramer-5bp recognition helix one after another
  • Helix in major groove, loop in minor groove
4 leucine zipper
4. Leucine zipper
  • Dimer (homo or hetero)
  • Two a helices wound around one another
  • Grip DNA like a clothespin
slide21
GCN4
  • Yeast transcriptional activator
  • Coiled coil packing of helices (knobs in hole)
  • homodimer
ap 1 fos jun
AP-1 Fos Jun
  • heterodimer
5 winged helix
5. Winged helix
  • Compact  structure
  • 2 wings, 3 helices and 3 strands
  • Helix 3 is recognition helix
6 beta ribbon group proteins
6. Beta ribbon group proteins
  • Bind via  structures
  • Major groove binding in ribbon helix helix family
  • Minor groove binding in DNA benders and TATA box binding proteins
arc repressor
Arc repressor
  • Homodimer
  • Monomer has pair of helices connected by  sheet
  •  sheet recognizes bases in major groove
integration host factor
Integration host factor
  • Beta sheets binds in minor groove
  • Pseudosymmetric
  • 180 degree bend in DNA
tata binding protein
TATA binding protein
  • Specifically recognize AT rich DNA seqeunces
  • 8 stranded  sheet binds to DNA
  • Hydrophobic side chains intercalate in minor groove
  • DNA kinked
references
References

http://www.acsu.buffalo.edu/~koudelka/Bio522_coursepage.html

questions
Questions
  • What features characterize the DNA-binding site of a protein?
  • How do proteins induce conformational changes in the DNA structures they bind?
datasets
Datasets
  • Two datasets selected from the NDB/PDB
      • 21 B-DNA structures
          • uncomplexed
          • unmodified
          • resolution range 1.4 Å-2.5Å
      • 26 protein-DNA complexes
slide34

Dataset Selection

NDB/PDB

Query “Protein/DNA <3.0”

132 Protein-DNA complexes

5 Unclassified

7 Single Helix

NDB Classification

3 Quadruple Helix

117 Double Helix

Full atom records

110 Protein-DNA complexes

Pairwise structure comparisons using SSAP

110 Protein-DNA complexes

grouped in 26 protein structure families

Select family representative

26 Protein-DNA complexes

nonhomologous by protein

dna binding sites on proteins
DNA-Binding Sites on Proteins

Computational analysis of

  • Size (ASA)
  • Packing
  • Polarity
  • Hydrogen Bonding
  • Bridging Water Molecules
  • Residue Propensities
protein and dna interaction footprints
Protein and DNA Interaction Footprints

Single headed binding proteins

slide38

Schematics of Protein-DNA Complexes

Single Headed Proteins

PU 1 ETS-domain

Endonuclease V

P53 Tumor Suppressor

Paired Domain

protein and dna interaction footprints1
Protein and DNA Interaction Footprints

Double headed binding proteins

schematics of protein dna complexes
Schematics of Protein-DNA Complexes

Double Headed Proteins

MyoD

bHLH

GCN4-bZIP bound to ATF/CREB

l repressor-

operator

GAL4

CAP

Glucocorticoid

PurR

Bovine

Papillomarvirus

Arc repressor-

operator

gd resolvase

RAP1

IHF

Metj

protein and dna interaction footprints2
Protein and DNA Interaction Footprints

Enveloping binding proteins

schematics of protein dna complex
Schematics of Protein-DNA Complex

EcoRV

endonuclease

EcoRI

endonuclease

HhaL

Methyltransferase

Endonuclease

BamHI

NFkB

Enveloping

Proteins

Zif268

Zinc Finger

PvuII

endonuclease

Yeast TBP/TATA

box

Hin Recombinase

slide43

Measuring DNA Distortion

(superposition onto canonical B-DNA)

rmsd = 3Å

rmsd = 10Å

rmsd = 22Å

 repressor

 resolvase

integration host factor

slide44

1ihf

1erl

1tsr

1igr

206l

1hci

1pvl

1bdl

1nfk

1glu

1rva

1ytb

1par

1gdt

1ber

1d29

1aay

1vas

1pnv

126d

252d

243d

1cgc

1d56

196d

167d

1d23

1d65

250d

1d49

1d98

119d

287d

194d

1d66

1dn9

1bna

2dgc

1pue

1lmb

5dnb

2bop

3mht

1oma

1mdy

1bhm

1pdm

Distortion in protein-bound and unbound DNA

RMSD DNA fitted to 40bp B-DNA

PDB Code