Transcript `Protein Nucleic Acid Interactions` lecture

Protein Nucleic Acid Interactions
September 28, 2006
Different types of recognition motifs
1.
2.
3.
4.
5.
6.
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
Dimerization required for full activity
Sequences separated by approximately one
turn of helix
 Major groove contact to DNA
 DNA sometimes bent
Proteins with HTH motif
Cro
 HTH 2nd and 3rd
helix
 17bp operator

 2 fold symmetry
 Recognition helices
34 A apart
 DNA slightly
distorted
434
 4 helix cluster, 2,3
HTH
 34 A between
recognition helices
 Slight distortion
Comparison of 434 and 
 Gln 33 H bonds to backbone
 Gln 44 H bonds to adenine
 Asn 52 H bonds to backbone
Relative orientation is different in
different complexes
2. Homeodomains
 HTH in eukaryotes
 60 amino acids
 Helix-loop-helixturn-helix
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
a)
b)
c)
d)
a
Hormone receptor
Gal4
Loop sheet helix
a. a
 Part of transcription
regulatory proteins
 30 residue motif
coordinating one
zinc via 2 cysteines
and 2 histidines
DNA binding of Zif268
 Monomer
 Major groove
 Finger bind to 3
base pair subsites
Different Zinc finger binding to DNA
 Zn fingers all have
similar structure
 Different contacts to
DNA
 Arginine guanine
contacts are
common
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
 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
 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
 Dimer (homo or
hetero)
 Two a helices
wound around one
another
 Grip DNA like a
clothespin
GCN4
 Yeast transcriptional
activator
 Coiled coil packing
of helices (knobs in
hole)
 homodimer
AP-1 Fos Jun
 heterodimer
5. Winged helix
 Compact a
structure
 2 wings, 3 helices
and 3 strands
 Helix 3 is
recognition helix
HNF 3
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
Beta ribbon proteins
Arc repressor
 Homodimer
 Monomer has pair of
helices connected
by  sheet
  sheet recognizes
bases in major
groove
Integration host factor
 Beta sheets binds in
minor groove
 Pseudosymmetric
 180 degree bend in
DNA
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
http://www.acsu.buffalo.edu/~koudelka/Bio522_coursepage.html
Systematic Studies
Questions
 What features characterize the DNAbinding site of a protein?
 How do proteins induce conformational
changes in the DNA structures they
bind?
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
Dataset Selection
NDB/PDB
Query “Protein/DNA <3.0”
132 Protein-DNA complexes
7 Single Helix
NDB Classification
5 Unclassified
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
Computational analysis of
•
•
•
•
•
•
Size (ASA)
Packing
Polarity
Hydrogen Bonding
Bridging Water Molecules
Residue Propensities
Comparisons of Residue Propensities
2.5
Protein-DNA
Propensity
Propensity
2
All Protein-Protein
1.5
1
0.5
0
ARG LYS ASP GLU ASN GLN SER GLY HIS THR ALA PRO TYR VAL MET CYS LEU PHE ILE TRP
Amino Acids (Hydrophillic --> Hydrophobic)
Protein and DNA Interaction Footprints
Single headed binding proteins
Schematics of Protein-DNA Complexes
Single Headed Proteins
PU 1 ETS-domain
Endonuclease V
P53 Tumor Suppressor
Paired Domain
Protein and DNA Interaction Footprints
Double headed binding proteins
Schematics of Protein-DNA Complexes
Double Headed Proteins
GAL4
CAP
Glucocorticoid
 repressoroperator
MyoD
bHLH
gd resolvase
Bovine
Papillomarvirus
RAP1
IHF
Arc repressoroperator
GCN4-bZIP bound
to ATF/CREB
Metj
PurR
Protein and DNA Interaction
Footprints
Enveloping binding proteins
Schematics of Protein-DNA Complex
NFkB
EcoRV
endonuclease
EcoRI
endonuclease
HhaL
Methyltransferase
Endonuclease
BamHI
Enveloping
Proteins
PvuII
endonuclease
Zif268
Yeast TBP/TATA Hin Recombinase
Zinc Finger
box
Measuring DNA Distortion
(superposition onto canonical B-DNA)
rmsd = 3Å
 repressor
rmsd = 10Å
gd resolvase
rmsd = 22Å
integration host factor
126d
252d
243d
1cgc
1d56
196d
167d
1d23
5dnb
1d65
250d
206l
1d49
1d98
119d
1dn9
1bna
1bdl
1d29
287d
1nfk
194d
1hci
1bhm
1mdy
1pdm
1d66
3mht
2dgc
1glu
1lmb
1tsr
1aay
1igr
1erl
2bop
1pue
1pvl
1rva
1par
1pnv
1oma
1vas
1ytb
1gdt
1ber
1ihf
Distortion in protein-bound and unbound DNA
PDB Code