Download DNA Structure and Protein

DNA Structure and Protein-DNA Interactions
siRNA
BINF6101/8101 Lecture 9
DNA Double Helix Structure
DNA double helix structure is stabilized by two major factors:
“base pairing” and “base stacking”
Base Stacking
The term “stacking” is normally related to π stacking (π-π interactions between
aromatic moieties), which represents the attractive, noncovalent interactions
between aromatic rings. Base stacking is considered the main stabilizing factor
in the DNA duplex.
http://www.chem.ucla.edu/harding/IGOC/
Yakovchuk et al NAR 34 (2): 564-574
DNA Double Helix Structure: base stacking
Forces: a combination
of non-covalent forces
-VDW dispersive force
-electrostatic effect
-hydrophobic
Phys. Chem. Chem. Phys., 2014, 16, 3238-3253
Intercalating Agent
Ethidium bromide (EB)
intercalating agent
Functions of DNA-binding Proteins
Protein-DNA Interaction Energies
Hydrogen-bonding Atoms
http://www.cryst.bbk.ac.uk/PPS2/course/section7/os_hres.gif
H-bonding to DNA Base Edges
Spatial Distribution of H-bonding Atoms Around Bases
Luscombe N M et al. Nucl. Acids Res. 2001;29:2860-2874
Schematic Diagrams of Bidentate Interactions
bidentate interactions: there are
two or more hydrogen bonds with
a base or base pair.
Luscombe N M et al. Nucl. Acids Res. 2001;29:2860-2874
Schematic Diagrams of Complex Interactions
complex bonds: an
amino acid interacts
with more than one
base step
simultaneously.
Luscombe N M et al. Nucl. Acids Res. 2001;29:2860-2874
Distributions of VDW-contacting Atoms Around Bases
Luscombe N M et al. Nucl. Acids Res. 2001;29:2860-2874
The Three Structures of Double Helical DNA
Protein-DNA Binding Specificity
DNA Sequence Motifs
Transcription factor, Rox1
Binding site sequence alignment
Consensus sequence
J
J
I i = log 2 (J) + ∑ pij log 2 ( pij ) = 2 +∑ pij log 2 ( pij )
j=1
j=1
D’haeseleer, Nature Biotechnology, 24, 423 – 425, 2006
IUPAC Nucleotide Code
Binding Affinity vs. Binding Specificity
Simple Code?----NO
Protein-DNA Binding Specificity
Direct readout
Indirect readout
Different DNA Shapes
Structural Features for Protein-DNA Binding Specificity
Distribution of Binding Residues
Corona, RI. Guo, J-T. Proteins: Structure, Function, and Bioinformatics, 2016
Protein-DNA Binding Specificity
-Amino acids that can form hydrogen bonds are enriched in specific protein-DNA interactions.
-Tyrosine is enriched in specific interactions.
Corona, RI. Guo, J-T. Proteins: Structure, Function, and Bioinformatics, 2016
Protein-DNA Contacts
Highly specific and multi-specific DNA binding proteins have more base contacts
Corona, RI. Guo, J-T. Proteins: Structure, Function, and Bioinformatics, 2016
Protein-DNA Contacts
Corona, RI. Guo, J-T. Proteins: Structure, Function, and Bioinformatics, 2016
Protein-DNA Contacts
Corona, RI. Guo, J-T. Proteins: Structure, Function, and Bioinformatics, 2016
Hydrogen Bonds between Protein and DNA
Corona, RI. Guo, J-T. Proteins: Structure, Function, and Bioinformatics, 2016
Hydrogen Bonds Between Asp/Glu and DNA
http://bioweb.uwlax.edu/
DNA Shape Features
DNA Shape Features
Dynamic Features in Protein-DNA Interactions
RMSD: root mean square deviation
Song, W. and Guo, J-T. Journal of Biomolecular Structure & Dynamics, 2015
Comparison of Dynamic Features
Conformational diversity of
apo Structures
Conformational differences after
binding to DNA
Corona, RI. Guo, J-T. Proteins: Structure, Function, and Bioinformatics, 2
Comparison of the Wild-type and Mutant Arc Structures
-The wild-type and the
mutant structures are
highly similar.
-The mutant has much
lower DNA binding
specificity, why?
Superimposition of the protein and DNA backbones from the protein-DNA cocrystal
structures of wild-type Arc (yellow) and the FV10 mutant (orange).
Schildbach J F et al. PNAS 1999;96:811-817
Protein and Protein-DNA Complex Structures
Song, W. and Guo, J-T. Journal of Biomolecular Structure & Dynamics, 2015
Molecular Dynamics (MD) Simulations
GROMACS,
at 298K, 1bar, NPT,
all-atom force field Charmm27,
Tip3p water
NaCl, 100mM
Time step: 2fs
Save a conformation every 10ps
Modeller, for modeling the
structures of missing residues
Song, W. and Guo, J-T. Journal of Biomolecular Structure & Dynamics, 2015
Structural Fluctuations of Residues 7-14
N11
R13
Check both Cα and Cβ positions
Song, W. and Guo, J-T. Journal of Biomolecular Structure & Dynamics, 2015
Q9
Structural Fluctuations of Residues 7-14
CV
Wildtype
FV10
mutant
A
0.23
0.15
B
0.17
0.19
C
0.18
0.10
D
0.15
0.19
* Unbound wild-type Arc is
more flexible than the FV10
mutant.
H-bonds Between Protein and DNA
-H-bonds are the
major contributor to
protein-DNA binding
specificity
-9000 snapshots
-Wild-type Arc forms
more H-bonds with
cognate DNA
H-bonds within Arc Dimers
***More H-bonds in both unbound
and bound FV10 mutant structures
than the wild-type Arc.
Song, W. and Guo, J-T. Journal of Biomolecular Structure & Dynamics, 2015
Different H-bond Formations between WT and Mutant
Wild-type
FV10 mutant