modeling dna unzipping in the presence of bound proteins
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Modeling DNA unzipping in the presence of DNA binding proteins
Farhat Habib, Dr. Ralf Bundschuh
Department of Physics,
The Ohio State University
Overview
Importance of understanding DNA-protein interactions
Single molecule experimental techniques The problem statement Theory and description of the applied model Results and conclusions Future directions
DNA
Carries genetic information Double stranded polymer
consisting of monomer units called nucleotides
4 nucleotides labeled A, G, C, and T
Basepairing A≡T, G≡C Each strand carries
complete information of the other
Proteins
Most diverse of macromolecules
Intermediaries in most biological reactions
Composed of smaller units called amino acids
Proteins play a vital role in DNA replication, transcription, recombination, repair, and in activating/inhibiting gene expression
Unzipping force analysis of protein association (UFAPA)
Single molecule experiment
Right sensitivity for probing DNA-protein interactions
F ~ 10 – 20 pN Distances ~ nm
Goals
To investigate the limitations of UFAPA The minimum binding energy for which the protein
can be detected Minimum distance between two proteins for which
they can be resolved
Theory and methods We describe the protein-DNA system’s
thermodynamic behavior or properties in terms of the partition function of the system
Model Break the DNA-protein system into two parts
The double stranded (ds)DNA with (or without) proteins
The single stranded (ss)DNA on which force is being applied
Model Partition function for dsDNA
The ssDNA In the highly stretched regime we will operate the
Extended Freely Jointed Chain (EFJC) model is the most accurate one
m
i
iE
N em)(
)(
Where E(i) is the stacking energy of the ith basepair
hRlml ehqR
hCmW pb /2)]([2
);(
R
Model (cont.) The protein
Include protein-DNA interaction by adding the extra free energy due to the presence of the protein at the binding site
Partition function for the entire system
where m0 is the protein binding site To obtain force at a given extension once we
have the partition function, we use
))(1)(;()()( /0
TkE
mNN
BprotemmmWmRZ R
)(log)( RZR
TkRf NB
Minimum protein strength
Top plot shows the force-extension curves from a protein of progressively lower binding energy at same position
Average force = 15.3 pN; Std deviation = 0.7 pN
At less than 10 kJ/mol the peak from the protein is within one standard deviation of the mean
Protein binding energy (kJ/mol)
GC:AT
20 40 60 80
1
2
3
4
25:75
50:5075:25
Cha
nge
in f
orce
(pN
)
30 kJ/mol
1300 1400 1500 1600 1700 1800
15
16
17
R(nm)
Fo
rce
(p
N)
-5 kJ/mol
30 kJ/mol
1300 1400 1500 1600 1700 1800
15
16
17
R(nm)
Fo
rce
(p
N)
-5 kJ/mol
Minimum resolvable distance between two proteins
14001500
1700
1800
50
40
20
10
121416182022
30
1600R(nm)
Prote
in s
epar
atio
n (b
p)
For
ce (
pN)
Averaged minimum resolvable distance
Minimum resolvable distance for pairs of proteins with 3 different relative binding energies
25 50 75 100
10
20
30
40
×2
×1
×½
Binding energy (kJ/mol)
Res
olva
ble
dist
ance
(ba
sepa
irs)
Conclusions and Future Directions We investigate the limits of the UFAPA technique by
considering the protein-DNA system thermodynamically Average force for bare DNA was found to be 15.3 pN with a
standard deviation of 0.7 pN Minimum binding energy for a protein to be detected using
UFAPA in the absence of FEC of bare DNA is around 10 kJ/mol
Minimum resolvable distance between two proteins can be up to 50 basepairs depending on relative protein strengths and the underlying DNA sequence
Future:Consider the kinetics of the process
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