Post on 03-Jan-2016
transcript
Correlation of DNA structural features with internal
dynamics and conformational flexibility
H. Peter Spielmann
University of Kentucky
Dept. of Molecular and Cellular Biochemistry
Molecular Structure From NMR
• Average inter-atomic distances measured for non-exchangeable hydrogens
Refined solution structure of self-complementary DNA molecule containing G-T mismatches
5’-CCATGCGTGG-3’3’-GGTGCGTACC-5’
Dynamic Processes on the ps-ns Timescale
Deoxyribose Re-puckering
Phosphate BI - BII Exchange
Internal Vibrational Modes
C2’-endo C3’-endo
• Also less well characterized motions• Bases also move, but less than backbone• Spontaneous base pair opening (“breathing”)• Rocking about the glycosidic linkage ()
What is DNA “Flexibility”
Internal Vibrational Modes
Order Parameters (S2)
Methine 13C Relaxation
Modelfree Analysis
Methine Carbons in DNA
How to Combine Disparate Dynamic Data to Obtain Information on Specific Motional Modes in DNA?
Molecular Dynamics Simulation• Newtonian model of a quantized system
• Atomic positions/velocities change in femtosecond steps, based on current velocities and inter-nuclear interactions, dependent on force field equations:
• Parameterized to reproduce experimental measurements of gross structural features
Time-Averaged Restraints
• Different than conventional restraints, in that deviations are allowed as long as the restraint is satisfied on average over a particular time frame (10-50 ps)
r (1/C) e( t t ) /
0
t
r( t ) i d t
1/ i
Effects of Smoothing
= No smoothing
= 5 ps interval smoothing
Computing Dynamics from MD
C(t)P2(( ) ( t)
r 3( )r 3( t)
C(t)S2 (1 Sf2 )e( t / f) (Sf
2 S2 )e( t / s )
C(t)S2 (1 S2 )e( t / e )
• Autocorrelation function:
• Lipari-Szabo modelfree formalism:
• Clore et al. extended model:
0.75
0.8
0.85
0.9
0.95
1
0 500 1000
0.75
0.8
0.85
0.9
0.95
1
0 500 1000
Effect of Smoothing on T8:C1’C(t)
t (ps)
Data 2-parameter 4-parameter
C(t)
t (ps)
Before After
Dynamics Correlations from NMR
• Correlations between S2, phosphate population, deoxyribose ring population, helical parameters
3’
5’
%BI vs. C1’5’ & %S5’
R2 = 0.79• Correlations not
evident in MD trajectories
Dynamics Relate to Recognition
Flexibility DynamicsNMR& MDDeformability
Sequence(Damage?)
Specific
Normal Mismatch
Biological Relevance
MutS:Mismatch
Recognition
Deformation:-Bend-Compressed, Deepened Major Groove-Widened Minor Groove
C G GC A T G C T G
CGG CATGCTG
GT-2
GT-5
C G GC A C G C T G
CGG CACGCTG
Normal vs. Mismatch
Maj
or G
roov
e W
idth
(Å
)
8
10
12
14
16
18
20
C4/T4 G5 C6 G7
Min
or G
roov
e W
idth
(Å
)
4
5
6
7
8
9
10
C4/T4 G5 C6 G7
= Normal
= Mismatch
Groove Widths & Flexibility
Mismatched DNA has more flexibility inmajor groove width
NH
HO
HO OH
NH
N
N
N
O
dR
1R-(-)-cis-anti-benzo[c]phenanthrene-N2-deoxyguanosine adduct
NH
HO
HO OH
NH
N
N
N
O
dR
1S-(+)-cis-anti-benzo[c]phenanthrene-N2-deoxyguanosine adduct
Diasteromeric carcinogen adducts
5’-CCATCGCTACC-3’3’-GGTAGCGATGG-5’
Conclusions
• Mechanical coupling exists in DNA
• Structure and dynamics are related
• Time-averaged restrained MD simulations are more accurate than are unrestrained MD simulations
• Smoothing improves accuracy of tarMD
• tarMD can reveal dynamic features of biological relevance
Acknowledgements
• Richard J. Isaacs
• William Rayens
• NSF
• Kentucky Center for Computational Sciences
• NCSA