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