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 B I - B II Exchange Internal Vibrational Modes

C2’-endoC3’-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 (S 2 ) Methine 13 C 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)

Effects of Smoothing = No smoothing = 5 ps interval smoothing

Computing Dynamics from MD Autocorrelation function: Lipari-Szabo modelfree formalism: Clore et al. extended model:

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 S 2, phosphate population, deoxyribose ring population, helical parameters 3’ 5’ %B I vs. C1’ 5’ & %S 5’ R 2 = 0.79 Correlations not evident in MD trajectories

Dynamics Relate to Recognition FlexibilityDynamics NMR & MD Deformability Sequence (Damage?) Specific

NormalMismatch Biological Relevance MutS: Mismatch Recognition Deformation: -Bend -Compressed, Deepened Major Groove -Widened Minor Groove

CGGCATGCTG CGGCATGCTG GT-2 GT-5 CGGCACGCTG CGGCACGCTG

Normal vs. Mismatch

Major Groove Width (Å) Minor Groove Width (Å) = Normal = Mismatch Groove Widths & Flexibility Mismatched DNA has more flexibility in major groove width

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