Correlation of DNA structural features with internal dynamics and conformational flexibility

1. Correlation of DNA structural features with internal dynamics and conformational flexibility H. Peter Spielmann University of Kentucky Dept. of Molecular and Cellular Biochemistry

2. 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’

3. Dynamic Processes on the ps-ns Timescale Deoxyribose Re-puckering Phosphate BI - BII Exchange Internal Vibrational Modes

4. What is DNA “Flexibility” 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 (c)

5. Internal Vibrational Modes Order Parameters (S2) Methine 13C Relaxation Modelfree Analysis

6. Methine Carbons in DNA

8. How to Combine Disparate Dynamic Data to Obtain Information on Specific Motional Modes in DNA?

9. 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

10. 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)

11. = No smoothing Effects of Smoothing = 5 ps interval smoothing

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

13. Effect of Smoothing on T8:C1’ Data 2-parameter 4-parameter After Before C(t) C(t) t (ps) t (ps)

14. 5’ 3’ Dynamics Correlations from NMR %BI vs. C1’5’ & %S5’ • Correlations between S2, phosphate population, deoxyribose ring population, helical parameters • Correlations not evident in MD trajectories R2 = 0.79

15. Deformability Sequence (Damage?) Specific Dynamics Relate to Recognition Flexibility Dynamics NMR & MD

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

17. C C C C A A T C G G C C G G T T G G G G G G G G T T G G C C G G T C A A C C C C GT-2 GT-5

18. Normal vs. Mismatch

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

20. 5’-CCATCGCTACC-3’ 3’-GGTAGCGATGG-5’

21. 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

22. Acknowledgements • Richard J. Isaacs • William Rayens • NSF • Kentucky Center for Computational Sciences • NCSA