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Correlation of DNA structural features with internal dynamics and conformational flexibility H. Peter Spielmann University of Kentucky Dept. of Molecular and Cellular Biochemistry
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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’
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Dynamic Processes on the ps-ns Timescale Deoxyribose Re-puckering Phosphate B I - B II Exchange Internal Vibrational Modes
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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”
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Internal Vibrational Modes Order Parameters (S 2 ) Methine 13 C Relaxation Modelfree Analysis
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Methine Carbons in DNA
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How to Combine Disparate Dynamic Data to Obtain Information on Specific Motional Modes in DNA?
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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
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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)
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Effects of Smoothing = No smoothing = 5 ps interval smoothing
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Computing Dynamics from MD Autocorrelation function: Lipari-Szabo modelfree formalism: Clore et al. extended model:
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Effect of Smoothing on T8:C1’ C(t) t (ps) Data 2-parameter 4-parameter C(t) t (ps) Before After
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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
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Dynamics Relate to Recognition FlexibilityDynamics NMR & MD Deformability Sequence (Damage?) Specific
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NormalMismatch Biological Relevance MutS: Mismatch Recognition Deformation: -Bend -Compressed, Deepened Major Groove -Widened Minor Groove
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CGGCATGCTG CGGCATGCTG GT-2 GT-5 CGGCACGCTG CGGCACGCTG
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Normal vs. Mismatch
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Major Groove Width (Å) Minor Groove Width (Å) = Normal = Mismatch Groove Widths & Flexibility Mismatched DNA has more flexibility in major groove width
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5’-CCATCGCTACC-3’ 3’-GGTAGCGATGG-5’
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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
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Acknowledgements Richard J. Isaacs William Rayens NSF Kentucky Center for Computational Sciences NCSA
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