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A critical evaluation of models for complex molecular dynamics: Application to NMR studies of double‐ and single‐stranded DNA
Author(s) -
Levy George C.,
Craik David J.,
Kumar Anil,
London Robert E.
Publication year - 1983
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360221214
Subject(s) - chemistry , molecular dynamics , crystallography , relaxation (psychology) , amplitude , dna , molecular physics , nuclear magnetic resonance , computational chemistry , physics , optics , social psychology , biochemistry , psychology
The nature of internal and overall motions in native (double‐stranded) and denatured (single‐stranded) DNA fragments 120–160 base pairs (bp) long is examined by molecular‐dynamics modeling using 13 C‐nmr spin‐relaxation data obtained over the frequency range of 37–125 MHz. The broad range of 13 C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T 1 values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double‐stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τ x = ∼10 −6 s;τ Z = ∼1.8 × 10 −8 s), which is in good agreement with values calculated from hydrodynamic theory (τ x = ∼1.8 × 10 −6 s; τ Z = ∼2.7 × 10 −8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual CH vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τ w = ∼4 × 10 −9 s, θ cone = ∼21°) or as a bistable jump (τ A = τ B = ∼2 × 10 −9 s, θ = ∼15°). We discuss the critical role in molecular‐dynamics modeling played by the angle (β) that individual CH vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τ W = ∼0.2 × 10 −9 s, θ cone = ∼50°), and overall motion is affected by becoming essentially isotropic (τ x = τ Z = ∼5 × 10 −8 s) for the single‐stranded molecules. Since 13 C‐nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.