Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA

Suzuki, Masashi; Amano, Naoki; Kakinuma, Jun; Tateno, Masaru

doi:10.1006/jmbi.1997.1406

Cited by 74 publications

(57 citation statements)

References 51 publications

(62 reference statements)

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“…RpR and RpY steps showed less intrinsic deformation and deformability, but trends were consistent with corresponding surveys of the crystallographic database. 63 The MD calculated flexibility by step correlated well with the bendability deduced independently from the protein-DNA crystal structures. 19 The MD results indicated that curvature and flexibility of base pair steps in uncomplexed DNA oligonucleotides are highly correlated, i.e., steps, which exhibit the most intrinsic deformation with respect to B-form DNA, turn out to be also the most deformable.…”

Section: Models Of Dna Structure In Solutionsupporting

confidence: 54%

Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting

et al. 2004

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Recent studies of DNA axis curvature and flexibility based on molecular dynamics (MD) simulations on DNA are reviewed. The MD simulations are on DNA sequences up to 25 base pairs in length, including explicit consideration of counterions and waters in the computational model. MD studies are described for ApA steps, A-tracts, for sequences of A-tracts with helix phasing. In MD modeling, ApA steps and A-tracts in aqueous solution are essentially straight, relatively rigid, and exhibit the characteristic features associated with the B'-form of DNA. The results of MD modeling of A-tract oligonucleotides are validated by close accord with corresponding crystal structure results and nuclear magnetic resonance (NMR) nuclear Overhauser effect (NOE) and residual dipolar coupling (RDC) structures of d(CGCGAATTCGCG) and d(GGCAAAAAACGG). MD simulation successfully accounts for enhanced axis curvature in a set of three sequences with phased A-tracts studied to date. The primary origin of the axis curvature in the MD model is found at those pyrimidine/purine YpR "flexible hinge points" in a high roll, open hinge conformational substate. In the MD model of axis curvature in a DNA sequence with both phased A-tracts and YpR steps, the A-tracts appear to act as positioning elements that make the helix phasing more precise, and key YpR steps in the open hinge state serve as curvature elements. Our simulations on a phased A-tract sequence as a function of temperature show that the MD simulations exhibit a premelting transition in close accord with experiment, and predict that the mechanism involves a B'-to-B transition within A-tracts coupled with the prediction of a transition in key YpR steps from the high roll, open hinge, to a low roll, closed hinge substate. Diverse experimental observations on DNA curvature phenomena are examined in light of the MD model with no serious discrepancies. The collected MD results provide independent support for the "non-A-tract model" of DNA curvature. The "junction model" is indicated to be a special case of the non-A-tract model when there is a Y base at the 5' end of an A-tract. In accord with crystallography, the "ApA wedge model" is not supported by MD.

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Section: Models Of Dna Structure In Solutionsupporting

confidence: 54%

Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting

et al. 2004

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“…Thus, genomic DNA molecules of hyperthermophiles are expected to be least flexible. In fact, statistical study of DNA crystal structures has shown that the positioning of purine and pyrimidine rings in the YR combinations creates the smallest conformational restrictions (17)(18)(19)(20). Indeed, DNA structures have the largest deviations at YR combinations, the DNA being largely bent at these points in many complexes with proteins.…”

Section: Resultsmentioning

confidence: 99%

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium

Kawashima

Amano

Koike

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

180

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The complete genomic sequence of the archaeon Thermoplasma volcanium, possessing optimum growth temperature (OGT) of 60°C, is reported. By systematically comparing this genomic sequence with the other known genomic sequences of archaea, all possessing higher OGT, a number of strong correlations have been identified between characteristics of genomic organization and the OGT. With increasing OGT, in the genomic DNA, frequency of clustering purines and pyrimidines into separate dinucleotides rises (e.g., by often forming AA and TT, whereas avoiding TA and AT). Proteins coded in a genome are divided into two distinct subpopulations possessing isoelectric points in different ranges (i.e., acidic and basic), and with increasing OGT the size of the basic subpopulation becomes larger. At the metabolic level, genes coding for enzymes mediating pathways for synthesizing some coenzymes, such as heme, start missing. These findings provide insights into the design of individual genomic components, as well as principles for coordinating changes in these designs for the adaptation to new environments.

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“…Although the nowadays most widely used theoretical approach to molecular structure, density functional theory (DFT), [8,9] includes EC in an approximate manner, it is now clear that almost all standard density functionals are unable to describe dispersive interactions (see, for example, reference [10] and references therein). Probably the earliest DFT study which reported significant overestimations of the [ 4,10 ] [7]metacyclophane are compared to experimental data from X-ray crystal structure determinations. In all cases, very accurate theoretical predictions are obtained from the recently developed spin-component-scaled MP2 (SCS-MP2) method, in which the deviations are within the experimental accuracy and expected crystal-packing or vibrational effects.…”

Section: Introductionmentioning

confidence: 99%

On the Importance of Electron Correlation Effects for the π‐π Interactions in Cyclophanes

Grimme

2004

Chemistry A European J

167

206

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Correlated ab initio quantum chemical methods based on second-order perturbation theory and density functional theory (DFT) together with large atomic orbital (AO) basis sets are used to calculate the structures of four cyclophanes with two aromatic rings and one sulphur-containing phane with one aromatic ring. The calculated geometrical data for [2.2]paracyclophane, cyclophane (superphane), 8,16-dimethyl[2.2]metacyclophane, 16-methyl[2.2]metaparacyclophane, and 2,6,15-trithia[3(4,10)][7]metacyclophane are compared to experimental data from X-ray crystal structure determinations. In all cases, very accurate theoretical predictions are obtained from the recently developed spin-component-scaled MP2 (SCS-MP2) method, in which the deviations are within the experimental accuracy and expected crystal-packing or vibrational effects. Especially the inter-ring distances, which are determined by a detailed balance between attractive van der Waals (dispersive) and repulsive (Pauli) contributions, are very sensitive to the level of theory employed. While standard MP2 theory in general overestimates the dispersive interactions (pi-pi correlations) between the two aromatic rings leading to too short distances (between 3 and 8 pm), the opposite is observed for DFT methods (errors up to 15 pm). This indicates that an explicit account of dispersive-type electron correlation effects between the clamped aromatic units is essential for a quantitative description of cyclophane structures. In order to distinguish these effects from "normal" van der Waals interactions, the term "overlap-dispersive" interaction may be employed. The popular B3 LYP hybrid density functional offers no advantage over the pure PBE functional that at least qualitatively accounts for some of the dispersive effects. The use of properly polarized AO basis sets of at least valence-triple-zeta quality is strongly recommended to obtain quantitative predictions with traditional wave function methods.

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Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA

Cited by 74 publications

References 51 publications

Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting

Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium

On the Importance of Electron Correlation Effects for the π‐π Interactions in Cyclophanes

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