Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids

Beckers, M.L.M.; Buydens, L.M.C.

doi:10.1002/(sici)1096-987x(199805)19:7<695::aid-jcc2>3.0.co;2-l

Cited by 20 publications

(16 citation statements)

References 19 publications

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“…For PC2, the α 2 and γ 2 torsions are dominant while their different signs reflect anti-correlated behaviour (7,9,19). The loadings of the torsions of the two sugar rings are much smaller than in PC1.…”

Section: Resultsmentioning

confidence: 99%

“…For example, within the B-DNA family, there exist the BI- and BII-forms (or states) which show differences in the two torsions ɛ (C4′–C3′–O3′–P) and ζ (C3′–O3′–P–O5′) (5). Within A-DNA, the A-form and the Crankshaft-forms differ in the torsions α (O3′–P–O5′–C5′) and γ (O5′–C5′–C4′–C3′) (6,7). …”

Section: Introductionmentioning

confidence: 99%

“…In both studies the number of data points used was limited and the focus was restricted to bivariate relationships. In an explicitly multivariate approach, a principal component analysis (PCA) of nine backbone torsion angles of dinucleotide monophosphates (DMs) fragments from duplex DNA crystal structures resulted in a 3D conformational space which exhibited a separation of an A-DNA class, two different B-DNA classes and one so-called Crankshaft class (7). This representation was considered by the authors as a multidimensional analogue to the Ramachandran plot used in protein analysis (10).…”

Section: Introductionmentioning

confidence: 99%

“…To achieve this, we needed an appropriate and tractable set of degrees of freedom to define the conformational space. Extending the statistical work of Becker and Buydens (7) in a similar way to Sims and Kim (11) we generated a descriptive set of collective coordinates for a dinucleotide fragment via a PCA of backbone and sugar torsion angle parameters from a sample of duplex crystal structures. These collective coordinates (which are linear combinations of proper torsion angles) span the principal conformational subspace (PCS) of the DM.…”

Section: Introductionmentioning

confidence: 99%

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The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA

Elsawy

2005

Nucleic Acids Research

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A multivariate analysis of the backbone and sugar torsion angles of dinucleotide fragments was used to construct a 3D principal conformational subspace (PCS) of DNA duplex crystal structures. The potential energy surface (PES) within the PCS was mapped for a single-strand dinucleotide model using an empirical energy function. The low energy regions of the surface encompass known DNA forms and also identify previously unclassified conformers. The physical determinants of the conformational landscape are found to be predominantly steric interactions within the dinucleotide backbone, with medium-dependent backbone-base electrostatic interactions serving to tune the relative stability of the different local energy minima. The fidelity of the PES to duplex DNA properties is validated through a correspondence to the conformational distribution of duplex DNA crystal structures and the reproduction of observed sequence specific propensities for the formation of A-form DNA. The utility of the PES is demonstrated through its succinct and accurate description of complex conformational processes in simulations of duplex DNA. The study suggests that stereochemical considerations of the nucleic acid backbone play a role in determining conformational preferences of DNA which is analogous to the role of local steric interactions in determining polypeptide secondary structure.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA

Elsawy

2005

Nucleic Acids Research

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“…Similar analysis problems are posed by nucleic acids. While it is now possible to describe the subtle variations in the geometry of the double helix [21], the number of signi®cant variables per nucleotide step makes it dicult to achieve the simplicity of the Ramachandran maps, although attempts continue to be made in this direction [22]. DNAs have recently been seen to adopt a surprising range of conformations [23,24], but it is once again RNAs and their protein complexes which represent the hardest challenge for future theoretical studies.…”

mentioning

confidence: 97%

Perspective on "Stereochemistry of polypeptide chain conformations"

Lavery¹

2000

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

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Despite its apparent simplicity the``Ramachandran map'' has been an enormously successful tool for describing and understanding protein structure. Thirty-®ve years after its invention, it is still used daily for checking the quality of experimental and modeled protein structures. It is, moreover, founded on a rational, reduced-coordinate model of the polypeptide chain which continues to be useful in computational attempts at predicting protein folding. PerspectivePerspective on``Stereochemistry of polypeptide chain conformations'' Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) J Mol Biol 7: 95±9

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Singular value decomposition of torsional angles of analogs of the dopamine reuptake inhibitor GBR 12909

et al. 2006

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Analysis of large, flexible molecules, such as the dopamine reuptake inhibitor GBR 12909 (1), is complicated by the fact that they can take on a wide range of closely related conformations. The first step in the analysis is to classify the conformers into groups. Here, Singular Value Decomposition (SVD) was used to group conformations of GBR 12909 analogs by the similarity of their nonring torsional angles. The significance of the present work, the first application of SVD to the analysis of very flexible molecules, lies in the development of a novel scaling technique for circular data and in the grouping of molecular conformations using a technique that is independent of molecular alignment. Over 700 conformers each of a piperazine (2) and piperidine (3) analog of 1 were studied. Analysis of the score and loading plots showed that the conformers of 2 separate into three large groups due to torsional angles on the naphthalene side of the molecule, whereas those of 3 separate into nine groups due to torsional angles on the bisphenyl side of the molecule. These differences are due to nitrogen inversion at the unprotonated piperazinyl nitrogen of 2, which results in a different ensemble of conformers than those of 3, where no inversion is possible at the corresponding piperidinyl carbon.

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Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids

Cited by 20 publications

References 19 publications

The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA

The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA

Perspective on "Stereochemistry of polypeptide chain conformations"

Singular value decomposition of torsional angles of analogs of the dopamine reuptake inhibitor GBR 12909

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