Theoretical studies of nucleic acid conformation: potential energies, chain statistics, and model building

Olson, Wilma K.

doi:10.1007/978-1-349-06007-8_1

Cited by 21 publications

(8 citation statements)

References 263 publications

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“…The limits of each envelope are determined by where the probability of observation drops to zero. Our method of empirical binning differs from previous methods that use ranges de®ned by equivalent limits on either side of ideal torsion angles (11). Thus, the descriptions anti, gauche+ and gauche± are not fully equivalent to the bins used here.…”

Section: Binningmentioning

confidence: 95%

“…Because of their multi-peaked nature, the remaining four torsion angles and P allow a straightforward separation into distinct con®guration classes. However, d and P are correlated, both by geometric de®nition (11,13), and from analysis of the HM 23S rRNA data. Thus, to avoid redundancy, we eliminate P and consider only four torsion angles, a, g, d and z.…”

Section: Binningmentioning

confidence: 99%

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Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA

Hershkovitz¹

2003

Nucleic Acids Research

102

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We develop novel methods for recognizing and cataloging conformational states of RNA, and for discovering statistical rules governing those states. We focus on the conformation of the large ribosomal subunit from Haloarcula marismortui. The two approaches described here involve torsion matching and binning. Torsion matching is a pattern-recognition code which finds structural repetitions. Binning is a classification technique based on distributional models of the data. In comparing the results of the two methods we have tested the hypothesis that the conformation of a very large complex RNA molecule can be described accurately by a limited number of discrete conformational states. We identify and eliminate extraneous and redundant information without losing accuracy. We conclude, as expected, that four of the torsion angles contain the overwhelming bulk of the structural information. That information is not significantly compromised by binning the continuous torsional information into a limited number of discrete values. The correspondence between torsion matching and binning is 99% (per residue). Binning, however, does have several advantages. In particular, we demonstrate that the conformation of a large complex RNA molecule can be represented by a small alphabet. In addition, the binning method lends itself to a natural graphical representation using trees.

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Section: Binningmentioning

confidence: 95%

Section: Binningmentioning

confidence: 99%

Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA

Hershkovitz¹

2003

Nucleic Acids Research

102

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“…These plots show a superposition of results for each step in the dodecamer, and thus generic rather than sequence-specific behavior. The shaded areas in these dials are the range of values of each torsion that have been deduced from independent model building considerations (Olson, 1982a,b) to be sterically unfavorable. The MD results strongly support the predicted conformationally allowed regions.…”

Section: Conformational Analysismentioning

confidence: 99%

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

Young

Ravishanker

Beveridge

1997

Biophysical Journal

285

303

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We report the results of four new molecular dynamics (MD) simulations on the DNA duplex of sequence d(CGCGAATTCGCG)2, including explicit consideration of solvent water, and a sufficient number of Na+ counterions to provide electroneutrality to the system. Our simulations are configured particularly to characterize the latest MD models of DNA, and to provide a basis for examining the sensitivity of MD results to the treatment of boundary conditions, electrostatics, initial placement of solvent, and run lengths. The trajectories employ the AMBER 4.1 force field. The simulations use particle mesh Ewald summation for boundary conditions, and range in length from 500 ps to 5.0 ns. Analysis of the results is carried out by means of time series for conformationalm, helicoidal parameters, newly developed indices of DNA axis bending, and groove widths. The results support a dynamically stable model of B-DNA for d(CGCGAATTCGCG)2 over the entire length of the trajectory. The MD results are compared with corresponding crystallographic and NMR studies on the d(CGCGAATTCGCG)2 duplex, and placed in the context of observed behavior of B-DNA by comparisons with the complete crystallographic data base of B-form structures. The calculated distributions of mobile solvent molecules, both water and counterions, are displayed. The calculated solvent structure of the primary solvation shell is compared with the location of ordered solvent positions in the corresponding crystal structure. The results indicate that ordered solvent positions in crystals are roughly twice as structured as bulk water. Detailed analysis of the solvent dynamics reveals evidence of the incorporation of ions in the primary solvation of the minor groove B-form DNA. The idea of localized complexation of otherwise mobile counterions in electronegative pockets in the grooves of DNA helices introduces an additional source of sequence-dependent effects on local conformational, helicoidal, and morphological structure, and may have important implications for understanding the functional energetics and specificity of the interactions of DNA and RNA with regulatory proteins, pharmaceutical agents, and other ligands.

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“…Helices in the A 2 B 2 hyperfamily adopt the conformational switch ®rst characterized in dimer steps at the ends of B-DNA dodecamer duplexes (Grzeskowiak et al, 1991) and anticipated in early DNA computations (Zhurkin et al, 1978;Olson, 1982b). We use the subscript 2 to emphasize the conformational similarity of our computed structures with these so-called B(II) states where the ez rotations about the C3 H ÐO3 H and O3 H Ð P bonds adopt g À t combinations rather than the tg À arrangements typical of canonical A 1 B 1 duplexes, the b angle about the O5 H ÐC5 H bond decreases by 30-70 , and the w angle orienting the sugar and base rises by 40-60 to the high anti range (see Table 1).…”

Section: A T B T Hyperfamilymentioning

confidence: 99%

DNA stretching and compression: large-scale simulations of double helical structures 1 1Edited by I. Tinoco

Kosikov

Gorin

Zhurkin

et al. 1999

Journal of Molecular Biology

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131

102

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Theoretical studies of nucleic acid conformation: potential energies, chain statistics, and model building

Cited by 21 publications

References 263 publications

Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA

Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

DNA stretching and compression: large-scale simulations of double helical structures 1 1Edited by I. Tinoco

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