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Low‐resolution models for nucleic acids from small‐angle X‐ray scattering with applications to electrostatic modeling
Author(s) -
Lipfert Jan,
Chu Vincent B.,
Bai Yu,
Herschlag Daniel,
Doniach Sebastian
Publication year - 2007
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889807001707
Subject(s) - scattering , poisson–boltzmann equation , resolution (logic) , nucleic acid , small angle scattering , ion , small angle x ray scattering , chemistry , macromolecule , molecular physics , statistical physics , physics , computational physics , quantum mechanics , computer science , biochemistry , artificial intelligence
Several algorithms are available to reconstruct low‐resolution electron density maps of biological macromolecules from small‐angle solution scattering data. These algorithms have been extensively applied to proteins and protein complexes. Here, we demonstrate their applicability to nucleic acids by reconstructing a set of RNA and DNA molecules of known three‐dimensional structure from their small‐angle X‐ray scattering profiles. The overall size and shape of the molecules get reproduced well in all tested cases. Furthermore, we show that the generated bead models can be used as inputs for electrostatic calculations. The number of ions bound under different solution conditions computed from numerical solutions of the Poisson–Boltzmann equation for bead models agrees very well with results of calculations on all atom models derived from crystallography. The predictions from Poisson–Boltzmann theory also agree generally well with experimentally determined ion binding numbers.