Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling
TLDR
In this paper, a set of RNA and DNA molecules of known three-dimensional structure from their small-angle X-ray scattering profiles were reconstructed by using the Poisson-Boltzmann equation to estimate the number of ions bound under different solution conditions.Abstract:
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.read more
Citations
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Journal ArticleDOI
Understanding Nucleic Acid–Ion Interactions
TL;DR: This review provides practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models and describes opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic Acid-ion interactions.
Journal ArticleDOI
Small-angle X-ray scattering from RNA, proteins, and protein complexes.
Jan Lipfert,Sebastian Doniach +1 more
TL;DR: Recently developed algorithms for 3-D structure modeling and applications to protein complexes are reviewed and SAXS is discussed as a tool to study membrane protein-detergent complexes and the folding of functional RNA molecules.
Journal ArticleDOI
Predicting the sizes of large RNA molecules
Aron M. Yoffe,Peter Prinsen,Ajaykumar Gopal,Charles M. Knobler,William M. Gelbart,Avinoam Ben-Shaul +5 more
TL;DR: It is argued that there has been evolutionary pressure for the genome to have overall spatial properties—including an appropriate radius of gyration, Rg—that facilitate this assembly process, and it is predicted the Rg values of viral ssRNAs are smaller than those of nonviral sequences.
Journal ArticleDOI
Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio cholerae
Jan Lipfert,Rhiju Das,Vincent B. Chu,Madhuri Kudaravalli,Nathan Boyd,Daniel Herschlag,Sebastian Doniach +6 more
TL;DR: A first glimpse into the structural conformations of the VCI-II aptamer is provided, rigorous constraints for further modeling are established, and a framework for future mechanistic studies is provided.
References
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CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
TL;DR: In this paper, a program for evaluating the solution scattering from macromolecules with known atomic structure is presented, which uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell.
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Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.
TL;DR: Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.
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Uniqueness of ab initio shape determination in small-angle scattering
TL;DR: In this article, scattering patterns from geometrical bodies with different shapes and anisometry (solid and hollow spheres, cylinders, prisms) are computed and the shapes are reconstructed using envelope function and bead modelling methods.