Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

Lipfert, Jan; Chu, Victor C.; Bai, Yu; Herschlag, Daniel; Doniach, Sebastian

doi:10.1107/s0021889807001707

Cited by 41 publications

(47 citation statements)

References 28 publications

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“…2E) suggested the RNA is folded and not a random coil. The ab initio model based on the SAXS data is elongated and similar to a previously published ab initio reconstruction for the P4-P6 domain (Lipfert et al 2007a); however, this model is inconsistent with the overall shape suggested by the X-ray crystal structure.…”

Section: Limitations To Saxs Analysis Due To Refolding Artifactsmentioning

confidence: 66%

Improving small-angle X-ray scattering data for structural analyses of the RNA world

Rambo¹,

Tainer²

2010

RNA

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Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNA val , and yeast tRNA phe that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways.

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Section: Limitations To Saxs Analysis Due To Refolding Artifactsmentioning

confidence: 66%

Improving small-angle X-ray scattering data for structural analyses of the RNA world

Rambo¹,

Tainer²

2010

RNA

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“…In a first approach, we constructed low-resolution models of the entire IRES and of its different fragments with the programme DAMMIN 34,35 ( Supplementary Fig. 2).…”

Section: Saxs Experimentsmentioning

confidence: 99%

Structure of the full-length HCV IRES in solution

et al. 2013

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The 5 0 -untranslated region of the hepatitis C virus genome contains an internal ribosome entry site (IRES) that initiates cap-independent translation of the viral RNA. Until now, the structural characterization of the entire (IRES) remained limited to cryo-electron microscopy reconstructions of the (IRES) bound to different cellular partners. Here we report an atomic model of free full-length hepatitis C virus (IRES) refined by selection against small-angle X-ray scattering data that incorporates the known structures of different fragments. We found that an ensemble of conformers reproduces small-angle X-ray scattering data better than a single structure suggesting in combination with molecular dynamics simulations that the hepatitis C virus (IRES) is an articulated molecule made of rigid parts that move relative to each other. Principal component analysis on an ensemble of physically accessible conformers of hepatitis C virus (IRES) revealed dominant collective motions in the molecule, which may underlie the conformational changes occurring in the (IRES) molecule upon formation of the initiation complex.

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“…Molecular geometries have been defined in previous studies by high-resolution models from crystallography (Chin et al 1999;Misra and Draper 2001;Tang et al 2007). Recently, however, we have shown that low-resolution models for RNA can be obtained from SAXS data (Lipfert et al 2007a(Lipfert et al ,b, 2008, and that PB theory applied to the lowresolution models can predict the composition of the ion atmosphere of RNA molecules with an accuracy that can be comparable to the predictions made from high-resolution models (Lipfert et al 2007a). …”

Section: +mentioning

confidence: 99%

“…The extension of the simulation grid was determined by increasing the default values from APBS's psize.py utility by 20 Å in each dimension. All other simulation parameters are as described elsewhere (Lipfert et al 2007a). …”

Section: Poisson-boltzmann Calculationsmentioning

confidence: 99%

Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

Lipfert

Sim

Herschlag

et al. 2010

RNA

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Riboswitches are gene-regulating RNAs that are usually found in the 59-untranslated regions of messenger RNA. As the sugarphosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested monoand divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg 2+ , Ca 2+ , and Mn 2+ facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how iondependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.

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Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

Cited by 41 publications

References 28 publications

Improving small-angle X-ray scattering data for structural analyses of the RNA world

Improving small-angle X-ray scattering data for structural analyses of the RNA world

Structure of the full-length HCV IRES in solution

Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

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