Automated matching of high- and low-resolution structural models

Kozin, M. B.; Svergun, Dmitri I.

doi:10.1107/s0021889800014126

Cited by 1,238 publications

(1,188 citation statements)

References 38 publications

(29 reference statements)

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“…The NSD parameter measure the proximity of two objects in the threedimensional space and is analogous to the error-weighted w-value used to characterized deviations within one-dimensional data sets 45 . Structural alignment can be performed by minimizing this parameter, and the NSD calculated between aligned structures provides a quantitative estimate of the similarity between the models.…”

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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Section: Saxs Experimentsmentioning

confidence: 99%

Structure of the full-length HCV IRES in solution

et al. 2013

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“…4). Averaging and filtering of several ab initio modeling runs led to poorly superimposed ensembles (Kozin and Svergun 2001;Volkov and Svergun 2003) or oblate shapes with no features that would be instructive for structural interpretation at the resolution of A-form helices or independently folding structural domains (Supplemental Fig. 4).…”

Section: Ab Initio Modeling Fails To Define Unique Scattering Envelopesmentioning

confidence: 99%

“…Ab initio modeling of the scattering envelopes was performed with DAMMIF (Franke and Svergun 2009) with P(r) distributions calculated with maximal reasonable value of D max (Supplemental Table S1). Ten individual reconstructions were calculated for each RNA, superimposed, averaged, and filtered with DAMSEL, DAMSUP, DAMAVER, and DAMFILT utilities as described elsewhere (Kozin and Svergun 2001;Volkov and Svergun 2003). Theoretical scattering profiles from all-atom models were calculated with CRYSOL (Svergun et al 1995) by assigning an electron density for solvent to 0.334 e/Å 3 and a thickness of the solvent shell to 3 Å .…”

Section: Saxs Data Collection and Processingmentioning

confidence: 99%

Solution structure of RNase P RNA

Kazantsev¹,

Rambo²,

Karimpour³

et al. 2011

RNA

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The ribonucleoprotein enzyme ribonuclease P (RNase P) processes tRNAs by cleavage of precursor-tRNAs. RNase P is a ribozyme: The RNA component catalyzes tRNA maturation in vitro without proteins. Remarkable features of RNase P include multiple turnovers in vivo and ability to process diverse substrates. Structures of the bacterial RNase P, including full-length RNAs and a ternary complex with substrate, have been determined by X-ray crystallography. However, crystal structures of free RNA are significantly different from the ternary complex, and the solution structure of the RNA is unknown. Here, we report solution structures of three phylogenetically distinct bacterial RNase P RNAs from Escherichia coli, Agrobacterium tumefaciens, and Bacillus stearothermophilus, determined using small angle X-ray scattering (SAXS) and selective 29-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. A combination of homology modeling, normal mode analysis, and molecular dynamics was used to refine the structural models against the empirical data of these RNAs in solution under the high ionic strength required for catalytic activity.

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“…Of the 10 models constructed, the structure with the 2 close to 1 between computed I(Q) for the modeled structure versus the experimental data was used for structure interpretation (supplemental Table S3). Using SUPCOMB20 program, the inertial axes of the resultant low resolution shapes for the proteins and known crystal structures from x-ray diffraction were superimposed (35). Open source programs PyMOL and SPDB viewer were used for graphical analysis, manual alignment of models, and figure generation.…”

Section: Cloning and Purification Of Recombinant Gelsolin Mutants-mentioning

confidence: 99%

Global Shapes of F-actin Depolymerization-competent Minimal Gelsolins

Peddada¹,

Sagar²,

Rathore³

et al. 2013

Journal of Biological Chemistry

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Background: Shape-function studies are necessary to design better therapeutic alternatives of the plasma gelsolin. Results: N-terminal fragment 30 -161 is the smallest segment with F-actin depolymerization potential, and G1-G3 can function independent of Ca 2ϩ ions or low pH. Conclusion: The g2-g3 linker plays a role in imparting pH/Ca 2ϩ insensitivity to G1-G3. Significance: We provide the first evidence that g2-g3 linker regulates mobility of the G1 domain.

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Automated matching of high- and low-resolution structural models

Cited by 1,238 publications

References 38 publications

Structure of the full-length HCV IRES in solution

Structure of the full-length HCV IRES in solution

Solution structure of RNase P RNA

Global Shapes of F-actin Depolymerization-competent Minimal Gelsolins

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