<i>CRYSOL</i>– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

Svergun, Dmitri I.; Barberato, Cláudio; Koch, Michel H. J.

doi:10.1107/s0021889895007047

Cited by 3,304 publications

(3,678 citation statements)

References 14 publications

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“…For macromolecules, we found that I(q) is well-represented by tens of points at small scattering amplitudes and up to hundreds of points at the larger values of q sampled in this study. When the number of grid points is not quite large enough, the current method seems to fail gracefully (the resulting error grows slowly with an increasing q), unlike the approach in which the scattering amplitude is expanded in terms of spherical harmonics (27).…”

Section: Methods and Theorymentioning

confidence: 89%

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

2007

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The structure and dynamics of the Dickerson DNA dodecamer [5′d(CGCGAATTCGCG) 2 ] in solution have been investigated by joint simulated annealing refinement against NMR and large-angle X-ray scattering data (extending from 0.25 to 3 Å -1 ). The NMR data comprise an extensive set of heteroand homonuclear residual dipolar coupling and 31 P chemical shift anisotropy restraints in two alignment media, supplemented by NOE and 3 J coupling data. The NMR and X-ray scattering data cannot be fully ascribed to a single structure representation, indicating the presence of anisotropic motions that impact the experimental observables in different ways. Refinement with ensemble sizes (N e ) of g2 to represent the atomic motions reconciles all the experimental data within measurement error. Cross validation against both the dipolar coupling and X-ray scattering data suggests that the optimal ensemble size required to account for the current data is 4. The resulting ensembles permit one to obtain a detailed view of the conformational space sampled by the dodecamer in solution and permit one to analyze fluctuations in helicoidal parameters, sugar puckers, and BI-BII backbone transitions and to obtain quantitative metrics of atomic motion such as generalized order parameters and thermal B factors. The calculated order parameters are in good agreement with experimental order parameters obtained from 13 C relaxation measurements. Although DNA behaves as a relatively rigid rod with a persistence length of ∼150 bp, dynamic conformational heterogeneity at the base pair level is functionally important since it readily permits optimization of intermolecular protein-DNA interactions.

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Section: Methods and Theorymentioning

confidence: 89%

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

2007

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“…In each MD trajectory, after a rapid rise in the first 2 ns, the RMSD evolved towards a stable value near 2.5 nm and the R g value decreases. Twothousand four-hundred conformers were obtained as snapshots taken at regular interval (50 ps) along the six first MD simulations, and the theoretical scattering profiles were calculated from the structures using the programme CRYSOL 58 and compared with the experimental data. The best agreement with the experimental curve yielded a w-value of 6, down from a value of 10 calculated for the initial structure.…”

Section: Methodsmentioning

confidence: 99%

“…For each of the 20 energy-minimized models, 140 models were generated with the torsion-based random conformational search functionality of Another Molecular Mechanics Program (AMMP) implemented in VEGA ZZ, leading to 2,800 additional conformers. A model with a w-value of 2.8 between the experimental and calculated curve was finally selected using CRYSOL 58 (Fig. 2).…”

Section: Methodsmentioning

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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“…33 Calculated form factors for BPTI monomer and decamer were obtained using the CRYSOL program 55 from a set of crystallographic coordinates (PDB entry 1BHC 34 ). At very low scattering vectors, (s < 0.02 Å -1 ), interparticle interactions may perturb the scattering intensity and affect the form factor.…”

Section: Simulation Procedures 4321 Form Factorsmentioning

confidence: 99%

Exploring Bovine Pancreatic Trypsin Inhibitor Phase Transitions

et al. 2006

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This paper presents an investigation of the phase diagram of BPTI (bovine pancreatic trypsin inhibitor)/350 mM KSCN at pH 4.9 by direct observation and numerical simulations. We report optical microscopy and light and X-ray scattering experiments coupled with theoretical data analysis using numerical tools. The phase diagram is thoroughly determined, as a function of temperature. Two polymorphs are observed by video microscopy and their solubility measured. In this phase diagram, the liquid-liquid phase separation (LLPS) is metastable with respect to the solid-liquid phase separation. Above the T L-L boundary curve, solutions are composed of a mixture of BPTI monomers and decamers. Attractive interactions are stronger between decamers than between monomers. Below the T L-L boundary curve, the dense phase is highly concentrated in protein and composed of BPTI decamers alone. Thus, the driving force for liquid-liquid or liquid-solid phase separation is the attraction between decamers at low pH. The structure factors of the dense phases are characteristic of repulsive dense phases because of a hard sphere repulsion core, meaning that in the dense phase proteins are actually in contact (interparticle distance of 53 Å). In agreement with the Oswald rule of stages, LLPS occurs prior to and impedes the solid nucleation.

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CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

Cited by 3,304 publications

References 14 publications

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

Structure of the full-length HCV IRES in solution

Exploring Bovine Pancreatic Trypsin Inhibitor Phase Transitions

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