New method for incorporating solvent influence into the evaluation of X-ray scattering intensity of proteins in solution

Soda, Kunitsugu; Miki, Yōichiro; Nakagawa, Takayuki; Seki, Yasutaka

doi:10.1016/s0301-4622(96)02228-4

Cited by 8 publications

(7 citation statements)

References 10 publications

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“…Scattering curves of GroES from crystal atomic Small-angle X-ray Scattering of GroES coordinates 16 were calculated using a radial distribution model 61,62 that introduces the effect of hydrated water. The first hydrated water layer is replaced with a layer that has a higher electron density than that of free water.…”

Section: Saxs Data Analysismentioning

confidence: 99%

Structural Stability and Solution Structure of Chaperonin GroES Heptamer Studied by Synchrotron Small-angle X-ray Scattering

Higurashi

Hiragi

Ichimura

et al. 2003

Journal of Molecular Biology

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Section: Saxs Data Analysismentioning

confidence: 99%

Structural Stability and Solution Structure of Chaperonin GroES Heptamer Studied by Synchrotron Small-angle X-ray Scattering

Higurashi

Hiragi

Ichimura

et al. 2003

Journal of Molecular Biology

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“…Sokolova et al (2003) have introduced a database of SAXS patterns from different proteins. The development of similar tools to couple molecular modeling with WAXS is more difficult; one of the most important challenges for accurately predicting scattering is the task of estimating the scattering from water in the immediate vicinity of protein (Svergun et al, 1995;Soda et al, 1997;Seki et al, 2002). Whereas for lowresolution experiments (SAXS) the water molecules in the hydration layer may not evidence significant structure, this is not necessarily true at higher resolutions.…”

Section: Introductionmentioning

confidence: 99%

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules

2009

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This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.

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“…To expand the possibility of comparing computation with experimental results quantitatively, it is necessary to obtain the following: (1) precise SXS data in the wide range of scattering angles including the forward scattering intensity 9 and (2) a method of accurately estimating SXS profiles that is applicable to unfolded proteins and incorporates solvent effects explicitly. 34,35 ' AUTHOR INFORMATION Corresponding Author *Tel. : þ81-78-940-5645.…”

Section: ' Discussionmentioning

confidence: 99%

A New Efficient Method for Generating Conformations of Unfolded Proteins with Diverse Main-Chain Dihedral-Angle Distributions

Seki

Shimbo

Nonaka

et al. 2011

J. Chem. Theory Comput.

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A new method for generating polypeptide-chain conformations has been developed for studying structural characteristics of unfolded proteins. It enables us to generate a large number of conformations very rapidly by avoiding atomic collisions efficiently with the use of main-chain dihedral-angle distributions derived from a crystal-structure database of proteins. In addition, combining main-chain dihedral-angle distributions for the amino acid residues incorporated in different secondary structures, we can obtain diverse conformational ensembles with different structural features. Structural characteristics of proteins denatured in high-concentration denaturant solution were analyzed by comparing predictions from this method with results from solution X-ray scattering (SXS) measurement. Analysis of the dependence of the mean square radius (Rsq) of protein on the number of residues and the shape of its Kratky profile has confirmed that the highly denaturing solvent serves as a good solvent in accordance with previous reports. It was also found that, in order for a conformational ensemble to reproduce experimental data, the percentage in which main-chain dihedral angles are found in the α region must be in the range of 20-40%. It agrees with studies on the (3)JHNα coupling constant using the multidimensional NMR method. These results confirm that our method for generating diverse conformations of polypeptide chains is very useful to the conformational analysis of unfolded protein, because it enables us to analyze comprehensively both of the local structural features obtained from NMR and the global ones obtained from SXS.

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New method for incorporating solvent influence into the evaluation of X-ray scattering intensity of proteins in solution

Cited by 8 publications

References 10 publications

Structural Stability and Solution Structure of Chaperonin GroES Heptamer Studied by Synchrotron Small-angle X-ray Scattering

Structural Stability and Solution Structure of Chaperonin GroES Heptamer Studied by Synchrotron Small-angle X-ray Scattering

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules

A New Efficient Method for Generating Conformations of Unfolded Proteins with Diverse Main-Chain Dihedral-Angle Distributions

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