Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

scholarly journals Obtaining tertiary protein structures by the ab-initio interpretation of small angle X-ray scattering data

2019 ◽  
Author(s):  
Christopher Prior ◽  
Owen R Davies ◽  
Daniel Bruce ◽  
Ehmke Pohl
Keyword(s):  
Ab Initio ◽  
Small Angle ◽  
Protein Structures ◽  
Scattering Data ◽  
Ab Initio Method ◽  
Primary Sequence ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

ABSTRACTSmall angle X-ray scattering (SAXS) has become an important tool to investigate the structure of proteins in solution. In this paper we present a novel ab-initio method to represent polypeptide chains as discrete curves that can be used to derive a meaningful three-dimensional model from only the primary sequence and experimental SAXS data. High resolution crystal structures were used to generate probability density functions for each of the common secondary structural elements found in proteins. These are used to place realistic restraints on the model curve’s geometry. To evaluate the quality of potential models and demonstrate the efficacy of this novel technique we developed a new statistic to compare the entangled geometry of two open curves, based on mathematical techniques from knot theory. The chain model is coupled with a novel explicit hydration shell model in order derive physically meaningful 3D models by optimizing configurations against experimental SAXS data using a monte-caro based algorithm. We show that the combination of our ab-initio method with spatial restraints based on contact predictions successfully derives a biologically plausible model of the coiled–coil component of the human synaptonemal complex central element protein.SIGNIFICANCESmall-angle X-ray scattering allows for structure determination of biological macromolecules and their complexes in aqueous solution. Using a discrete curve representation of the polypeptide chain and combining it with empirically determined constraints and a realistic solvent model we are now able to derive realistic ab-initio 3-dimensional models from BioSAXS data. The method only require a primary sequence and the scattering data form the user.

Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering

2010 ◽  
Vol 43 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Shuji Akiyama
Keyword(s):  
Quality Control ◽  
Molecular Mass ◽  
Small Angle ◽  
Biological Macromolecules ◽  
Average Deviation ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Standard Quality ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) is a powerful technique with which to evaluate the size and shape of biological macromolecules in solution. Forward scattering intensity normalized relative to the particle concentration,I(0)/c, is useful as a good measure of molecular mass. A general method for deducing the molecular mass from SAXS data is to determine the ratio ofI(0)/cof a target protein to that of a standard protein with known molecular mass. The accuracy of this interprotein calibration is affected considerably by the monodispersity of the prepared standard, as well as by the precision in estimating its concentration. In the present study, chromatographic fractionation followed by hydrodynamic characterization is proposed as an effective procedure by which to prepare a series of monodispersed protein standards. The estimation of molecular mass within an average deviation of 8% is demonstrated using monodispersed bovine serum albumin as a standard. The present results demonstrate the importance of protein standard quality control in order to take full advantage of interprotein calibration.

Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer

2014 ◽  
Vol 67 (12) ◽  
pp. 1786 ◽  
Author(s):  
Lachlan W. Casey ◽  
Alan E. Mark ◽  
Bostjan Kobe
Keyword(s):  
Structural Biology ◽  
Small Angle ◽  
Significant Risk ◽  
Macromolecular Crystallography ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The role of small-angle X-ray scattering (SAXS) in structural biology is now well established, and its usefulness in combination with macromolecular crystallography is clear. However, the highly averaged SAXS data present a significant risk of over-interpretation to the unwary practitioner, and it can be challenging to frame SAXS results in a manner that maximises the reliability of the conclusions drawn. In this review, a series of recent examples are used to illustrate both the challenges for interpretation and approaches through which these can be overcome.

Influence of polychromaticity on particle structure determination in small-angle X-ray scattering

2015 ◽  
Vol 48 (6) ◽  
pp. 1935-1942 ◽  
Author(s):  
Wenjia Wang ◽  
Eleonora V. Shtykova ◽  
Vladimir V. Volkov ◽  
Guangcai Chang ◽  
Lianhui Zhang ◽  
...  
Keyword(s):  
Small Angle ◽  
Structural Parameters ◽  
Shape Reconstruction ◽  
The Body ◽  
Particle Structure ◽  
Saxs Data ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Pink beams are now widely used for small-angle X-ray scattering (SAXS) data collection owing to their high intensity. However, the wavelength spread of a pink beam is a factor of 100 higher than that of a monochromatic beam, thus causing the experimental data to be smeared. To reveal the influence of polychromaticity on shape reconstruction, four geometric bodies (sphere, cube, helix and long cylinder) were used for SAXS data analysis. The results reveal that the influence of polychromaticity on the process of shape reconstruction is significantly more dependent on the geometry of the body than on its size. Scattering objects with smoothed scattering curves can tolerate a higher wavelength spread than those with tortuous curves. It is further demonstrated that the structural parameters calculated from the smeared data sets have little deviation from the ideal ones, which indicates the possibility of using a light source with a greater wavelength spread than a conventional pink beam for special time-resolved SAXS experiments. Finally, it is concluded that SAXS data collected in pink-beam mode can be used directly for structural calculations and model reconstructions without a desmearing procedure.

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