Direct detection of the protein quaternary structure and denatured entity by small-angle scattering: guanidine hydrochloride denaturation of chaperonin protein GroEL

2002 ◽  
Vol 35 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Yuzuru Hiragi ◽  
Yasutaka Seki ◽  
Kaoru Ichimura ◽  
Kunitsugu Soda
Keyword(s):  
Small Angle ◽  
Quaternary Structure ◽  
Direct Detection ◽  
Guanidine Hydrochloride ◽  
Average Molecular Weight ◽  
Higher Order ◽  
Small Angle Scattering ◽  
Radius Of Gyration ◽  
Order Structure ◽  
Angle Scattering

A change in the higher-order structure of an oligomeric protein is directly detectable by small-angle scattering. A small-angle X-ray scattering (SAXS) study of the denaturation process of the chaperonin protein GroEL by guanidine hydrochloride (GdnHCl) showed that the disappearance of the quaternary structure can be monitored by using a Kratky plot of the scattered intensities, demonstrating the advantage of the SAXS method over other indirect methods, such as light scattering, circular dichroism (CD), fluorescence and sedimentation. The collapse of the quaternary structure was detected at a GdnHCl concentration of 0.8 Mfor a solution containing ADP (adenosine diphosphate)/Mg2+(2 mM)/K+. From pairwise plots of the change in forward scattering intensityJ(0)/C(weight-average molecular weight) and thez-average (root mean square) radius of gyration against the GdnHCl concentration, the stability and nature of the denatured protein can be determined. The SAXS results suggest that the GroEL tetradecamer directly dissociates to the unfolded coil without going through a globular monomer state. The denatured ensemble is not a single unfolded monomer coil particle, but some mixture of entangled aggregates and a monomer of the coil molecules. Small-angle scattering is a powerful method for the detection and study of changes in quaternary and higher-order structures of oligomeric proteins.

Information retrieval from X-ray small-angle scattering with polychromatic (`white') synchrotron radiation

1983 ◽  
Vol 16 (1) ◽  
pp. 42-46 ◽  
Author(s):  
O. Glatter ◽  
P. Laggner
Keyword(s):  
Synchrotron Radiation ◽  
Small Angle ◽  
Particle Shape ◽  
Structural Information ◽  
Small Angle Scattering ◽  
Radius Of Gyration ◽  
X Ray ◽  
Angle Scattering ◽  
Slit Length ◽  
Hinge Bending

The possibilities of obtaining structural information from X-ray small-angle scattering experiments with `white' polychromatic synchrotron radiation using line collimation are investigated by numerical simulation. Theoretical scattering curves of geometrical models were smeared with the appropriate wavelength distributions and slit-length functions, afflicted by statistical noise, and then evaluated by identical methods as normally used for experimental data, as described previously [program ITP; Glatter (1977). J. Appl. Cryst. 10, 415–421]. It is shown that even for a wavelength distribution of 50% half width, the information content is not limited to the parameters derived from the central part of the scattering curves, i.e. the radius of gyration and the zero-angle intensity, but also allows qualitative information on particle shape via the distance distribution function p(r). By a `hinge-bending model' consisting of two cylinders linked together at different angles it is demonstrated that changes in the radius of gyration amounting to less than 5% can be detected and quantified, and the qualitative changes in particle shape be reproduced.

Phenylalanyl-tRNA Synthetase from Baker'Yeast: Structural Organization of the Enzyme and Its Complex with tRNAPhe as Determined by X-Ray Small-Angle Scattering

1979 ◽  
Vol 34 (1-2) ◽  
pp. 20-26 ◽  
Author(s):  
Ingrid Pilz ◽  
Karin Goral ◽  
Friedrich v. d. Haar
Keyword(s):  
Molecular Weight ◽  
Small Angle ◽  
Quaternary Structure ◽  
Trna Synthetase ◽  
Distribution Functions ◽  
Maximum Diameter ◽  
Radius Of Gyration ◽  
X Ray ◽  
Angle Scattering ◽  
The Difference

Abstract The quaternary structure of the phenylalanyl-tRNA synthetase and its complex with tRNAPhe was studied in dilute solutions by small angle X-ray scattering. For the free synthetase the radius of gyration was determined as 5.5 nm, the volume 523 nm3, the maximum diameter 17.5 nm and the molecular weight as 260 000 using an isopotential specific volume of 0.735. The overall shape could be best approximated by a flat cylinder with dimensions 18.2 nm X 11.5 nm X 4 nm ; the loose structure was approximated by building up the cylinder by spheres (diameter 4.2 nm).The corresponding parameters of the enzyme tRNA complex were the following: radius of gyration 5.9 nm, volume 543 nm 3, maximum diameter 21 nm and molecular weight 290 000. These parameters suggest an 1:1 complex, whereby it must be assumed that the tRNA molecule is attached in the extension of the longer axis. From the difference in the distance distribution functions of the free enzyme and the complex it is evident that we have to assume a change of conformation (contraction) of the enzyme upon the binding of the specific tRNA.

scholarly journals Scattering from generalized Cantor fractals

2010 ◽  
Vol 43 (4) ◽  
pp. 790-797 ◽  
Author(s):  
A. Yu. Cherny ◽  
E. M. Anitas ◽  
A. I. Kuklin ◽  
M. Balasoiu ◽  
V. A. Osipov
Keyword(s):  
Fractal Dimension ◽  
Small Angle ◽  
Cantor Set ◽  
Small Angle Scattering ◽  
Three Dimensions ◽  
Radius Of Gyration ◽  
Large Wave ◽  
Fractal Sets ◽  
Power Law Decay ◽  
Angle Scattering

A fractal with a variable fractal dimension, which is a generalization of the well known triadic Cantor set, is considered. In contrast with the usual Cantor set, the fractal dimension is controlled using a scaling factor, and can vary from zero to one in one dimension and from zero to three in three dimensions. The intensity profile of small-angle scattering from the generalized Cantor fractal in three dimensions is calculated. The system is generated by a set of iterative rules, each iteration corresponding to a certain fractal generation. Small-angle scattering is considered from monodispersive sets, which are randomly oriented and placed. The scattering intensities represent minima and maxima superimposed on a power law decay, with the exponent equal to the fractal dimension of the scatterer, but the minima and maxima are damped with increasing polydispersity of the fractal sets. It is shown that, for a finite generation of the fractal, the exponent changes at sufficiently large wave vectors from the fractal dimension to four, the value given by the usual Porod law. It is shown that the number of particles of which the fractal is composed can be estimated from the value of the boundary between the fractal and Porod regions. The radius of gyration of the fractal is calculated analytically.

scholarly journals Reduction of small-angle scattering profiles to finite sets of structural invariants

2017 ◽  
Vol 73 (4) ◽  
pp. 317-332
Author(s):  
Jérôme Houdayer ◽  
Frédéric Poitevin
Keyword(s):  
Small Angle ◽  
Shape Reconstruction ◽  
Theoretical Description ◽  
Small Angle Scattering ◽  
Radius Of Gyration ◽  
Comprehensive Description ◽  
Model Free ◽  
Angle Scattering ◽  
Object Of Study ◽  
Pair Distance Distribution Function

This paper shows how small-angle scattering (SAS) curves can be decomposed in a simple sum using a set of invariant parameters calledKnwhich are related to the shape of the object of study. TheseKn, together with a radiusR, give a complete theoretical description of the SAS curve. Adding an overall constant, these parameters are easily fitted against experimental data giving a concise comprehensive description of the data. The pair distance distribution function is also entirely described by this invariant set and theDmaxparameter can be measured. In addition to the understanding they bring, these invariants can be used to reliably estimate structural moments beyond the radius of gyration, thereby rigorously expanding the actual set of model-free quantities one can extract from experimental SAS data, and possibly paving the way to designing new shape reconstruction strategies.

scholarly journals Effects of multiple scattering encountered for various small-angle scattering model functions

2018 ◽  
Vol 51 (5) ◽  
pp. 1455-1466 ◽  
Author(s):  
Grethe Vestergaard Jensen ◽  
John George Barker
Keyword(s):  
Multiple Scattering ◽  
Small Angle ◽  
Gaussian Function ◽  
Small Angle Scattering ◽  
Radius Of Gyration ◽  
Scattering Function ◽  
Angle Scattering ◽  
Scattering Effects ◽  
The Impact ◽  
Multiple Scattering Effects

In small-angle scattering theory and data modeling, it is generally assumed that each scattered ray – photon or neutron – is only scattered once on its path through the sample. This assumption greatly simplifies the interpretation of the data and is valid in many cases. However, it breaks down under conditions of high scattering power, increasing with sample concentration, scattering contrast, sample path length and ray wavelength. For samples with a significant scattering power, disregarding multiple scattering effects can lead to erroneous conclusions on the structure of the investigated sample. In this paper, the impact of multiple scattering effects on different types of scattering pattern are determined, and methods for assessing and addressing them are discussed, including the general implementation of multiple scattering effects in structural model fits. The modification of scattering patterns by multiple scattering is determined for the sphere scattering function and the Gaussian function, as well as for different Sabine-type functions, including the Debye–Andersen–Brumberger (DAB) model and the Lorentzian scattering function. The calculations are performed using the semi-analytical convolution method developed by Schelten & Schmatz [J. Appl. Cryst. (1980). 13, 385–390], facilitated by analytical expressions for intermediate functions, and checked with Monte Carlo simulations. The results show how a difference in the shape of the scattering function plotted versus momentum transfer q results in different multiple scattering effects at low q, where information on the particle mass and radius of gyration is contained.

Small-angle scattering: the Guinier technique underestimates the size of hard globular particles due to the structure-factor effect

2015 ◽  
Vol 48 (4) ◽  
pp. 1089-1093 ◽  
Author(s):  
Alexander V. Smirnov ◽  
Ivan N. Deryabin ◽  
Boris A. Fedorov
Keyword(s):  
Small Angle ◽  
Structure Factor ◽  
Hard Spheres ◽  
Small Angle Scattering ◽  
Radius Of Gyration ◽  
Concentration Effects ◽  
Factor Effect ◽  
Calculated Correction ◽  
Angle Scattering ◽  
Guinier Plot

The straightforward calculation of small-angle scattering intensity by hard spheres at different concentrations is performed. For the same system of hard spheres, the scattering intensities were found both using the product of the form factor and the structure factor {based on the work of Kinning & Thomas [Macromolecules, (1984),17, 1712–1718]} and using the correlation function {based on the work of Kruglov [J. Appl. Cryst.(2005),38, 716–720] and Hansen [J. Appl. Cryst.(2011),44, 265–271;J. Appl. Cryst.(2012),45, 381–388]}. All three intensities are in agreement at every concentration. The values of the radii of gyration found from the Guinier plot are shown to be noticeably underestimated compared to the true radius of gyration of a single sphere. Presented are the calculated correction factors that should be applied to the experimentally found radius of gyration of spheres. Also, the concentration effects are shown to have an even greater impact on the radius of gyration of prolate particles that is found from the Guinier plot.

A comparison of X-ray small-angle scattering results to crystal structure analysis and other physical techniques in the field of biological macromolecules

1978 ◽  
Vol 11 (1) ◽  
pp. 39-70 ◽  
Author(s):  
O. Kratky ◽  
I. Pilz
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Small Angle ◽  
Quaternary Structure ◽  
Heavy Atom ◽  
Crystal Structure Analysis ◽  
Small Angle Scattering ◽  
Biological Macromolecules ◽  
X Ray ◽  
Angle Scattering

In principle, there exist two ways to contribute to structure determination of macromolecules by X-ray diffraction: (a) by analysing diffraction data obtained from the crystalline state, and (b) by interpretation of X-ray small-angle scattering from particles in solution.The brilliant achievements of X-ray crystal-structure analysis of macromolecules, initiated by the works of Perutz on heamoglobin and Kendrew on myoglobin, are well known and it is evident that its detailed elution of secondary, tertiary and quaternary structure cannot be matched by any other means. However, a number of necessary prerequisites for a successful application, as, for example, the availability of well-defined crystals and heavy atom labelled derivatives thereof to surmount the problem of phase determination are not always given.

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