Small-angle X-ray and neutron scattering as a tool for structural systems biology

2010 ◽  
Vol 391 (7) ◽  
Author(s):  
Dmitri I. Svergun
Keyword(s):  
Systems Biology ◽  
Neutron Scattering ◽  
Conformational Changes ◽  
Small Angle ◽  
Structural Systems ◽  
Biological Macromolecules ◽  
X Rays ◽  
Hierarchical Systems ◽  
X Ray ◽  
Structural Systems Biology

Abstract Small-angle scattering (SAS) of X-rays and neutrons reveals low-resolution structures of biological macromolecules in solution. With the recent experimental and methodological advances, SAS became a unique tool for characterising biological systems. The method covers an extremely broad range of molecule sizes (from a few kDa to hundreds of MDa) and experimental conditions (temperature, pH, salinity, ligand addition, etc.), which is of primary importance for a systemic approach in structural biology. The method provides unique information about the overall structure and conformational changes of native individual proteins, functional complexes, flexible macromolecules and hierarchical systems. New developments in small-angle X-ray and neutron scattering studies of biological macromolecules in solution are briefly reviewed, with a special emphasis on technical and methodological approaches useful for structural systems biology. Possibilities of synergistic use of the method with other techniques are considered.

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution

2003 ◽  
Vol 36 (2) ◽  
pp. 147-227 ◽  
Author(s):  
Michel H. J. Koch ◽  
Patrice Vachette ◽  
Dmitri I. Svergun
Keyword(s):  
High Resolution ◽  
Neutron Scattering ◽  
Small Angle ◽  
Structure Factor ◽  
Structural Changes ◽  
Biological Macromolecules ◽  
Time Resolved ◽  
Scattering Intensity ◽  
X Ray ◽  
Angle Scattering

1. Introduction 1482. Basics of X-ray and neutron scattering 1492.1 Elastic scattering of electromagnetic radiation by a single electron 1492.2 Scattering by assemblies of electrons 1512.3 Anomalous scattering and long wavelengths 1532.4 Neutron scattering 1532.5 Transmission and attenuation 1553. Small-angle scattering from solutions 1563.1 Instrumentation 1563.2 The experimental scattering pattern 1573.3 Basic scattering functions 1593.4 Global structural parameters 1613.4.1 Monodisperse systems 1613.4.2 Polydisperse systems and mixtures 1633.5 Characteristic functions 1644. Modelling 1664.1 Spherical harmonics 1664.2 Shannon sampling 1694.3 Shape determination 1704.3.1 Modelling with few parameters: molecular envelopes 1714.3.2 Modelling with many parameters: bead models 1734.4 Modelling domain structure and missing parts of high-resolution models 1784.5 Computing scattering patterns from atomic models 1844.6 Rigid-body refinement 1875. Applications 1905.1 Contrast variation studies of ribosomes 1905.2 Structural changes and catalytic activity of the allosteric enzyme ATCase 1916. Interactions between molecules in solution 2036.1 Linearizing the problem for moderate interactions: the second virial coefficient 2046.2 Determination of the structure factor 2057. Time-resolved measurements 2118. Conclusions 2159. Acknowledgements 21610. References 216A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies – on ribosomes and on the allosteric protein aspartate transcarbamoylase – illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

Neutron scattering studies of biological macromolecules in solution

1977 ◽  
Vol 10 (4) ◽  
pp. 485-527 ◽  
Author(s):  
G. G. Kneale ◽  
J. P. Baldwin ◽  
E. M. Bradbury
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Structural Information ◽  
Biological Macromolecules ◽  
X Rays ◽  
X Ray Scattering ◽  
Time Position ◽  
Position Sensitive ◽  
Biological Complexes ◽  
Position Sensitive Detectors

Small-angle neutron scattering studies of biological macromolecules have developed rapidly in recent years due to the advent of high neutron-flux reactors,† efficient position-sensitive area detectors for neutrons (Allemand et al. 1975) and novel design of instruments (Ibel, 1976). At the same time position-sensitive detectors for X-rays (Gabriel & Dupont, 1972) have revitalized the small-angle X-ray scattering field (Kratky & Pilz, 1972; Luzzati et al. 1976) and it is now becoming clear that neutrons and X-rays can provide complementary structural information on biological complexes.

Isotope effects in solution small-angle X-ray scattering

1999 ◽  
Vol 32 (1) ◽  
pp. 113-114 ◽  
Author(s):  
Stephen J. Henderson
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Isotope Effects ◽  
X Rays ◽  
Light Water ◽  
X Ray ◽  
X Ray Scattering ◽  
The Difference ◽  
Ray Scattering

While the difference between using heavy and light water as solvents for small-angle neutron scattering experiments is well known, the lesser difference for the case of small-angle X-ray scattering with these same isotopes of water has, as yet, not been reported. This difference for the case of X-rays is discussed and quantified for several familiar materials: polystyrene latexes, proteins and lipids.

scholarly journals Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5624
Author(s):  
Domenico Lombardo ◽  
Pietro Calandra ◽  
Mikhail A. Kiselev
Keyword(s):  
Light Scattering ◽  
Neutron Scattering ◽  
Conformational Changes ◽  
Small Angle ◽  
Structural Information ◽  
Imaging Techniques ◽  
Structure Characterization ◽  
Full Potential ◽  
X Rays ◽  
Wide Range

Scattering techniques represent non-invasive experimental approaches and powerful tools for the investigation of structure and conformation of biomaterial systems in a wide range of distances, ranging from the nanometric to micrometric scale. More specifically, small-angle X-rays and neutron scattering and light scattering techniques represent well-established experimental techniques for the investigation of the structural properties of biomaterials and, through the use of suitable models, they allow to study and mimic various biological systems under physiologically relevant conditions. They provide the ensemble averaged (and then statistically relevant) information under in situ and operando conditions, and represent useful tools complementary to the various traditional imaging techniques that, on the contrary, reveal more local structural information. Together with the classical structure characterization approaches, we introduce the basic concepts that make it possible to examine inter-particles interactions, and to study the growth processes and conformational changes in nanostructures, which have become increasingly relevant for an accurate understanding and prediction of various mechanisms in the fields of biotechnology and nanotechnology. The upgrade of the various scattering techniques, such as the contrast variation or time resolved experiments, offers unique opportunities to study the nano- and mesoscopic structure and their evolution with time in a way not accessible by other techniques. For this reason, highly performant instruments are installed at most of the facility research centers worldwide. These new insights allow to largely ameliorate the control of (chemico-physical and biologic) processes of complex (bio-)materials at the molecular length scales, and open a full potential for the development and engineering of a variety of nano-scale biomaterials for advanced applications.

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