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E-grāmata: Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules

(Department of Chemistry, University of Leuven), (Long-term Visitor, Institut Laue-Langevin, Grenoble), (Long-term Visitor, Institut Laue-Langevin, Gr), (Group Leader and Senior Scientist, European Molecular Biology Laboratory, Hamburg)
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Small-angle scattering of X-rays (SAXS) and neutrons (SANS) is an established method for the structural characterization of biological objects in a broad size range from individual macromolecules (proteins, nucleic acids, lipids) to large macromolecular complexes. SAXS/SANS is complementary to the high resolution methods of X-ray crystallography and nuclear magnetic resonance, allowing for hybrid modeling and also accounting for available biophysical and biochemical data. Quantitative characterization of flexible macromolecular systems and mixtures has recently become possible. SAXS/SANS measurements can be easily performed in different conditions by adding ligands or binding partners, and by changing physical and/or chemical characteristics of the solvent to provide information on the structural responses. The technique provides kinetic information about processes like folding and assembly and also allows one to analyze macromolecular interactions.
The major factors promoting the increasingly active use of SAXS/SANS are modern high brilliance X-ray and neutron sources, novel data analysis methods, and automation of the experiment, data processing and interpretation.

In this book, following the presentation of the basics of scattering from isotropic macromolecular solutions, modern instrumentation, experimental practice and advanced analysis techniques are explained. Advantages of X-rays (rapid data collection, small sample volumes) and of neutrons (contrast variation by hydrogen/deuterium exchange) are specifically highlighted. Examples of applications of the technique to different macromolecular systems are considered with specific emphasis on the synergistic use of SAXS/SANS with other structural, biophysical and computational techniques.

Recenzijas

This book is a masterly treatment by four authors with many decades of experience of SAXS and SANS and who are from world class synchrotron X-ray and neutron research facilities. From the basics and on through the instrumentation and data analysis descriptions, as well as numerous research themes and examples, this book will be invaluable to newcomers and be useful to the specialists. It also should be read in detail by structural biology researchers whether principally from crystallography, bio NMR, EM or bioinformatics. It's surely going to be a classic book. * John Helliwell, University of Manchester * Small angle X-ray and neutron scattering from solutions of biological macromolecules is an essential book covering the theory, experiment, data analysis, and applications of small-angle scattering (SAS) ... No laboratory interested in SAS should be without a copy and it provides a good background to the capabilities, limitations, and practical application of the technique. The authors should be commended and the book is strongly recommended. * Crystallography Reviews *

Introduction 1(8)
References 9(4)
PART I THEORY AND EXPERIMENT
1 Basics of small angle scattering
13(14)
1.1 Elastic scattering of X-rays and neutrons
13(5)
1.2 Scattering by macromolecular solutions
18(3)
1.3 Resolution and contrast
21(4)
1.4 Absorption and anomalous X-ray scattering
25(2)
References
26(1)
2 X-ray and neutron scattering instruments
27(38)
2.1 Characteristics of sources
27(2)
2.2 X-ray sources
29(8)
2.3 Neutron sources
37(6)
2.4 SAXS instruments
43(9)
2.5 SANS instruments
52(5)
2.6 Special instruments
57(8)
References
62(3)
3 Experimental practice and data processing
65(28)
3.1 Sample requirements for SAXS and SANS
65(3)
3.2 Experimental protocols and instrumental corrections
68(4)
3.3 Special features of SAXS: radiation damage
72(3)
3.4 Special features of SANS: the use of H2O/D2O mixtures
75(4)
3.5 Random and systematic errors
79(2)
3.6 Basic structural information and data quality
81(4)
3.7 Calibration to absolute scale and molecular mass
85(8)
References
88(5)
PART II DATA ANALYSIS METHODS
4 Monodisperse systems
93(59)
4.1 Overall parameters of particles
93(15)
4.2 Multipole representation of SAS intensity
108(2)
4.3 Shannon sampling
110(2)
4.4 Ab initio shape analysis
112(13)
4.5 Computation of scattering patterns from atomic models
125(3)
4.6 Hybrid methods
128(6)
4.7 Labelling and triangulation
134(18)
References
145(7)
5 Polydisperse and interacting systems
152(19)
5.1 Size, shape and conformation polydispersity
152(1)
5.2 Size distribution functions
153(2)
5.3 Shape polydispersity and oligomeric mixtures
155(4)
5.4 Conformational polydispersity and flexible systems
159(4)
5.5 Interacting systems and structure factor
163(8)
References
166(5)
PART III BIOLOGICAL APPLICATIONS OF SOLUTION SAS
6 Static structural studies
171(49)
6.1 Applications of ab initio shape determination
171(10)
6.2 Quaternary structure analysis of proteins and complexes
181(11)
6.3 Equilibrium mixtures and oligomeric composition
192(6)
6.4 Membrane proteins and lipoproteins
198(7)
6.5 Flexible systems
205(15)
References
212(8)
7 Kinetic and perturbation studies
220(39)
7.1 Dynamics and kinetics
221(2)
7.2 Perturbation methods
223(7)
7.3 Temperature scans and T-jumps
230(3)
7.4 High-pressure experiments
233(4)
7.5 Stopped-flow and continuous-flow mixing
237(10)
7.6 Light-triggered processes
247(12)
References
250(9)
8 Analysis of interparticle interactions
259(27)
8.1 Basic physical chemistry of interactions
259(6)
8.2 Experimental SAS studies of protein-protein interactions
265(1)
8.3 Structure factor calculations for proteins
266(14)
8.4 Interactions in nucleic acids
280(6)
References
281(5)
9 SAS in multidisciplinary studies
286(37)
9.1 Automation and high-throughput SAS
286(5)
9.2 Joint use with high-resolution methods
291(7)
9.3 SAS and low-resolution crystallography
298(5)
9.4 Complementary biophysical methods
303(6)
9.5 Bioinformatics and model validation
309(11)
References
314(6)
Conclusions and future prospects
320(3)
Appendices
323(30)
Appendix 1 Basic physics and mathematics of wave phenomena
323(15)
Appendix 2 Spherical harmonics and their applications for SAS
338(5)
Appendix 3 Interactions between spherical molecules
343(6)
Appendix 4 Web resources
349(4)
Abbreviations list 353(2)
Index of computer programs 355(2)
Index 357
Dmitri I.Svergun: MSc in Solid state physics (1980), Physics Department, Moscow State University, Russia; PhD in Physics and Mathematics (1982) and Dr. of Science (1997), Institute of Crystallography, Moscow, Russia; Engineer, Researcher, Senior Scientist at the Institute of Crystallography, Russian Academy of Sciences, Moscow (1980 - 2008); Guest scientist, GKSS Research Centre, Geesthacht, Germany (1990-1991); Visitor, Staff Scientist, Group Leader, at the European Molecular Biology Laboratory Hamburg Outstation (1991-present).

Michel, H.J. Koch: PhD in chemistry, University of Louvain (1970), Neutron scattering on biological macromolecules in solution (1974-1976). Consultant (1975-1976), Group leader at the European Molecular Biology Laboratory outstation at DESY, Hamburg (1977-2006), Visiting professor at the Faculty of Engineering and Natural Science, Sabanci University, Turkey (2008-2009) and the Chemistry Department, University of Leuven (2006 - present).

Roland May: Diploma in Physics (Technische Universität München); Thesis work at the Max-Planck Institut für Biochemie, Martinsried; PhD Technische Universität München 1978; scientist in the Large-Scale Structures group of the Institut Laue-Langevin, Grenoble until 2008; retired.

Peter Timmins: BSc in Chemistry (1967), MSc in Crystallography (1968) and PhD in Crystallography (1972) - Birkbeck College, University of London. Instrument Scientist, Institut Laue-Langevin, 1975 - 1993, Head, Large Scale Structures Group, Institut Laue-Langevin, 1993 - 2010. Since 2010, retired.