Structural Biology Using Electrons and X-rays

Structural Biology Using Electrons and X-rays, 1st Edition

An Introduction for Biologists

Structural Biology Using Electrons and X-rays, 1st Edition,Michael F Moody,ISBN9780123705815

M Moody   

Academic Press




235 X 191

An accessible introduction to the two major diffraction-based techniques of structural biology

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Key Features

*Emphasis on common principles underlying all diffraction-based methods

*Thorough grounding in theory requires understanding of only simple algebra

*Visual representations and explanations of challenging content

*Mathematical detail offered in short-course form to parallel the text


Structural Biology Using Electrons and X-Rays discusses the diffraction and image-based methods used for the determination of complex biological macromolecules. The book focuses on the Fourier transform theory, which is a mathematical function that is computed to transform signals between time and frequency domain. Composed of five parts, the book examines the development of nuclear magnetic resonance (NMR), which allows the calculation of the images of a certain protein. Parts 1 to 4 provide the basic information and the applications of Fourier transforms, as well as the different methods used for image processing using X-ray crystallography and the analysis of electron micrographs. Part 5 focuses entirely on the mathematical aspect of Fourier transforms. In addition, the book examines detailed structural analyses of a specimen’s symmetry (i.e., crystals, helices, polyhedral viruses and asymmetrical particles). This book is intended for the biologist or biochemist who is interested in different methods and techniques for calculating the images of proteins using nuclear magnetic resonance (NMR). It is also suitable for readers without a background in physical chemistry or mathematics.


Graduate and advanced undergraduate students in biochemistry, molecular biology, and biological and medical physics; research biologists using electron microscopy

Michael F Moody

Structural Biology Using Electrons and X-rays, 1st Edition

Preface Chapter 1: Overview 1.1 Role of Structural (Molecular) Biology 1.2 A Short History of Structural (Molecular) Biology 1.2.1 The Nature of the Problem 1.2.2 ‘Imaging’ Techniques 1.2.3 Nuclear Magnetic Resonance 1.2.4 Fundamental Limitations to Finding Macromolecule Structures Part I: Fourier Transforms Chapter 2: Correlations and Convolutions 2.1 Introducing Correlations 2.2 Function Parity 2.3 Auto-Correlation Function Chapter 3: Fourier Fundamentals 3.1 Component Functions 3.2 Fourier Analysis of Periodic Even Functions 3.3 Sines and Phasors 3.4 Fourier Transforms 3.5 Summary of Rules Chapter 4: Digital Fourier Transforms 4.1 Data Preparation 4.2 Digital Fourier Transform Features 4.3 Digital Fourier Transform Calculations 4.4 Appendix Chapter 5: Filters 5.1 Introduction 5.2 Blurring Filters 5.3 Digital-to-Analog Conversion 5.4 Correcting Blurring Filters 5.5 Gradients and Derivatives Chapter 6: Two-Dimensional FTs 6.1 Two-Dimensional Fourier Transforms Rules 6.2 Points and Lines 6.3 Polygons 6.4 Polar Coordinates Part II: Optics Chapter 7: Microscopy with Rays 7.1 Light Microscopy 7.2 Electron Microscopy 7.3 Electron Lens Aberrations 7.4 Contrast Mechanisms Chapter 8: Waves 8.1 Wave Properties 8.2 The Quantum Electron 8.3 Fresnel Diffraction 8.4 Fraunhofer Diffraction 8.5 Appendix Chapter 9: Wave Imaging 9.1 Overview of Wave Imaging 9.2 Defocus 9.3 Other Aberrations 9.4 Appendix: Aberration Phase-Shift Geometry Part III: General Structural Methods Chapter 10: Symmetry 10.1 Principles 10.2 One-Translation Groups 10.3 Two-Translation Groups 10.4 Three-Translation Groups 10.5 Fourier Transforms of Crystallographic Symmetry Operations Chapter 11: Statistics and Matrices 11.1 Statistics 11.2 Matrices 11.3 Structure Optimization and Simulation 11.4 Appendix Chapter 12: The Third Dimension 12.1 Depth Through Tilting 12.2 Aligning Particle Images 12.3 Information Content of Particle Images 12.4 Three-Dimensional Reconstruction: Principles Part IV: Symmetry-Based Methods Chapter 13: X-Ray Crystallography 13.1 Introduction 13.2 Specimen and Data Collection 13.3 Ab Initio Phasing 13.4 Other Phasing Methods Chapter 14: Crystalline Sheets 14.1 Electrons Versus X-Rays 14.2 Electron Diffraction 14.3 Two-Dimensional Imaging 14.4 Three-Dimensional Imaging Chapter 15: Helices 15.1 Helical Symmetry and Structure 15.2 Helical Fourier Transforms 15.3 Getting a Structure from Helical Diffraction Data Chapter 16: Icosahedral Particles 16.1 Deltahedra 16.2 Projections 16.3 Three-Dimensional Reconstruction 16.4 Appendix: Calculation of T-numbers Chapter 17: Unsymmetrical (‘Single’) Particles 17.1 Introduction 17.2 Alignment 17.3 Multivariate Statistical Analysis 17.4 Reconstruction Chapter 18: Distortion Correction 18.1 Introduction 18.2 Crystalline Sheets 18.3 Helices Part V: Mathematical Basis Chapter 19: FT Mathematics 19.1 Introduction 19.2 Algebra 19.3 Geometry 19.4 Infinitesimals 19.5 Calculus Chapter 20: Elementary Matrices 20.1 Introducing Matrices 20.2 Matrix Inversion 20.3 Eigenvectors 20.4 Least-Squares Fits References Index

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