Three-Dimensional Electron Microscopy of Macromolecular Assemblies Visualization of Biological Molecules in Their Native State

by Frank, Joachim

• ISBN13: 9780195150964
• ISBN10: 0195150961
• Edition: 2nd
• Format: Hardcover
• Copyright: 2006-02-02
• Publisher: Oxford University Press

Summary

Cryoelectron microscopy of biological molecules is among the hottest growth areas in biophysics and structural biology at present, and Frank is arguably the most distinguished practitioner of this art. CryoEM is likely over the next few years to take over much of the structural approachescurrently requiring X-ray crystallography, because one can now get good and finely detailed images of single molecules down to as little as 200,000 MW, covering a substantial share of the molecules of greatest biomedical research interest. This book, the successor to an earlier work published in1996 with Academic Press, is a natural companion work to our forthcoming book on electron crystallography by Robert Glaeser, with contributions by six others, including Frank. A growing number of workers will employ CryoEM for structural studies in their own research, and a large proportion ofbiomedical researchers will have a growing interest in understanding what the capabilities and limits of this approach are.

Table of Contents

Introduction	1	(14)
The Electron Microscope and Biology	1	(4)
General Remarks	1	(1)
Three-Dimensional Electron Microscopy	2	(3)
Single-Particle Versus Crystallographic Analysis	5	(2)
Crystallography without Crystals	7	(2)
Toward a Unified Approach to Structural Analysis of Macromolecules	9	(1)
Single-Particle Reconstruction, Macromolecular Machines, and Structural Proteomics	10	(2)
The Electron Microscope and the Computer	12	(3)
Electron Microscopy of Macromolecular Assemblies	15	(56)
Principle of the Transmission Electron Microscope	15	(4)
Specimen Preparation Methods	19	(15)
Introduction	19	(1)
Negative Staining	20	(7)
Glucose Embedment	27	(1)
Use of Tannic Acid	28	(1)
Ice-Embedded Specimens	28	(3)
Hybrid Techniques: Cryo-Negative Staining	31	(2)
Labeling with Gold Clusters	33	(1)
Support Grids	33	(1)
Principle of Image Formation in the Transmission Electron Microscope	34	(30)
Introduction	34	(1)
The Weak-Phase Object Approximation	35	(4)
The Contrast Transfer Theory	39	(8)
Amplitude Contrast	47	(2)
Formulation of Bright-Field Image Formation Using Complex Atomic Scattering Amplitudes	49	(1)
Optical and Computational Diffraction Analysis---The Power Spectrum	50	(3)
Determination of the Contrast Transfer Function	53	(4)
Instrumental Correction of the Contrast Transfer Function	57	(1)
Computational Correction of the Contrast Transfer Function	58	(4)
Locally Varying CTF and Image Quality	62	(2)
Special Imaging Techniques and Devices	64	(7)
Low-Dose Electron Microscopy	64	(2)
Spot Scanning	66	(1)
Energy Filtration	67	(1)
Direct Image Readout and Automated Data Collection	68	(3)
Two-Dimensional Averaging Techniques	71	(74)
Introduction	72	(11)
The Different Sources and Types of Noise	72	(2)
Principle of Averaging: Historical Notes	74	(1)
Equivalence between Averaging and Quasi-Optical Fourier Filtration	75	(3)
A Discourse on Terminology: Views Versus Projections	78	(1)
The Role of Two-Dimensional Averaging in the Three-Dimensional Analysis of Single Molecules	78	(1)
Origins of Orientational Preferences	79	(4)
Digitization and Selection of Particles	83	(8)
Hardware for Digitization	83	(1)
The Sampling Theorem	84	(2)
Interactive Particle Selection	86	(1)
Automated Particle Selection	87	(4)
Alignment Methods	91	(24)
Quantitative Definitions of Alignment	91	(1)
Homogeneous Versus Heterogeneous Image Sets	92	(2)
Translational and Rotational Cross-Correlation	94	(6)
Reference-Based Alignment Techniques	100	(9)
Reference-Free Alignment Techniques	109	(6)
Alignment Using the Radon Transform	115	(1)
Averaging and Global Variance Analysis	115	(9)
The Statistics of Averaging	115	(2)
The Variance Map and the Analysis of Statistical Significance	117	(4)
Signal-to-Noise Ratio	121	(3)
Resolution	124	(18)
The Concept of Resolution	124	(2)
Resolution Criteria	126	(11)
Resolution and Cross-Resolution	137	(1)
Resolution-Limiting Factors	138	(1)
Statistical Requirements following the Physics of Scattering	139	(1)
Noise Filtering	140	(2)
Validation of the Average Image	142	(3)
Multivariate Data Analysis and Classification of Images	145	(48)
Introduction	145	(8)
Heterogeneity of Image Sets	146	(1)
Images as a Set of Multivariate Data	147	(1)
The Principle of Making Patterns Emerge from Data	148	(1)
Multivariate Data Analysis: Principal Component Analysis Versus Correspondence Analysis	149	(4)
Theory of Correspondence Analysis	153	(9)
Analysis of Image Vectors in RJ	154	(1)
Analysis of Pixel Vectors in RN	155	(1)
Factorial Coordinates and Factor Maps	156	(1)
Reconstitution	157	(4)
Computational Methods	161	(1)
Significance Test	161	(1)
Correspondence Analysis in Practice	162	(14)
A Model Image Set Used for Demonstration	162	(1)
Definition of the Image Region to Be Analyzed	162	(4)
Eigenvalue Histogram and Factor Map	166	(3)
Case Study: Ribosome Images	169	(3)
Use of Explanatory Tools	172	(4)
Classification	176	(17)
Background	176	(1)
Overview over Different Approaches and Goals of Classification	177	(1)
K-Means Clustering	178	(2)
Hierarchical Ascendant Classification	180	(2)
Hybrid Clustering Techniques	182	(2)
Inventories	184	(1)
Analysis of Trends	185	(1)
Nonlinear Mapping	185	(1)
Self-Organized Maps	186	(2)
Supervised Classification: Use of Templates	188	(1)
Inference from Two to Three Dimensions	189	(4)
Three-Dimensional Reconstruction	193	(84)
Introduction	193	(1)
General Mathematical Principles	194	(7)
The Projection Theorem and Radon's Theorem	194	(2)
Object Boundedness, Shape Transform, and Resolution	196	(2)
Definition of Eulerian Angles, and Special Projection Geometries: Single-Axis and Conical Tilting	198	(3)
The Rationales of Data Collection: Reconstruction Schemes	201	(12)
Introduction	201	(1)
Cylindrically Averaged Reconstruction	202	(3)
Compatibility of Projections	205	(1)
Relating Projections to One Another Using Common Lines	206	(4)
The Random-Conical Data Collection Method	210	(2)
Comparison of Common Lines Versus Random-Conical Methods	212	(1)
Reconstruction Schemes Based on Uniform Angular Coverage	213	(1)
Overview of Existing Reconstruction Techniques	213	(9)
Preliminaries	213	(1)
Weighted Back-Projection	214	(5)
Fourier Reconstruction Methods	219	(2)
Iterative Algebraic Reconstruction Methods	221	(1)
The Random-Conical Reconstruction in Practice	222	(10)
Overview	222	(1)
Optical Diffraction Screening	222	(3)
Interactive Tilted/Untilted Particle Selection	225	(1)
Optical Density Scaling	226	(1)
Processing of Untitled-Particle Images	227	(1)
Processing of Tilted-Particle Images	228	(3)
Carrying Out the Reconstruction	231	(1)
Common-Lines Methods (or ``Angular Reconstitution'') in Practice	232	(1)
Reference-Based Methods and Refinement	232	(15)
Introduction	232	(4)
Three-Dimensional Projection Matching	236	(4)
Numerical Aspects	240	(2)
Three-Dimensional Radon Transform Method	242	(1)
The Size of Angular Deviations	243	(3)
Model Dependence of the Reconstruction	246	(1)
Consistency Check by Reprojection	247	(1)
Resolution Assessment	247	(8)
Theoretical Resolution of the 3D Reconstruction	247	(1)
Practically Achieved Resolution	248	(5)
Cross-Validation Using Excision of Fourier Data from the 3D Reference	253	(2)
Contrast Transfer Function and Fourier Amplitude Correction	255	(6)
Introduction	255	(1)
Contrast Transfer Function Correction	255	(4)
Fourier Amplitude Correction	259	(2)
Three-Dimensional Restoration	261	(5)
Introduction	261	(1)
Theory of Projection onto Convex Sets	262	(2)
Projection onto Convex Sets in Practice	264	(2)
Reconstructions from Heterogeneous Data Sets	266	(4)
Introduction	266	(1)
Separating Ligand-Bound from Ligand-Free Complexes	266	(1)
Separating Populations with Different Conformations	267	(3)
Merging and Averaging of Reconstructions	270	(7)
The Rationale for Merging	270	(1)
Negatively Stained Specimens: Complications due to Preparation-Induced Deformations	271	(1)
Alignment of Volumes	272	(3)
Merging of Reconstructions through Merging of Projection Sets into a Common Coordinate Frame	275	(1)
Classification of 3D Volumes	276	(1)
Interpretation of Three-Dimensional Images of Macromolecules	277	(42)
Introduction	277	(2)
Assessment of Statistical Significance	279	(7)
Introduction	279	(1)
Three-Dimensional Variance Estimation from Projections	280	(4)
Use of the 3D Variance Estimate to Ascertain the Statistical Significance	284	(2)
Validation and Consistency	286	(7)
Internal Consistency	286	(1)
Reconstructions from the Same Data Set with Different Algorithms	286	(1)
Consistency with X-Ray Structures	287	(4)
Concluding Remarks	291	(2)
Visualization and Rendering	293	(5)
Surface Rendering	294	(2)
Definition of Boundaries	296	(1)
Volume Rendering	297	(1)
Segmentation of Volumes	298	(10)
Manual (Interactive) Segmentation	299	(1)
Segmentation Based on Density Alone	299	(4)
Knowledge-Based Segmentation, and Identification of Regions	303	(5)
Methods for Docking and Fitting	308	(8)
Manual Fitting	309	(2)
Quantitative Fitting	311	(5)
Classification of Volumes	316	(3)
Appendix 1 Some Important Definitions and Theorems	319	(8)
Appendix 2 Profiles, Point-Spread Functions, and Effects of Commonly Used Low-Pass Filters	327	(4)
Appendix 3 Bibliography of Methods	331	(6)
Appendix 4 Bibliography of Structures	337	(6)
Appendix 5 Special Journal Issues on Image Processing Techniques	343	(2)
References	345	(54)
Index	399