Dynamics and Kinetics in Structural Biology

Keith Moffat, PhD is the Louis Block Distinguished Service Professor of Biochemistry and Molecular Biology and a founding member of the Institute for Biophysical Dynamics, University of Chicago, USA. He pioneered the technique of time-resolved crystallography and has published very widely in the fields of biophysics and biochemistry. Eaton E. Lattman, PhD has served as Professor at the Johns Hopkins University and the University at Buffalo, among other roles. He was director of BioXFEL, an NSF-sponsored center for the application of X-ray lasers to biology. He has years of experience in the fields of X-ray crystallography, structural biology, and related areas.

• List of Figures xiiAcknowledgments xivAcronyms/Abbreviations xviUnits xix1 Introduction: Principles of Kinetics and Dynamics 11.1 Structure, Function, and Mechanism 11.2 Activity in the Crystal 31.3 Other Structure-informing Techniques 71.4 Dynamics, Kinetics, Movies, Pathways, and Functional Trajectories 81.5 The Time-resolved Experiment: An Overview 122 Physical Chemistry of Reactions 192.1 Introduction 192.2 Thermodynamics: States and Equilibria 192.3 Kinetics, Rates, and Rate Coefficients 252.4 Enzyme Kinetics 282.5 Transition State Theory and Energy Landscapes 342.6 Trapping of Intermediates 383 The Experiment 433.1 Introduction 433.2 Signal and Noise 433.3 Reaction Initiation 484 The Sample 704.1 Crystal and Solution Samples 704.2 Introduction of the Sample to the X-ray Beam: Injection and Fixed Targets 724.3 Radiation Damage 764.4 Optogenetics and Photopharmacology 825 Time-resolved Crystallography, Solution Scattering, and Molecular Dynamics 925.1 Time-resolved Crystallography 925.2 Time-resolved X-ray Solution Scattering 1045.3 Molecular Dynamics Simulations 1166 X-ray Sources, Detectors, and Beamlines 1266.1 Introduction 1266.2 Sources of Synchrotron Radiation 1276.3 X-ray Free Electron Lasers 1366.4 Detectors 1416.5 Beamlines and Experimental Stations 1437 Data Analysis and Interpretation 1507.1 Introduction 1507.2 General Constraints on Analysis and Interpretation 1527.3 Difference Electron Density Maps 1547.4 Singular Value Decomposition (SVD) 1607.5 Features Commonly Found in DED Maps 1677.6 Refinement of Intermediate Structures 1687.7 Example: The Photosynthetic Reaction Center 1697.8 Making a Molecular Movie 1727.9 Does the Mechanism in the Crystal Represent the Mechanism in Solution? 1738 Other Structural Biology Techniques 1788.1 Introduction 1788.2 Single-Particle Cryo-Electron Microscopy 1788.3 Energy Landscape Analysis 1818.4 X-ray Spectroscopy 1938.5 Nuclear Magnetic Resonance: Joseph Sachleben (University of Chicago) 2028.6 Hydrogen-Deuterium Exchange 2139 Looking Forward 2229.1 Overview: Unraveling Function and Mechanism 2229.2 Single Particle Imaging, Energy Landscape Analysis, and Functional Trajectories 2239.3 Artificial Intelligence and Machine Learning 2239.4 Experimental Approaches 2279.5 Evolutionary Relevance of Trajectories 232References 233Appendix A Review of Crystallography 235Index 246