Contents. Part I Elastic Techniques
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- Ἱεριχώ Παπαστεφάνου
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1 1 Neutron Scattering for Biology T.A. Harroun, G.D. Wignall, J. Katsaras Introduction Production of Neutrons Elements of Neutron Scattering Theory Properties of Neutrons Energy and Momentum Transfer Diffraction Scattering Length and Cross-Section Coherent and Incoherent Cross-Sections Neutron Diffraction and Contrast Contrast and Structure Contrast and Dynamics Contrast and Biology Conclusions References Part I Elastic Techniques 2 Single Crystal Neutron Diffraction and Protein Crystallography C.C. Wilson, D.A. Myles Introduction Single Crystal Neutron Diffractometers: BasicPrinciples Development of Single Crystal Neutron Diffractometers Achievements of Neutron Macromolecular Crystallography at Reactor Sources Developments at Spallation Sources
2 X Contents Forward Look for Instrumentation for Neutron Macromolecular Crystallography Improvements in Sources Information from Neutron Crystallography Neutron Crystallography of Molecular Materials Neutron Crystallography in Structural Biology Sample and Data Requirements for Single Crystal Neutron Diffraction Brief Review of the Use of Neutron Diffraction in the Study of Biological Structures Location of Hydrogen Atoms Solvent Structure Hydrogen Exchange Low Resolution Studies Other Biologically Relevant Molecules Recent Developments and Future Prospects References Neutron Protein Crystallography: Hydrogen and Hydration in Proteins N. Niimura Introduction Complementarity of Neutrons and X-rays Refinement of Hydrogen Positions Hydrogen Atoms Which Cannot be Predicted Stereochemically HydrogenBonding Weak and Strong Hydrogen Bonding Bifurcated Hydrogen Bonds H/DExchange Hydration in Proteins Experimental Observation of Hydration Molecules Classification of Hydration Dynamic Behavior of Hydration Crystallization ConclusionsandFutureProspects References Neutron Protein Crystallography: Technical Aspects and Some Case Studies at Current Capabilities and Beyond M. Blakeley, A.J.K. Gilboa, J. Habash, J.R. Helliwell, D. Myles, J. Raftery Introduction Data Collection Perspectives
3 XI 4.3 Realizing a Complete Structure: The Complementary Roles of X-ray and Neutron Protein Crystallography Cryo-Neutron Protein Crystallography Current Technique, Source, andapparatusdevelopments PlansfortheESSandnPX ConclusionsandFutureProspects References Detergent Binding in Membrane Protein Crystals by Neutron Crystallography P. Timmins Introduction Advantages of Neutrons Instrumentation and Data Reduction The Crystallographic Phase Problem Comparison of Protein Detergent Interactions in Several Membrane Protein Crystals Reaction Centers and Light Harvesting Complexes Porins Conclusions References High-Angle Neutron Fiber Diffraction in the Study of Biological Systems V.T. Forsyth, I.M. Parrot Introduction Fibers and Fiber Diffraction Neutron Fiber Diffraction: General Issues Facilities for Neutron Fiber Diffraction NucleicAcids Cellulose ConclusionsandFutureProspects References Neutron Scattering from Biomaterials in Complex Sample Environments J. Katsaras, T.A. Harroun, M.P. Nieh, M. Chakrapani, M.J. Watson, V.A. Raghunathan Introduction Alignment in a Magnetic Field Magnetic Alignment of Lipid Bilayers Neutron Scattering in a Magnetic Field: Other Examples HighPressureStudies Hydrostatic Pressure and Aligned Lipid Bilayers
4 XII Contents High Pressure Neutron Scattering Experiments: OtherExamples Shear Flow Induced Structures in Biologically Relevant Materials Shear Cells Suitable for Neutron Scattering Shear Studies of Biologically Relevant Systems Comparison of a Neutron and X-ray Sample Environment % Relative Humidity Sample Cells Conclusions References Small-Angle Neutron Scattering from Biological Molecules J.K. Krueger, G.D. Wignall Introduction Why Neutron Scattering is Appropriate and Comparison with Other Low-Q Scattering Techniques Complementary Aspects of Light, Small-Angle Neutron and X-ray Scattering for Solution Studies Elements of Neutron Scattering Theory Coherent and Incoherent Cross-Sections Scattering Length Density Contrast Variation Practical Aspects of SANS Experiments and Data Analysis SANS Instrumentation The Importance of Absolute Calibration and Having Well-Characterized Samples Instrumental Resolution Other Experimental Considerations and Potential Artifacts Data Analysis: Extracting Structural and Shape Parameters from SANS Data and P (r)analysis SANS Application: Investigating Conformational Changes ofmyosinlightchainkinase Solvent Matching of a Specifically Deuterated CaM Bound to a Short Peptide Sequence Contrast Variation of Deuterated CaM BoundtoMLCKEnzyme Mechanism of the CaM-Activation Step: SAXS/SANS Studies of a (Deuterated) Mutant CAM ConclusionsandOutlook References
5 XIII 9 Small Angle Neutron Scattering from Proteins, Nucleic Acids, and Viruses S. Krueger, U.A. Perez-Salas, S.K. Gregurick, D. Kuzmanovic Introduction Modeling SANS Data Contrast Variation Experimental Examples NucleicAcids:RNAFolding Compaction of a Bacterial Group I Ribozyme RNA Compaction and Helical Assembly Protein Complexes: Multisubunit Proteins and Viruses Conformation of a Polypeptide Substrate in Model GroEL/GroES Chaperonin Complexes Spatial Distribution and Molecular Weight of the Protein and RNA Components of Bacteriophage MS References Structure and Kinetics of Proteins Observed by Small Angle Neutron Scattering M.W. Roessle, R.P. May Introduction Solution Scattering Specific Aspects of Neutron Scattering Time-Resolved Experiments: Dynamics vs. Steady State Protein Motions and Kinetics Cooperative Control of Protein Activity Protein Kinetic Analysis by Neutron Scattering Experiments Trapping of Reaction Intermediates: The (αβ)-thermosome Quasi-static Analysis of Reaction Kinetics The Symmetric GroES GroEL GroES Complex Chasing Experiments (Slow Kinetics) Time Resolved Small-Angle Neutron Scattering Conclusions and Outlook References Complex Biological Structures: Collagen and Bone P. Fratzl, O. Paris Introduction Collagenous Connective Tissue Structure and Dynamics by Neutron Scattering
6 XIV Contents Elastic and Visco-elastic Behavior of Collagen from In situ Mechanical Experiments with Synchrotron Radiation Bone and other Calcified Tissue Structure of Mineralized Collagen Contributions from Neutron Scattering Investigating the Hierarchical Structure of Bone References Structural Investigations of Membranes in Biology by Neutron Reflectometry C.F. Majkrzak, N.F. Berk, S. Krueger, U.A. Perez Salas Introduction Theory The Exact ( Dynamical ) Solution The Born Approximation Multilayers Scale of Spatial Resolution Basic Experimental Methods Instrumental Configuration Instrumental Resolution and the Intrinsic Coherence Lengths of the Neutron In-Plane Averaging Q-Resolution for Specular Reflectivity, Assuming anincoherentbeam Measurement of the Reflectivity Sample Cell Designs Sources of Background Multilayer Samples: Secondary Extinction and Mosaic Data Collection Strategies for Time-Dependent Phenomena Phase Determination Techniques Reference Films Surround Variation Refinement An Illustrative Example References Protein Adsorption and Interactions at Interfaces J.R. Lu Introduction Neutron Reflection and Concept of Isotopic Contrast Variation Adsorption of Other Proteins at the Air Water Interface
7 XV 13.4 Adsorption at the Solid Water Interface: The Effect of Surface Chemistry Interaction Between Surfactant and Protein Future Prospects References Complex Biomimetic Structures at Fluid Surfaces and Solid Liquid Interfaces T. Gutberlet, M. Lösche Introduction Surface-Sensitive Scattering Specular Reflectivity Structure-Based Model Refinement Floating Lipid Monolayers: Structural Investigations and the Interaction of Peptides and Proteins with Lipid Interfaces Single Phospholipid LMs Functionalized Phospholipid LMs Lipopolymers Protein Adsorption and Stability at Functionalized Solid Interfaces Hydrophobic Modified Interfaces Hydrophilic Modified Interfaces Functionalized Lipid Interfaces and Supported Lipid Bilayers Solid-Supported Phospholipid Bilayers Hybrid Bilayer Membranes Polymer-Supported Phospholipid Bilayers Conclusions References Part II Inelastic Techniques 15 Quasielastic Neutron Scattering in Biology, Part I: Methods R.E. Lechner, S. Longeville Introduction Basic Theory of Neutron Scattering Van Hove Scattering Functions and Correlation Functions The Elastic Incoherent Structure Factor Experimental Energy Resolution Instruments for QENS Spectroscopy in (Q,ω)-Space XTL TOF Spectrometers TOF TOF Spectrometers
8 XVI Contents XTL XTL Spectrometers TOF XTL Spectrometers Instruments for QENS Spectroscopy in (Q,t)-Space NSE Spectrometers Spin 1/2 and Larmor Precession The Neutron Spin-Echo Principle Transmission of Polarizers and Analyzers Getting a Spin-Echo, as a Measure of the Polarization Measuring Quasielastic Neutron Scattering Neutron Resonance Spin-Echo Spectrometry Observation Function, Effect of Wavelength Distribution on Spin-Echo Time Miscellaneous Technical Points: MSC, Calibration, Contrast Conclusions References Quasielastic Neutron Scattering in Biology, Part II: Applications R.E. Lechner, S. Longeville Introduction Dynamical Models Dynamical-Independence Approximation The Gaussian Approximation Simple Translational Diffusion Three-Dimensional Diffusion of Protein Molecules in Solution (Crowded Media) Vibrational Motions, Phonon-Expansion and Debye Waller factor (DWF), Dynamic Susceptibility Vibrational Density of States of the Light-Harvesting Complex II of Green Plants Non-Gaussian Motion Atomic Jump Motions Described by Rate Equations Confined or Localized Diffusive Atomic and Molecular Motions Environment-Dependence of Confined Diffusive Protein Motions: ExampleLysozyme Change of Protein Dynamics on Ligand Binding: Example Dihydrofolate Reductase Low-Dimensional Systems Two-Dimensional Long-Range Diffusion of Rotating Molecules Dynamical Transition and Temperature-Dependent Hydration: Example Purple Membrane
9 XVII 16.6 Conclusions References Conformational Dynamics Measured with Proteins in Solution J. Fitter Introduction Dynamics in Proteins: Types of Motions and Their Biological Relevance Samples in Neutron Spectroscopy: Sample Preparation, Sample Characterization, andsampleenvironment From Spectra to Results: Data Acquisition, Data Analysis, and Data Interpretation Applications and Examples Comparison of Folded and Unfolded States Conformational Entropy Calculation from Neutron Scattering Data Conclusions and Outlook References Relating Protein Dynamics to Function and Structure: The Purple Membrane U. Lehnert, M. Weik Introduction Elastic Incoherent Neutron Scattering Methods of Investigation Elastic Incoherent Neutron Scattering on Powder Samples Models for Describing Thermal Protein Dynamics H/D Labeling Techniques Relating Thermal Motions in Purple Membranes to Structural and Functional Characteristics ofbacteriorhodopsin Thermal Motions in Bacteriorhodopsin and the Purple Membrane Hydration Dependence of Thermal Motions Local Core Motions Lipid Environment Relation Between PM Dynamics and Crystallographic B-factors Comparison of Force Constants with Forces Measured byafm Protein Dynamics and Function in Some Other Proteins Conclusions References
10 XVIII Contents 19 Biomolecular Spectroscopy Using Pulsed-Source Instruments H.D. Middendorf Introduction Why Pulsed Sources? Pulsed Source vs. Reactor Instruments Backscattering Spectrometers Hydration Dynamics Low-Temperature Dynamics and Glass-Like Transitions Enzyme Dynamics and Folding Unfolding Processes Inelastic Scattering at1mev< ω <1eV(8< ω <8, 000 cm 1 ) Chopper Spectrometers Crystal-Analyzer and Filter-Difference Spectrometers Building Blocks and Model Compounds Interpretational Aspects Proteins and Biomaterials Biopolymers Nucleotides and Nucleosides Neutron Compton Scattering (NCS) Conclusions and Outlook References Brownian Oscillator Analysis of Molecular Motions in Biomolecules W. Doster Introduction Dynamics of Protein Solvent Interactions Properties of the Intermediate Scattering Function Relevant Time and Spatial Scales The Brownian Oscillator as a Model of Protein-Residue Motion The Visco-Elastic Brownian Oscillator Moment Analysis of Hydration Water Displacements Analysis of Protein Displacements Data Analysis Conclusions References Internal Dynamics of Proteins and DNA: Analogy to Glass-Forming Systems A.P. Sokolov, R.B. Gregory Introduction Analysis of Relaxation Spectra: Susceptibility Presentation vs. Dynamic Structure Factor
11 XIX 21.3 Slow Relaxation Process The Nature of the Dynamical Transition in Proteins and DNA Fast Picosecond Relaxation Conclusions and Future Prospects References Structure and Dynamics of Model Membrane Systems Probed by Elastic and Inelastic Neutron Scattering T. Salditt, M.C. Rheinstädter Introduction Sample Preparation and Sample Environment Specular Neutron Reflectivity Nonspecular Neutron Reflectivity Models of Bilayer Undulations Monochromatic NSNR Experiments White-Beam NSNR Experiments Change of Fluctuations by Added Antimicrobial Peptides Elastic and Inelastic Studies of the Acyl Chain Correlation Peak Inelastic Neutron Scattering Elastic Neutron Scattering Collective Dynamics Conclusions References Subnanosecond Dynamics of Proteins in Solution: MD Simulations and Inelastic Neutron Scattering M. Tarek, D.J. Tobias Introduction MD Simulations Systems Set-up and Simulations Generating Neutron Spectra Overall Protein Structure and Motion in Solution Internal Protein Dynamics Dynamics of Proteins in Solution from MD Simulations Conclusions References Index...549
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