1. Fluorescence Anisotropy: Theory and Applications Robert F. Steiner 1.1. 1.2. 1.3. 1.4. 1.5. 1.6. Introduction... Theory... 1.2.1. Meaning of Anisotropy... 1.2.2. Influence of Excitation Pulse Shape... 1.2.3. The Time Decay of Anisotropy... 1.2.4. The Rotational Diffusion of Ellipsoids of Revolution... 1.2.5. The Anisotropy Decay of Ellipsoidal Particles... 1.2.6. Partially Immobilized Systems... 1.2.7. The Influence of Internal Rotation... Experimental Analysis of Anisotropy Decay... 1.3.1. Analysis of Time-Domain Data... 1.3.2. Time-Domain Measurements of Anisotropy Decay... 1.3.3. Frequency-Domain Measurements of Anisotropy Decay... Anisotropy Decay of Heterogeneous Systems... 1.4.1. 1.4.2. Anisotropy-Resolved Emission Spectra... The Meaning of Correlation Times for Associative and Nonassociative Heterogeneity... Anisotropy Decay of Intrinsic Protein Fluorophores... 1.5.1. 1.5.2. Anisotropy Decay of a Rigid Protein: S. Nuclease... Rotational Dynamics of Flexible Polypeptides: Adrenocorticotropin and Melittin... 1.5.3. Anisotropy Decay of a Tightly Bound Fluorophore: Lumazine Protein... 1.5.4. Anisotropy Decay of a Transfer RNA... Anisotropy Decay of Biopolymers Labeled with an Extrinsic Fluorophore... 1.6.1. 1.6.2. 1.6.3. Anisotropy Decay and Internal Flexibility of Myosin... Anisotropy Decay of a Fibrous Protein: F-Actin... Anisotropy Decay for Proteins Displaying Internal Rotation Involving a Well-Defined Domain: The Immunoglobulins.. 1 2 2 5 6 8 10 14 18 22 22 25 26 28 28 31 32 32 33 37 39 41 41 43 44 ix
x Contents 1.6.4. Anisotropy Decay of Calmodulin Complexes with TNS... References... 48 51 2. Fluorescence Quenching: Theory and Applications Maurice R. Eftink 2.1. 2.2. 2.3. 2.4. 2.5. 2.6. Introduction... Basic Concepts...... 2.2.1. The Stern Volmer Equation... 2.2.2. 2.2.3. 2.2.4. Quenching Mechanisms and Efficiency... Diffusional Nature of Quenching... Static Quenching... 2.2.5. Various Quenchers... Quenching Studies with Proteins... 2.3.1. Exposure of Fluorophores... 2.3.2. Effect of the Macromolecule s Size... 2.3.3. Electrostatic Effects... 2.3.4. Tryptophan Residues in Proteins... 2.3.5. 2.3.6. Ligand Binding and Conformational Changes... Mechanism of Quenching in Proteins Penetration versus Unfolding Mechanisms... 2.3.7. Interaction of Quenchers with Proteins... 2.3.8. Transient Effects... 2.3.9. Multiple Quenching Rate Constants and Fluorescence Lifetimes... Studies with Membranes and Nucleic Acids... 2.4.1. Partitioning of Quenchers into Membranes/Micelles... 2.4.2. Two-Dimensional Diffusion in Membranes... 2.4.3. Quencher Moieties Attached to Lipid Molecules... 2.4.4. Membrane Transport and Surface Potential... 2.4.5. Nucleic Acids... Uses to Resolve Other Fluorescence Properties... 2.5.1. Resolution of Steady-State Spectra... 2.5.2. Resolution of Fluorescence Lifetimes... 2.5.3. Resolution of Anisotropy Measurements... 2.5.4. Resolution of Energy Transfer Experiments... 2.5.5. Other Uses of Solute Quenching.... Recent Developments in Data Analysis... 2.6.1. 2.6.2. 2.6.3. 2.6.4. Simultaneous Analyses of Quenching Data... Nonlinear Least-Squares Fits... Distribution of Lifetimes or Rate Constants... Experimental Improvements... 53 55 55 58 60 64 67 68 68 68 71 72 75 78 85 87 91 92 92 96 97 99 100 101 102 103 105 108 109 112 112 113 114 116
2.7. 2.8. Phosphorescence Quenching... Conclusion... References... xi 117 120 120 3. Resonance Energy Transfer Herbert C. Cheung 3.1. 3.2. 3.3. 3.4. 3.5. 3.6. 3.7. 3.8. 3.9. Long-Range Dipole Dipole Interaction... Determination of Energy Transfer... Proximity Mapping of Molecular Assembly... Experimental Strategy... 3.4.1. Sample Preparation... 3.4.2. Measurement of Transfer Efficiency... 3.4.3. The Orientation Factor... Selected Applications... 3.5.1. Myosin and Actomyosin... 3.5.2. Troponin Subunits... 3.5.3. Ribosomal Proteins... Comparison of FRET Results with Results from Other Techniques... 3.6.1. Comparison with Crystallographic Data... 3.6.2. Comparison with Cross-Linking Data... Application of FRET to Enzyme Kinetics... Time-Resolved Energy Transfer Measurements... Distribution of Distances... 3.9.1. Theory... 3.9.2. Examples... 3.10. Summary and Prospects... References... 128 130 132 132 132 133 135 140 140 145 147 148 148 151 152 155 157 158 161 170 171 4. Least-Squares Analysis of Fluorescence Data Martin Straume, Susan G. Frasier-Cadoret, and Michael L. Johnson 4.1. 4.2. 4.3. 4.4. 4.5. Introduction... Basic Terminology... Assumptions of Least-Squares Analysis... Least-Squares Parameter Estimation Procedures... 4.4.1. Modified Gauss Newton Algorithm... 4.4.2. Nelder Mead Simplex Algorithm... An Example of the Least-Squares Procedures Collisional Quenching... 177 179 181 186 187 193 199
xii Contents 4.5.1.Example of the Gauss Newton Procedure... 4.5.2.Example of the Nelder Mead Simplex Procedure... 4.6. Joint Confidence Intervals Estimation and Propagation... 4.6.1. 4.6.2. 4.6.3. 4.6.4. 4.7. 4.8. 4.9. Asymptotic Standard Errors... Linear Joint Confidence Intervals... Support Plane Confidence Intervals... Approximate Nonlinear Support Plane Joint Confidence Intervals... 4.6.5. A Monte Carlo Method for the Evaluation of Confidence Intervals... 4.6.6. Propagation of Confidence Intervals... Analysis of Residuals... 4.7.1. 4.7.2. 4.7.3. 4.7.4. 4.7.5. 4.7.6. Plots... Distributions... Trends... Outliers... Influential Observations... Common Quantitative Tests... Implementation Notes... In Summary... References... 202 205 207 208 208 209 211 214 215 216 218 221 226 228 229 230 235 238 239 5. The Global Analysis of Fluorescence Intensity and Anisotropy Decay Data: Second-Generation Theory and Programs Joseph M. Beechem, Enrico Gratton, Marcel Ameloot, Jay R. Knutson, and Ludwig Brand 5.1. 5.2. 5.3. Introduction... 5.1.1. Multiexcitation/Multitemperature Studies of Anisotropic Rotation... 5.1.2. Multiexcitation/Emission Wavelength Studies of Total Intensity Data... 5.1.3. Double-Kinetic Studies... The Global Analysis Philosophy... 5.2.1. Evolution of the Global Analysis Approach... 5.2.2. Global Analysis Implementation Strategy... General Elements of the Global Analysis Program... 5.3.1. 5.3.2. 5.3.3. 5.3.4. Mapping to the Physical Observables... Empirical Description of the Fluorescence Decay... Compartmental Description of Photophysical Events... Overview of Nonlinear Minimization (The Basic Equations) 241 242 243 244 244 244 248 249 252 252 253 258
xiii 5.4. In-Depth Flow Chart of a General-Purpose Global Analysis Program... 5.4.1. Overview of the Global Analysis Procedure... 5.4.2. Flow Chart for the LFD Global Analysis Program Global... 5.5. Case Studies of the Application of Global Analysis to Experimental Data... 5.5.1. Case Study of a Two-State Excited State Reaction... 5.5.2. Distributions of Distances and Energy Transfer Analysis... 5.6. Anisotropy Decay Data Analysis... 5.6.1. 5.6.2. 5.6.3. 5.6.4. 5.6.5. 5.6.6. 5.7. 5.8. General Equations and Experimental Linkages... Changes in Anisotropy Data Collection Schemes... Associative versus Nonassociative Modeling of Anisotropy Anisotropy Decay-Associated Spectra (ADAS)... Multidye Global Anisotropy Decay Analysis... Distributed Lifetimes and Distributed Rotational Correlation Times... 5.6.7. Multiexcitation Anisotropy Experiments... 5.6.8. Example of Distributed Rotations: Fluorophore Rotations Gated by Packing Fluctuations in Lipid Bilayers... Error Analysis and the Identifiability Problem... 5.7.1. 5.7.2. 5.7.3. The Identifiability Problem... Identifiability Study Using Laplace Identifiability Analysis.. Error Analysis... Conclusions... References... 259 259 260 272 272 277 280 280 283 283 284 285 285 286 287 288 288 291 294 298 301 6. Fluorescence Polarization from Oriented Systems Thomas P. Burghardt and Katalin Ajtai 6.1. 6.2. 6.3. Overview... Theory and Application... 6.2.1. 6.2.2. 6.2.3. 6.2.4. The Angular Probability Density N... Fluorescence Polarization in Homogeneous Space... Time-Resolved Fluorescence Depolarization Determination of the High-Resolution Angular Probability Density... Relation of Electron Spin Resonance Spectra to Fluorescence Polarization... Biochemical Techniques of Specific Labeling... 6.2.5. Discussion... References... 307 308 309 311 320 331 332 338 340
xiv Contents 7. Fluorescence-Based Fiber-Optic Sensors Richard B. Thompson 7.1. 7.2. 7.3. 7.4. 7.5. 7.6. 7.7. 7.8. 7.9. 7.10. 7.11. Introduction... Fiber-Optic Fundamentals... Sensor Design... Sensing Tip Configurations... Fiber Characteristics... Separating Excitation and Emission... Launching Optics... Light Sources... Time-Resolved Fluorescence in Fibers... Polarization... Conclusion... References... 345 346 349 350 353 357 359 359 361 362 362 363 8. Inhomogeneous Broadening of Electronic Spectra of Dye Molecules in Solutions Nicolai A. Nemkovich, Anatolyi N. Rubinov, and Vladimir I. Tomin 8.1. 8.2. 8.3. 8.4. Introduction... Theoretical Considerations of Inhomogeneous Broadening... 8.2.1. 8.2.2. Solvate Configurational Energy... Field Diagram of a Polar Solution... 8.2.3. Solvate Distribution in Configurational Sublevels... 8.2.4. Nonpolar Solutions... 8.2.5. Selective Excitation with Vibrational Spectral Broadening.. 8.2.6. Absorption and Fluorescence Spectra: Dependence on Exciting Light Frequency... Stationary Inhomogeneous Broadening... 8.3.1. Universal Relationship between Fluorescence and Absorption Spectra of Polar Solutions... 8.3.2. Luminescence Spectra at Red-Edge Excitation... 8.3.3. Directed Nonradiative Energy Transfer in Organic Solutions Dynamic Inhomogeneous Broadening in Liquid Solutions... 8.4.1. 8.4.2. 8.4.3. 8.4.4. Analysis of Configurational Relaxation in Liquid Solutions Experimental Study of the Luminescence Kinetics of Liquid Solutions... The Solution Spectrochronogram... The Effect of Light-Induced Molecular Rotation in Solution.... 367 369 369 371 374 376 378 383 387 387 388 390 395 395 401 404 406
xv 8.5. 8.6. Selective Kinetic Spectroscopy of Fluorescent Molecules in Phospholipid Membranes... 8.5.1. 8.5.2. Energy Levels of an Electric Dipole Probe in a Membrane Inhomogeneous Broadening in Steady-State Fluorescence Spectra of Probes... Kinetics of Probe Fluorescence... Rotational Dynamics of the Probe in the Membrane... 8.5.3. 8.5.4. Conclusions... References.... 413 413 416 419 422 423 425 Index... 429