Topics in Fluorescence Spectroscopy. Volume 2 Principles

Transcription

1 Topics in Fluorescence Spectroscopy Volume 2 Principles

2 Topics in Fluorescence Spectroscopy Edited by JOSEPH R. LAKOWICZ Volume 1: Techniques Volume 2: Principles Volume 3: Biochemical Applications

3 Topics in Fluorescence Spectroscopy Volume 2 Principles Edited by JOSEPH R. LAKOWICZ Center for Fluorescence Spectroscopy Department of Biological Chemistry University of Maryland School of Medicine Baltimore, Maryland KLUWER ACADEMIC PUBLISHERS NEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW

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5 Contributors Katalin Ajtai Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, Minnesota 55905; permanent address: Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary Marcel Ameloot Limburgs Universitair Centrum, Universitaire Campus, B-3610 Diepenbeek, Belgium Joseph M. Beechem Department of Physics, University of Illinois Urbana Champaign, Urbana, Illinois 61801; present address: Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee Ludwig Brand Department of Biology, The John Hopkins University, Baltimore, Maryland Thomas P. Burghardt Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, Minnesota Herbert C. Cheung Department of Biochemistry, University of Alabama at Birmingham, Birmingham, Alabama Maurice R. Eftink Department of Chemistry, University of Mississippi, University, Mississippi Susan G. Frasier-Cadoret Departments of Pharmacology and Internal Medicine, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908; present address: Office of Interdisciplinary Graduate Studies, University of Virginia Health Sciences Center, Charlottesville, Virginia Enrico Gratton Department of Physics, University of Illinois Urbana Champaign, Urbana, Illinois Michael L. Johnson Departments of Pharmacology and Internal Medicine, University of Virginia Health Sciences Center, Charlottesville, Virginia Jay R. Knutson National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland v

6 vi Contributors s Nicolai A. Nemkovich Institute of Physics of the B.S.S.R. Academy of Sciences, Minsk , U.S.S.R. Anatolyi N. Rubinov Institute of Physics of the B.S.S.R., Academy of Sciences, Minsk , U.S.S.R. Robert F. Steiner Department of Chemistry, University of Maryland Baltimore County, Baltimore, Maryland Martin Straume Departments of Pharmacology and Internal Medicine, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908; present address: Department of Biology, The Johns Hopkins University, Baltimore, Maryland Richard B. Thompson Department of Biological Chemistry, University of Maryland School of Medicine, Baltimore, Maryland Vladimir I. Tomin Institute of Physics of the B.S.S.R., Academy of Sciences, Minsk , U.S.S.R.

7 Preface Fluorescence spectroscopy and its applications to the physical and life sciences have evolved rapidly during the past decade. The increased interest in fluorescence appears to be due to advances in time resolution, methods of data analysis, and improved instrumentation. With these advances, it is now practical to perform time-resolved measurements with enough resolution to compare the results with the structural and dynamic features of macromolecules, to probe the structures of proteins, membranes, and nucleic acids, and to acquire two-dimensional microscopic images of chemical or protein distributions in cell cultures. Advances in laser and detector technology have also resulted in renewed interest in fluorescence for clinical and analytical chemistry. Because of these numerous developments and the rapid appearance of new methods, it has become difficult to remain current on the science of fluorescence and its many applications. Consequently, I have asked the experts in particular areas of fluorescence to summarize their knowledge and the current state of the art. This has resulted in the initial two volumes of Topics in Fluorescence Spectroscopy, which is intended to be an ongoing series which summarizes, in one location, the vast literature on fluorescence spectroscopy. The third volume will appear shortly. The first three volumes are designed to serve as an advanced text. These volumes describe the more recent techniques and technologies (Volume 1), the principles governing fluorescence and the experimental observables (Volume 2), and applications in biochemistry and biophysics (Volume 3). Additional volumes will be published as warranted by further advances in this field. I welcome your suggestions for future topics or volumes, offers to contribute chapters on specific topics, or comments on the present volumes. Finally, I thank all the authors for their patience with the delays incurred in release of the first three volumes. Baltimore, Maryland Joseph R. Lakowicz vii

8 Contents 1. Fluorescence Anisotropy: Theory and Applications Robert F. Steiner Introduction... Theory Meaning of Anisotropy Influence of Excitation Pulse Shape The Time Decay of Anisotropy The Rotational Diffusion of Ellipsoids of Revolution The Anisotropy Decay of Ellipsoidal Particles Partially Immobilized Systems The Influence of Internal Rotation... Experimental Analysis of Anisotropy Decay Analysis of Time-Domain Data Time-Domain Measurements of Anisotropy Decay Frequency-Domain Measurements of Anisotropy Decay... Anisotropy Decay of Heterogeneous Systems Anisotropy-Resolved Emission Spectra... The Meaning of Correlation Times for Associative and Nonassociative Heterogeneity... Anisotropy Decay of Intrinsic Protein Fluorophores Anisotropy Decay of a Rigid Protein: S. Nuclease... Rotational Dynamics of Flexible Polypeptides: Adrenocorticotropin and Melittin Anisotropy Decay of a Tightly Bound Fluorophore: Lumazine Protein Anisotropy Decay of a Transfer RNA... Anisotropy Decay of Biopolymers Labeled with an Extrinsic Fluorophore 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 ix

9 x Contents Anisotropy Decay of Calmodulin Complexes with TNS... References Fluorescence Quenching: Theory and Applications Maurice R. Eftink Introduction... Basic Concepts The Stern Volmer Equation Quenching Mechanisms and Efficiency... Diffusional Nature of Quenching... Static Quenching Various Quenchers... Quenching Studies with Proteins Exposure of Fluorophores Effect of the Macromolecule s Size Electrostatic Effects Tryptophan Residues in Proteins Ligand Binding and Conformational Changes... Mechanism of Quenching in Proteins Penetration versus Unfolding Mechanisms Interaction of Quenchers with Proteins Transient Effects Multiple Quenching Rate Constants and Fluorescence Lifetimes... Studies with Membranes and Nucleic Acids Partitioning of Quenchers into Membranes/Micelles Two-Dimensional Diffusion in Membranes Quencher Moieties Attached to Lipid Molecules Membrane Transport and Surface Potential Nucleic Acids... Uses to Resolve Other Fluorescence Properties Resolution of Steady-State Spectra Resolution of Fluorescence Lifetimes Resolution of Anisotropy Measurements Resolution of Energy Transfer Experiments Other Uses of Solute Quenching.... Recent Developments in Data Analysis Simultaneous Analyses of Quenching Data... Nonlinear Least-Squares Fits... Distribution of Lifetimes or Rate Constants... Experimental Improvements

10 Contents Phosphorescence Quenching... Conclusion... References... xi Resonance Energy Transfer Herbert C. Cheung Long-Range Dipole Dipole Interaction... Determination of Energy Transfer... Proximity Mapping of Molecular Assembly... Experimental Strategy Sample Preparation Measurement of Transfer Efficiency The Orientation Factor... Selected Applications Myosin and Actomyosin Troponin Subunits Ribosomal Proteins... Comparison of FRET Results with Results from Other Techniques Comparison with Crystallographic Data Comparison with Cross-Linking Data... Application of FRET to Enzyme Kinetics... Time-Resolved Energy Transfer Measurements... Distribution of Distances Theory Examples Summary and Prospects... References Least-Squares Analysis of Fluorescence Data Martin Straume, Susan G. Frasier-Cadoret, and Michael L. Johnson Introduction... Basic Terminology... Assumptions of Least-Squares Analysis... Least-Squares Parameter Estimation Procedures Modified Gauss Newton Algorithm Nelder Mead Simplex Algorithm... An Example of the Least-Squares Procedures Collisional Quenching

11 xii Contents Example of the Gauss Newton Procedure Example of the Nelder Mead Simplex Procedure Joint Confidence Intervals Estimation and Propagation Asymptotic Standard Errors... Linear Joint Confidence Intervals... Support Plane Confidence Intervals... Approximate Nonlinear Support Plane Joint Confidence Intervals A Monte Carlo Method for the Evaluation of Confidence Intervals Propagation of Confidence Intervals... Analysis of Residuals Plots... Distributions... Trends... Outliers... Influential Observations... Common Quantitative Tests... Implementation Notes... In Summary... References 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 Introduction Multiexcitation/Multitemperature Studies of Anisotropic Rotation Multiexcitation/Emission Wavelength Studies of Total Intensity Data Double-Kinetic Studies... The Global Analysis Philosophy Evolution of the Global Analysis Approach Global Analysis Implementation Strategy... General Elements of the Global Analysis Program Mapping to the Physical Observables... Empirical Description of the Fluorescence Decay... Compartmental Description of Photophysical Events... Overview of Nonlinear Minimization (The Basic Equations)

12 Contents xiii 5.4. In-Depth Flow Chart of a General-Purpose Global Analysis Program Overview of the Global Analysis Procedure Flow Chart for the LFD Global Analysis Program Global Case Studies of the Application of Global Analysis to Experimental Data Case Study of a Two-State Excited State Reaction Distributions of Distances and Energy Transfer Analysis Anisotropy Decay Data Analysis 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 Multiexcitation Anisotropy Experiments Example of Distributed Rotations: Fluorophore Rotations Gated by Packing Fluctuations in Lipid Bilayers... Error Analysis and the Identifiability Problem The Identifiability Problem... Identifiability Study Using Laplace Identifiability Analysis.. Error Analysis... Conclusions... References Fluorescence Polarization from Oriented Systems Thomas P. Burghardt and Katalin Ajtai Overview... Theory and Application 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 Discussion... References

13 xiv Contents 7. Fluorescence-Based Fiber-Optic Sensors Richard B. Thompson 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 Inhomogeneous Broadening of Electronic Spectra of Dye Molecules in Solutions Nicolai A. Nemkovich, Anatolyi N. Rubinov, and Vladimir I. Tomin Introduction... Theoretical Considerations of Inhomogeneous Broadening Solvate Configurational Energy... Field Diagram of a Polar Solution Solvate Distribution in Configurational Sublevels Nonpolar Solutions Selective Excitation with Vibrational Spectral Broadening Absorption and Fluorescence Spectra: Dependence on Exciting Light Frequency... Stationary Inhomogeneous Broadening Universal Relationship between Fluorescence and Absorption Spectra of Polar Solutions Luminescence Spectra at Red-Edge Excitation Directed Nonradiative Energy Transfer in Organic Solutions Dynamic Inhomogeneous Broadening in Liquid Solutions 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

14 Contents xv Selective Kinetic Spectroscopy of Fluorescent Molecules in Phospholipid Membranes 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 Conclusions... References Index