Biomedical Applications of Biophysics

250 Pages·2010·8.04 MB·English

by  Patrice Koehl (auth.)

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Thomas Jue
Editor
Biomedical Applications
of Biophysics
Volume 3
Editor
Thomas Jue, Ph.D.
Department of Biochemistry and Molecular Medicine
University of California Davis
One Shields Avenue
Davis, CA 95616, USA
[email protected]
ISBN 978-1-60327-232-2 e-ISBN 978-1-60327-233-9
DOI 10.1007/978-1-60327-233-9
Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2010932766
© Springer Science+Business Media, LLC 2010
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P
REFACE
In the Biomedical Applications of Biophysics, Volume 3 of the Handbook of Modern Biophysics,
the authors have added to the topics introduced in Volume 1, Fundamental Concepts in Bio-
physics. These additional topics help trace the broad field of biophysics.
Patrice Koehl starts the book with an introduction to protein structure prediction based on
energetics, homology modeling, and ab-initio calculations. Dickey and Faller follow with a
“how-to approach” to model biomembranes. Brynda and Ames present the principles of mag-
netic resonance techniques, which researchers often use to solve protein and biomembrane
structure. Brynda encapsulates the theoretical and methodological concepts of electron para-
magnetic resonance spectroscopy. James Ames covers correspondingly the theory and applica-
tion of biomolecular NMR spectroscopy. Because optical techniques can also reveal biomolecu-
lar structure, Jie Zheng discusses the commonly used fluorescence resonance energy transfer
(FRET) in determining molecular distance. Chu and Lebrilla then turn their attention to a piv-
otal method of analytical chemistry, mass spectrometry. Green and Cheng show how transmis-
sion electron microscopy and computer-aided image processing can help visualize macromole-
cules in three dimensions. Finally, Weeks and Huser introduce to the reader the use of inelastic
scattering of Raman spectroscopy to investigate the living cell.
Each chapter presents the fundamental physics concepts, describes the instrumentation or
technique, and illustrates the application in studying current biomedical problems. With the ad-
dition of problem sets, further study, and references, the interested reader can use the chapters to
launch an independent exploration of the ideas presented.
Thomas Jue
Biochemistry & Molecular Medicine
University of California Davis

v
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C
ONTENTS
1 Protein Structure Prediction
Patrice Koehl
1.1. Introduction......................................................................................................................... 1
1.2. Basic Principles of Protein Structure................................................................................... 3
1.3. The Energetics of Protein Structure..................................................................................... 8
1.4. Homology Modeling........................................................................................................... 10
1.5. Ab-Initio Protein Structure Prediction................................................................................. 20
1.6. The CASP Experiment........................................................................................................ 25
1.7. Conclusions......................................................................................................................... 26
2 Molecular Modeling of Biomembranes:
A How-to Approach
Allison N. Dickey and Roland Faller
2.1. Introduction to Molecular Dynamics................................................................................... 35
2.2. Specifics of the Molecular Modeling of Biomembranes..................................................... 37
2.3. Force Fields: Simulation Models......................................................................................... 38
2.4. Degree of Detail: Atomistic versus Coarse-Grained........................................................... 39
2.5. Visualizations...................................................................................................................... 41
2.6. Area per Molecule and Thickness, Comparison
to X-Ray Data...................................................................................................................... 41
2.7. Order Parameters and Other Single-Lipid Properties.......................................................... 42
2.8. Radial Distribution Functions.............................................................................................. 44
2.9. Hydrogen Bonding and Advanced Static Analysis.............................................................. 44
2,10, Pressure and Pressure Profiles............................................................................................. 46
2.11. Two-Dimensional Diffusion................................................................................................ 46
2.12. Reorientations and NMR..................................................................................................... 48
2.13. Dynamics of Individual Molecules: Correlations
of Distribution Functions..................................................................................................... 49
2.14. Interactions with Small Molecules...................................................................................... 49
2.15. Summary............................................................................................................................. 51

vii
viii CONTENTS

3 Introduction to Electron Paramagnetic
Resonance Spectroscopy
Marcin Brynda
3.1. Introduction......................................................................................................................... 59
3.2. Historical Background......................................................................................................... 60
3.3. Basic Equations................................................................................................................... 61
3.4. Spin Hamiltonian................................................................................................................. 63
3.5. Continuous Wave (CW) versus Pulsed
EPR Techniques.................................................................................................................. 70
3.6. EPR Instrumentation........................................................................................................... 75
37. EPR Measurements in Solution and Solid State.................................................................. 79
3.8. Time-Resolved EPR............................................................................................................ 82
3.9. Dynamic Processes Observed by EPR................................................................................ 83
3.10. Multifrequency Experiments............................................................................................... 85
3.11. Quantum Chemistry Calculations........................................................................................ 88
3.12. EPR in Biology and in Bioinorganic Chemistry.................................................................. 91
4 Theory and Applications of
Biomolecular NMR Spectroscopy
James B. Ames
4.1. Introduction......................................................................................................................... 99
4.2. Nuclear and Electronic Spin................................................................................................ 100
4.3. Quantum Description of Nuclear Spin................................................................................ 100
4.4. Spin-State Populations in Ensembles.................................................................................. 101
4.5. Nuclear Shielding and Chemical Shift................................................................................ 103
4.6. NMR Scalar Coupling......................................................................................................... 103
4.7. Dipolar Coupling................................................................................................................. 104
4.8. NMR Relaxation and Dynamics.......................................................................................... 105
4.9. Neuronal Calcium Sensor Proteins...................................................................................... 108
4.10. NMR Structural Analysis of Ca2+-Myristoyl
Switch Proteins.................................................................................................................... 110
4.11. Summary............................................................................................................................. 114
5 FRET and Its Biological Application
as a Molecular Ruler
Jie Zheng
5.1. Introduction......................................................................................................................... 119
5.2. Distance Dependence of FRET Efficiency.......................................................................... 121
HANDBOOK OF MODERN BIOPHYSICS, VOLUME 3 ix

5.3. Spectra Overlap between FRET Pairs................................................................................. 122
5.4. Orientation Factor................................................................................................................ 122
5.5. Advantages of FRET for Biological Applications............................................................... 123
5.6. Donor Dequenching............................................................................................................. 125
5.7. Enhanced Acceptor Emission.............................................................................................. 125
5.8. Three-Cube FRET............................................................................................................... 126
5.9. Spectra FRET...................................................................................................................... 126
5.10. Fluorescence Intensity Ratio between
Donor and Acceptor............................................................................................................ 126
5.11. Lifetime Measurements....................................................................................................... 127
5.12. FRET Quantification through Photobleaching
Rate Measurements............................................................................................................. 127
5.13. Protein Complex Formation................................................................................................ 128
5.14. Subunit Stoichiometry of Protein Complex......................................................................... 129
5.15. Binding of Ligands or Modulatory Molecules.................................................................... 129
5.16. Conformational Rearrangements......................................................................................... 130
5.17. Intracellular Event Indicators.............................................................................................. 131

6 Introduction to Modern Techniques in Mass Spectrometry
Caroline S. Chu and Carlito B. Lebrilla
6.1. Introduction......................................................................................................................... 137
6.2. Ionization Techniques (Ion Sources)................................................................................... 138
6.3. Electron Impact................................................................................................................... 138
6.4. Chemical Ionization............................................................................................................. 139
6.5. Electrospray Ionization........................................................................................................ 139
6.6. Matrix-Assisted Laser Desorption/Ionization...................................................................... 141
6.7. Fourier Transform Ion Cyclotron Resonance...................................................................... 143
6.8. Time of Flight...................................................................................................................... 146
6.9. Tandem Mass Spectrometry................................................................................................ 148
6.10. Collision-Induced Dissociation........................................................................................... 148
6.11. Infrared Multiphoton Dissociation...................................................................................... 149
6.12. Electron Capture Dissociation............................................................................................. 150
6.13. Electron Transfer Dissociation............................................................................................ 150
6.14. Summary............................................................................................................................. 150