Methods in Molecular Biophysics: Structure, Dynamics, Function

Front Cover
Cambridge University Press, Mar 29, 2007 - Science
1 Review
Our knowledge of biological macromolecules and their interactions is based on the application of physical methods, ranging from classical thermodynamics to recently developed techniques for the detection and manipulation of single molecules. These methods, which include mass spectrometry, hydrodynamics, microscopy, diffraction and crystallography, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, are complementary; each has its specific advantages and limitations. Organised by method, this textbook provides descriptions and examples of applications for the key physical methods in modern biology. It is an invaluable resource for undergraduate and graduate students of molecular biophysics in science and medical schools, as well as research scientists looking for an introduction to techniques beyond their specialty. As appropriate for this interdisciplinary field, the book includes short asides to explain physics aspects to biologists and biology aspects to physicists.
 

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Contents

Part A Biological macromolecules and physical tools 19
38
Chapter A3 Understanding macromolecular structures
65
Part B Mass spectrometry 109
111
Introduction to biological applications
113
Ions in electric and magnetic fields
114
Mass resolution and mass accuracy
115
Ionisation technique
118
Instrumentation and innovative techniques
124
Introduction to biological problems
483
Dynamic light scattering as a spectroscopy of very high resolution
484
Dynamic light scattering under Gaussian statistics
493
DLS under nonGaussian statistics
499
Chapter D11 Fluorescence correlation spectroscopy
505
spectroscopy
512
PartE Optical spectroscopy 517
519
Brief theoretical outline
522

Checklist of key ideas
134
Suggestions for further reading
135
Chapter B2 Structure function studies
136
Functional proteomics
151
Nucleic acids
153
Carbohydrates
158
Subcellular complexes and organelles
163
Mass spectrometry in medicine
164
Imaging mass spectrometry
166
Checklist of key ideas
168
PartC Thermodynamics 171
173
Chapter C2 Differential scanning calorimetry
194
Chapter C3 Isothermal titration calorimetry
221
Chapter C4 Surface plasmon resonance and interferometrybased
234
Hydrodynamics 247
268
Chapter D3 Macromolecular diffusion
318
Translational friction and diffusion coefficients
328
Checklist of key ideas
336
Suggestions for further reading
337
Chapter D4 Analytical ultracentrifugation
339
Instrumentation and innovative technique
342
The Lamm equation
347
Solutions of the Lamm equation for different boundary conditions
348
Sedimentation velocity
352
Molecular mass from sedimentation and diffusion data
365
The partial specific volume
370
Density gradient sedimentation
372
Molecular shape from sedimentation data
376
Checklist of key ideas
385
Suggestions for further reading
386
Chapter D5 Electrophoresis
388
Introduction to biological problems
390
Electrophoretic experiments
391
free electrophoresis
395
zonal electrophoresis
397
Capillary electrophoresis CE
402
Capillary electrochromatography CEC
409
Checklist of key ideas
411
Suggestions for further reading
412
Chapter D6 Electric birefringence
414
Macromolecules in an electric field
415
Theoretical background of TEB measurements
417
Measurement of TEB
420
Global structure and flexibility of proteins
423
Global structure and flexibility of nucleic acids
425
Chapter D7 Flow birefringence
435
Introduction to biological problems
436
Steadystate flow birefringence
437
Decay of flow dichroism
440
Oscillatory flow birefringence
441
Orientation of macromolecules in flow as a dynamic phenomenon
442
Checklist of key ideas
443
Suggestions for further reading
444
Chapter D8 Fluorescence depolarisation
446
Introduction to biological problems
447
Theory of fluorescent depolarisation
448
Instrumentation
453
Depolarised fluorescence and Brownian motion
455
Depolarised fluorescence and molecular interactions
462
Checklist of key ideas
463
Suggestions for further reading
464
Chapter D9 Viscosity
466
Application to biological problems
467
Comparison of theory with experiment
472
homologous series
473
Monitoring of conformational change in proteins and nucleic acids
477
Checklist of key ideas
478
Suggestions for further reading
479
Chapter D10 Dynamic light scattering
481
The UVvisible spectral range
524
IR absorption spectroscopy
540
Checklist of key ideas
558
Suggestions for further reading
560
Chapter E2 Twodimensional IR spectroscopy
562
Linear and multidimensional spectroscopy
563
From amide bands to protein tertiary structure
566
Checklist of key ideas
570
Suggestions for further reading
571
Chapter E3 Raman scattering spectroscopy
573
Resonance Raman spectroscopy RRS
585
Surface enhanced Raman spectroscopy SERS
586
Vibrational Raman optical activity
587
Differential Raman spectroscopy
592
Timeresolved resonance Raman spectroscopy
593
Chapter E4 Optical activity
601
Part F Optical microscopy 625
627
Light microscopy inside the classical limit
629
Subwavelength resolution within the restrictions of geometrical optics
635
Lensless microscopy
636
Checklist of key ideas
639
Chapter F2 Atomic force microscopy
641
Introduction to biological problems
642
Imaging of biological structures
646
Combination of NSOM and AFM
654
Checklist of key ideas
655
Suggestions for further reading
656
Chapter F3 Fluorescence microscopy
658
Introduction to biological problems
660
Fluorescence microscopy outside the classical limits
666
Fluorescence resonance energy transfer FRET
670
Green fluorescent protein GFP
675
seeing the machinery of live cells
678
Chapter F4 Singlemolecule detection
683
Optical detection of single molecules in the solid state
690
Optical detection of single molecules at a surface
696
Singlemolecule studies tell more than ensemble
702
Chapter F5 Singlemolecule manipulation
709
Part G Xray and neutron diffraction 765
767
Chapter G2 Smallangle scattering
794
Chapter G3 Xray and neutron macromolecular crystallography
838
Part H Electron diffraction 883
885
Introduction to biological problems
886
Principles of electron diffraction and imaging
887
Electron microscopes
893
Techniques in specimen preparation
897
Data collection
899
Immunochemistry
902
Suggestions for further reading
903
Chapter H2 Threedimensional reconstruction from
904
EM data preparation
905
Singleparticle reconstruction procedures
907
Reconstruction procedures for one and twodimensional crystals
912
Classification procedures
915
Determination of the resolution
916
Map enhancement
919
Applications and examples
920
Checklist of key ideas
926
Suggestions for further reading
927
Molecular dynamics 929
931
Chapter I2 Neutron spectroscopy
948
Part J Nuclear magnetic resonance 969
971
Chapter J2 Experimental techniques
1000
Chapter J3 Structure and dynamics studies
1039
Suggestions for further reading 169
1060
Checklist of key ideas 432
1065
Checklist of key ideas 680
1068
References 1076
1076
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About the author (2007)

Igor N. Serdyuk is Professor of Molecular Biology and Head of the Laboratory of Nucleoprotein Physics at the Institute of Protein Research, Pushchino, Russia.

Nathan R. Zaccai is a research associate at the Department of Chemical Engineering, University of Cambridge.

Jospeh Zaccai is Senior Fellow for Biology at the Institut Laue-Langevin and Directeur de Recherche of the Centre Nationale de la Recherche Scientifique.

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