Molecular biophysics: structures in motion
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| 1. Verfasser: | |
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| Format: | Buch |
| Sprache: | German English |
| Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2006
|
| Ausgabe: | Reprinted |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Klappentext |
| Beschreibung: | XXII, 499 S. Ill., graph. Darst. |
| ISBN: | 0198577834 0198577826 |
Internformat
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| 100 | 1 | |a Daune, Michel |e Verfasser |4 aut | |
| 240 | 1 | 0 | |a Biophysique moléculaire |
| 245 | 1 | 0 | |a Molecular biophysics |b structures in motion |c Michel Daune |
| 250 | |a Reprinted | ||
| 264 | 1 | |a Oxford [u.a.] |b Oxford Univ. Press |c 2006 | |
| 300 | |a XXII, 499 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 2 | |a Biofizika | |
| 650 | 2 | |a Biopolimeri - Fiziologija | |
| 650 | 2 | |a Molekularna biologija | |
| 650 | 4 | |a Biophysics | |
| 650 | 4 | |a Biopolymers |x Physiology | |
| 650 | 4 | |a Molecular biology | |
| 650 | 0 | 7 | |a Molekulare Biophysik |0 (DE-588)4170391-1 |2 gnd |9 rswk-swf |
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Datensatz im Suchindex
| _version_ | 1804139917752664065 |
|---|---|
| adam_text | Contents
General
introduction
1
Part I Conformation of biopolymers
Introduction
7
Geometry of a polymer chain
9
1.1
Distance between the ends of a chain
9
1.2
Radius of gyration
10
1.3
Constraints on the valence bond
11
1.4
Torsionai
potential
14
Intermolecular forces
15
2.1
Introduction
15
2.2
Electrical origin of the interaction energy
15
2.3
Interactions between charges and permanent dipoles
1
б
2.3.1
Ion-ion
16
2.3.2
lon-dipole
18
2.3 3
Dipole-dipole
19
2.4
Induced dipoles
19
2.4.1
Ion-molecule interaction
20
2.4.2
Dipole-molecule interaction
21
2.4.3
Interaction between two induced dipoles
21
2.5
Forms of potential energy
22
2.5.1
General table
22
2.5.2
Spherically symmetric potential functions
2 2
x¡v
CONTENTS
2.6
The hydrogen bond
23
2.6.1
Definition and properties
24
2.6.2
Geometry and bifurcated bond
24
2.6.3
Empirical analytical form for the potential
26
3
Calculation of conformations
27
3.1
Bound atoms
27
3.1.1
Valence bonds
27
3.1.2
Torsionai
potential
28
3.2
Non-bonded atoms
28
3.3
Topological constraints
29
3.4
Helical structures
29
3.5
The helix-coil conformational transition
30
3.5.1
Review of thermodynamics
30
3.5.2
Zip model
31
3.5.3
Matrix model (Zimm and Bragg)
32
4
Conformation of nucleic acids
38
4.1
Introduction
38
4.2
Primary structure
39
4.3
Structure of the nucleotide chain
40
4.3.1
The bases
40
4.3.2
The sugars
42
4.3.3
Rotation angles of the phosphodiester chain
44
4.4
The double-helix structure
48
4.4.1
The canonical
В
and A forms
48
4.4.2
The
Z
form
51
4.4.3
Distortion of the helix and new parameters
53
4.4.4
Polymorphism
56
4.5
Properties of circular
DNA 58
4.5.1
Modelling and topology
58
4.5.2
Physical properties of circular
DNA 61
4.5.3
Gel electrophoresis
62
4.6
Polymorphism and flexibility of
DNA 64
4.6.1
The double helix: a theme with variations
64
4.6.2
Flexibility
67
CONTENTS xv
4.6.3
The double-strand to
single-strand
transition
72
4.6.4
B-Z transition
75
4.6.5
Formation of a cruciform structure
78
4.6.6
Three-stranded and four-stranded helices
78
4.6.7
Intercalation
81
4.7
Structure of ribonucleic acids
90
4.7.1
Modelling
90
4.7.2
Three-dimensional structure
92
5
Conformation of proteins
101
5.1
Sequence
101
5.2
Conformational parameters of the
peptide
bond
104
5.3
Spatial organization and related problems
104
5.4
Analysis of some secondary structures
106
5.4.1
α
-helices
106
5.4.2
310 helices and 0-turns
107
5.4.3
Polyproline helices
108
5.4.4
^-pleated sheets
108
5 5
Prediction of secondary structures
109
5.5.1
Ramachandran s method
109
5.5.2
Use of potential functions
111
5.5.3
Statistical predictions
111
5.6
Tertiary structure
115
5.6.1
Intramolecular interactions
116
5.6.2
Folding forces
120
5.6.3
Folding theory
122
5.6.4
Modes of representation
122
5.6.5
Folding mechanisms
132
5.6.6
The structure-function relationship
134
Conclusion to Part I
135
References and further reading
137
Part II Dynamics of biopolymers
Introduction
143
6
Fluctuations around an equilibrium conformation
147
xv¡
CONTENTS
6.1
The harmonie
oscillator model
147
6.1.1
The shape of the potential well
148
6.1.2
Strong damping
149
6.1.3
The concept of an attractor
149
6.2
Coupled oscillators and normal modes
150
7
Brownian motion
155
7.1
Random variables and the autocorrelation function
15 5
7.1.1
Random variables
155
7.1.2
Stochastic processes
156
7.1.3
The autocorrelation function
159
7.2
Brownian motion and coefficients of diffusion
160
7.2.1
Mathematical analysis
161
7.2.2
Correspondence with macroscopic laws
163
7.3
Langevin s equation
165
7.3.1
Establishing the equation
165
7.3.2
Harmonic oscillator with Brownian motion
168
7.4
Brownian motion with external forces
169
7.4.1
General equation for a transport process
171
7.4.2
Sedimentation
172
7.4.3
Electrophoresis
173
7.4.4 Biopolymer
in an electrochemical potential
174
8
Conformational changes
176
8.1
Kinetics of a conformational change
176
8.1.1
Simple change of conformation
176
8.1.2
Diffusion-controlled bimolecular reactions
179
8.2
Chemical relaxation
182
8.2.1
Basic principle
182
8.2.2
Application to a bimolecular reaction
183
8.2.3
Multi-step reactions
184
8.2.4
Transition from double helix to single strand
187
8.3
Kinetics of the helix-coil transition
188
8.4
Crossing a potential barrier
188
8.4.1
Activated complex theory
190
CONTENTS xvii
8.4.2 Kramers
theory
192
9
Experimental methods
195
9.1
Raman spectroscopy
195
9.1.1
Introduction
195
9.1.2
An elementary treatment
196
9.1.3
Comments on the problem
197
9.1.4
Resonance Raman scattering
198
9.2
Fluorescence depolarization
198
9.2.1
Definitions and calculations
198
9.2.2
Measurements
204
9.3
Proton exchange
207
9.3.1
Introduction
207
9.3.2
Exchange mechanism
207
9.3.3
Nucleic acids: coupling with an opening-closing
mechanism
209
9.3.4
Proteins
211
9.3.5
Technical aspects
215
9.4
X-rays and temperature factors
216
9.4.1
Determination and significance of
В
218
9.4.2
Interpretation of
В
218
9.4.3
Results and molecular dynamics
218
9.5
Flash photolysis
219
9.5.1
General aspects
219
9.5.2
Application to protein dynamics
222
9.6
Inelastic scattering of light
223
9.6.1
General principle
223
9.6.2
Calculation of the scattered intensity
224
9.7
Inelastic neutron scattering
227
9.8
Fast-reaction kinetics
227
9.8.1
Stopped-flow
228
9.8.2
Temperature jump
230
9.8.3
Other experimental aspects
232
10
Methods of modelling intramolecular dynamics
235
10.1
Dynamics in terms of normal modes
235
xv¡¡¡
CONTENTS
10.2
Molecular
dynamics
237
10.3
Stochastic dynamics
240
Conclusion to Part II
242
References and further reading
243
Part III
Hydration
of biopolymers
Introduction
247
11
Properties of water
249
11.1
The water molecule
249
11.2
Ice
250
11.2.1
Structure
250
11.2.2
Antifreeze peptides
252
11.3
Liquid water
252
11.3.1
Structural study
253
11.3.2
Models of liquid water
257
12 Hydrophobie
and hydrophilic molecules
260
12.1 Hydration
of hydrophobic groups
260
12.2 Hydration
of ions
263
12.2.1
Structural aspect
263
12.2.2
Thermodynamic aspect
263
12.2.3
Lyotropicseries
266
12.3 Hydration
of amphiphilic molecules
269
12.3.1
Definition and properties of amphiphilic
molecules
269
12.3.2
Quaternary ammonium ions
269
12.3.3
Micellar organization
271
13 Hydration
of proteins
277
13.1
Micellar model
278
13 2
Solvent accessibility
279
13.3
The hydropathy index
282
13.4
Protein hydration and stability
284
13.5
Structural aspect
287
13.5.1
External water
288
13.5.2
Internal water
289
CONTENTS xix
14 Hydration
of nucleic
acids
290
14.1
Experimental measurements
290
14.2
Thermodynamic model
293
14.3
Crystal studies
294
Conclusion to Part III
298
References and further reading
299
Part IV
Biopolymers
as polyelectrolytes
15
Charge distributions: general laws
303
15.1
Introduction
303
15.2
Electrostatics in
vacuo
306
15.2.1
Field and potential of a charge and
a dipole
306
15.2.2
Gauss s theorem and continuous distributions of
charge
308
15.2.3
Divergence and Poisson s equation
310
15.3
Electrostatics in a medium
311
15.3.1
Polarization and dielectric constant
311
15.3.2
Water as a dielectric
313
15.3.3
Boundary between two dielectric media
316
15.3.4
Poisson s equation and its consequences
321
16
Electrolytic solutions and the
Debye-Hückel
theory
323
16.1
Differential equation for the potential: assumptions and
approximations
323
16.2
Solutions and consequences
326
16.2.1
Electrostatic shielding
327
16.2.2
The dielectric constant of water near an ion
327
16.2.3
Ionic distribution
328
16.3
Limits to the validity of the
Debye-Hückel
theory
329
16.4
Ion pairs
331
17
Polyelectrolyte solutions
332
17.1
General properties of polyelectrolytes
332
17.1.1
Charge accumulation
332
17.1.2
Fluctuations
332
17.1.3
Counter-ions
333
xx
CONTENTS
17.1.4
Polyelectrolyte
conformation
333
17.1.5
Transport
phenomena
333
17.2
Activity of
a polyelectrolyte solution
334
17.2.1
Osmotic
coefficient
334
17.2.2
Donnan
equilibrium
334
17.2.3 Titration
curves
336
17.3
Modelling
338
18
Continuum model
340
18.1
Establishing the Poisson-Boitzmann equation
340
18.2
Examples of modelling
342
18.2.1
The non-linear Poisson-Boitzmann equation
342
18.2.2
The linearized Poisson-Boitzmann equation
342
18.3
Numerical solutions
349
18.4
Condensation model for a charged line
351
18.4.1
Concept of condensation
351
18.4.2
Applications of the model
353
18.5
Comparison between counter-ion condensation (CC) and
Poisson-Boitzmann
(PB)
models
357
19
Mixed models
360
19.1
The generalized Poisson-Boitzmann equation
360
19.2
Tanford and Kirkwood s model
361
19.3
Other models
365
19.4
Finite-difference model
368
20
Molecular models
377
20.1
Monte Carlo method
377
20.2
Molecular dynamics
378
21
Cellular permeability and ion transport
379
21.1
Introduction
379
21.2
Ionic conductivity
380
21.3
Transport mechanisms in ion channels
381
21.3.1
Electrochemical potential
382
21.3.2
Nernst-Planck model
385
21.4
Functioning of an ion pump
391
CONTENTS xxi
21.4.1
Introduction
391
21.4.2 Proton
transfer
392
21.4.3 Proton
transfer
and
electron
transfer
392
21.4.4
Mitchell s theory
394
Conclusion to Part IV
396
References and further reading
398
Part V Association between molecules
Introduction
405
22
Equilibrium studies
407
22.1
Two simple molecules
407
22.2
A ligand and
a
macromolecule
408
22.2.1
Equivalent sites
408
22.2.2
Non-equivalent sites
410
22.3
Binding energy
414
22.4
Large ligands
416
23
Kinetic study and facilitated diffusion
424
23.1
Introduction
424
23.2
Model of DNA-repressor recognition
425
23.3
Results
428
23.4
Transition from one model to another
430
23.5
Processivity
430
23.6
Guided diffusion of a substrate (channelling)
430
24
Mechanisms and specificity of recognition
432
24.1
Calcium transport and the EF hand
432
24.2
Protein dimerization and leucine zippers
433
24.3
Recognition of nucleic acids by proteins
434
24.3.1
Interacting groups in proteins
434
24.3.2
Interacting groups in nucleic acids
436
24.4
Operator-repressor interaction and the HTH motif
440
24.5
Zinc fingers
444
24.6
Polymerase-nucleic acid interactions
447
24.7
Specif ¡city of recognition
448
xii CONTENTS
25 Formation
of
subcellular
structures
456
25.1 Formation
of polymeric
structures
456
25.1.1
Cycle
of conformational
change
457
25.1.2
Polymerization at the end of a polymer
458
25.1.3
Copolymerization
460
25.2
The nucleus and chromatin
462
25.3
Viruses
465
25.4
Ribosome
467
Conclusion to Part V
468
References and further reading
470
Mathematical appendix
473
A.1 Evaluation of some integrals
473
A.
2
Legendre polynomials
474
A.
2.1
Definition and notation
474
A.2.2 Potential due to
a dipole
475
A.
2.3
Potential due to a quadrupole
476
A.2.4 Generalization and spherical functions
476
A3
Bessel functions
477
A.
3.1
Bessel functions (of the first kind) of zero order
477
A.3.2 Bessel functions (of the first kind) of first order
478
A.
3.3
Bessel functions of the second kind or Neumann
functions
479
A.
3.4
Modified Bessel functions
480
A4
Fourier transforms
481
A.4.1 Fourier series
481
A.4.2 Definition of the Fourier transform
483
A.4.3 Properties of Fourier transforms
484
A.4.4 The Dirac delta function
485
A4.5
Examples of Fourier transforms
487
A.
4.6
Convolution integrals
488
A.
5
Wiener-Khinchin relations
490
Index
493
This textbook, the first new text on this subject for some time,
offers a comprehensive introduction to the molecular physics of
biological systems: it seeks to explain how the laws and concepts
of physics apply to the living world at the molecular and subcellular
level, with an emphasis on electrical and dynamical behaviour.
The book is organized into five parts:
•
conformation of biopolymers
•
dynamics of biopolymers
•
hydration of biopolymers
•
biopolymers as polyelectrolytes
•
association between molecules
The author adopts a multi-disciplinary approach and limits the
mathematics only to what is strictly necessary for the development
of the subject. The text should be suitable for students, instructors
and researchers from a wide range of backgrounds in biology,
physics or chemistry taking or teaching an advanced course in bio¬
physics, molecular biophysics or biophysical chemistry.
|
| any_adam_object | 1 |
| author | Daune, Michel |
| author_facet | Daune, Michel |
| author_role | aut |
| author_sort | Daune, Michel |
| author_variant | m d md |
| building | Verbundindex |
| bvnumber | BV035711210 |
| classification_rvk | WD 2200 |
| classification_tum | PHY 821f PHY 820f |
| ctrlnum | (OCoLC)441783406 (DE-599)HBZHT015584524 |
| discipline | Physik Biologie |
| edition | Reprinted |
| format | Book |
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| genre | (DE-588)4123623-3 Lehrbuch gnd-content |
| genre_facet | Lehrbuch |
| id | DE-604.BV035711210 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T21:51:42Z |
| institution | BVB |
| isbn | 0198577834 0198577826 |
| language | German English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017988138 |
| oclc_num | 441783406 |
| open_access_boolean | |
| owner | DE-703 |
| owner_facet | DE-703 |
| physical | XXII, 499 S. Ill., graph. Darst. |
| publishDate | 2006 |
| publishDateSearch | 2006 |
| publishDateSort | 2006 |
| publisher | Oxford Univ. Press |
| record_format | marc |
| spelling | Daune, Michel Verfasser aut Biophysique moléculaire Molecular biophysics structures in motion Michel Daune Reprinted Oxford [u.a.] Oxford Univ. Press 2006 XXII, 499 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biofizika Biopolimeri - Fiziologija Molekularna biologija Biophysics Biopolymers Physiology Molecular biology Molekulare Biophysik (DE-588)4170391-1 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content Molekulare Biophysik (DE-588)4170391-1 s DE-604 Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017988138&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017988138&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext |
| spellingShingle | Daune, Michel Molecular biophysics structures in motion Biofizika Biopolimeri - Fiziologija Molekularna biologija Biophysics Biopolymers Physiology Molecular biology Molekulare Biophysik (DE-588)4170391-1 gnd |
| subject_GND | (DE-588)4170391-1 (DE-588)4123623-3 |
| title | Molecular biophysics structures in motion |
| title_alt | Biophysique moléculaire |
| title_auth | Molecular biophysics structures in motion |
| title_exact_search | Molecular biophysics structures in motion |
| title_full | Molecular biophysics structures in motion Michel Daune |
| title_fullStr | Molecular biophysics structures in motion Michel Daune |
| title_full_unstemmed | Molecular biophysics structures in motion Michel Daune |
| title_short | Molecular biophysics |
| title_sort | molecular biophysics structures in motion |
| title_sub | structures in motion |
| topic | Biofizika Biopolimeri - Fiziologija Molekularna biologija Biophysics Biopolymers Physiology Molecular biology Molekulare Biophysik (DE-588)4170391-1 gnd |
| topic_facet | Biofizika Biopolimeri - Fiziologija Molekularna biologija Biophysics Biopolymers Physiology Molecular biology Molekulare Biophysik Lehrbuch |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017988138&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017988138&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT daunemichel biophysiquemoleculaire AT daunemichel molecularbiophysicsstructuresinmotion |