Molecular and cellular biophysics:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge [u.a.]
Cambridge Univ. Press
2010
|
| Ausgabe: | 1. publ., transferred to digital printing, with corrections |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIII, 512 S. Ill., graph. Darst. |
| ISBN: | 9780521624411 9780521624701 |
Internformat
MARC
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| 020 | |a 9780521624701 |c (pbk) |9 978-0-521-62470-1 | ||
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| 100 | 1 | |a Jackson, Meyer B. |e Verfasser |0 (DE-588)155093851 |4 aut | |
| 245 | 1 | 0 | |a Molecular and cellular biophysics |c Meyer B. Jackson |
| 250 | |a 1. publ., transferred to digital printing, with corrections | ||
| 264 | 1 | |a Cambridge [u.a.] |b Cambridge Univ. Press |c 2010 | |
| 300 | |a XIII, 512 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
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Datensatz im Suchindex
| _version_ | 1804148951639654400 |
|---|---|
| adam_text | Contents
ľrejace
page xu
Acknowledgements
xiv
Chapter
1
Global transitions in proteins
1
1.1
Defining a global state
2
1.2
Equilibrium between two global states
4
1.3
Global transitions induced by temperature
5
1.4
Lysozyme unfolding
7
1.5
Steepness and enthalpy
9
1.6
Cooperativity and thermal transitions
11
1.7
Transitions induced by other variables
12
1.8
Transitions induced by voltage
14
1.9
The voltage sensor of voltage-gated channels
17
1.10
Gating current
18
1.11
Cooperativity and voltage-induced transitions
19
1.12
Compliance of a global state
21
Chapter
2 1
Molecular forces in biological structures
25
2.1
The Coulomb potential
25
2.2
Electrostatic self-energy
27
2.3
Image forces
29
2.4
Charge-dipole interactions
31
2.5
Induced dipoles
32
2.6
Cation
-π
interactions
33
2.7
Dispersion forces
35
2.8 Hydrophobie
forces
36
2.9 Hydration
forces
39
2.10
Hydrogen bonds
39
2.11
Steric repulsions
43
2.12
Bond flexing and harmonic potentials
44
2.13
Stabilizing forces in proteins
46
2.14
Protein force fields
50
2.15
Stabilizing forces in nucleic acids
52
2.16
Lipid bilayers
and membrane proteins
53
Chapter
3
Conformations of macromolecules
56
3.1
n-Butane
56
3.2
Configurational partition functions and
polymer chains
58
3.3
Statistics of random coils
60
3.4
Effective segment length
62
3.5 Nonideal
polymer chains and theta solvents
63
CONTENTS
3.6
Probability distributions
65
3.7
Loop formation
66
3.8
Stretching a random coil
67
3.9
When do molecules act like random coils?
68
3.10
Backbone rotations in proteins: secondary
Structure
68
3.11
The entropy of protein
denatura
tion
71
3.12
The helix-coil transition
73
3.13
Mathematical analysis of the helix-coil
transition
74
3.14
Results of helix-coil theory
78
3.15
Helical propensities
80
3.16
Protein folding
82
3.17
Cooperativity in protein folding
86
Chapter
4
Molecular associations
89
4.1
Association equilibrium in solution
89
4.2
Cooperativity
91
4.2.1
Concerted binding
91
4.2.2
Sequential binding
93
4.2.3
Nearest neighbor interactions
94
4.3
Thermodynamics of associations
94
4.4
Contact formation
95
4.5
Statistical mechanics of association
96
4.6
Translational free energy
98
4.7
Rotational free energy
юі
4.8
Vibrational free energy
Ю2
4.9
Solvation effects
Ю5
4.10
Configurational free energy
Ю6
4.11
Protein association in membranes
-
reduction of
dimensionality W7
4.12
Binding to membranes W8
Chapter
5
I Allosteric interactions
ш
5.1
The allosteric transition
П2
5.2
The simplest case: one binding site and one
allosteric transition H2
5.3
Binding and response H5
5.4
Energy balance in the one-site model 116
5.5
G-protein coupled receptors H7
5.6
Binding site interactions
121
5.7
The Monod-Wyman-Changeux (MWC) model
123
5.8
Hemoglobin
126
5.9
Energetics of the MWC model
127
5.10
Macroscopic and microscopic additivity l28
5.11
Phosphofructokinase 130
5.12
Ligand-gated channels 132
CONTENTS
5.13 Subunit-subunit
interactions:
the
Koshland-Nemethy-Filmer (KNF)
model
134
5.14 The Szabo-Karplus
(SK)
model
137
Chapter
6
I Diffusion and Brownian motion
142
6.1
Macroscopic diffusion: Fick s laws
142
6.2
Solving the diffusion equation
143
6.2.1
One-dimensional diffusion from a point
144
6.2.2
Three-dimensional diffusion from a point
146
6.2.3
Diffusion across an interface
146
6.2.4
Diffusion with boundary conditions
148
6.3
Diffusion at steady state
150
6.3.1
A long pipe
151
6.3.2
A small hole
152
6.3.3
A porous membrane
153
6.4
Microscopic diffusion
-
random walks
154
6.5
Random walks and the Gaussian distribution
156
6.6
The diffusion equation from microscopic theory
159
6.7
Friction
160
6.8
Stokes law
162
6.9
Diffusion constants of macromolecules
163
6.10
Lateral diffusion in membranes
164
Chapter
7
Fundamental rate processes
167
7.1
Exponential relaxations
167
7.2
Activation energies
169
7.3
The reaction coordinate and detailed balance
170
7.4
Linear free energy relations
172
7.5
Voltage-dependent rate constants
175
7.6
The Marcus free energy relation
177
7.7
Eyring theory
179
7.8
Diffusion over a barrier
-
Kramers theory
180
7.9
Single-channel kinetics
183
7.10
The reaction coordinate for a global transition
186
Chapter
8
Association kinetics
194
8.1
Bimolecular association
194
8.2
Small perturbations
195
8.3
Diffusion-limited association
197
8.4
Diffusion-limited dissociation
200
8.5
Site binding
201
8.6
Protein-ligand association rates
203
8.6.1
Evolution of speed
205
8.6.2
Acetylcholinesterase
205
8.6.3
Horseradish peroxidase
206
8.7
Proton transfer
207
CONTENTS
8.8
Binding to membrane receptors
208
8.9
Reduction in dimensionality
212
8.10
Binding to
DNA 214
Chapter
9
Multi-state kinetics
216
9.1
The three-state model
216
9.2
Initial conditions
219
9.3
Separation of timescales
220
9.4
General solution to multi-state systems
221
9.5
The three-state model in matrix notation
225
9.6
Stationarity, conservation, and detailed balance
226
9.7
Single-channel kinetics: the three-state model
229
9.8
Separation of timescales in single channels: burst
analysis
232
9.9
General treatment of single-channel kinetics: state
counting
235
9.10
Relation between single-channel and macroscopic
kinetics
236
9.11
Loss of stationarity, conservation, and detailed balance
237
9.12
Single-channel correlations: pathway counting
240
9.13
Multisubunit kinetics
242
9.14
Random walks and stretched kinetics
244
Chapter 1
0
Enzyme catalysis
248
10.1
Basic mechanisms
-
serine
proteases
248
10.2
Michaelis-Menten kinetics
251
10.3
Steady-state approximations
254
10.4
Pre-steady-state kinetics
256
10.5
Allosteric enzymes
257
10.6
Utilization of binding energy
258
10.7
Kramers rate theory and catalysis
259
10.8
Proximity and translational entropy
260
10.9
Rotational entropy
263
10.10
Reducing
Eu.
transition state complementarity
264
10.11
Friction in an enzyme-substrate complex
267
10.12
General-acid-base catalysis and Bronsted slopes
268
10.13
Acid-base catalysis in
ß-galactosidase 270
10.14
Catalysis in
serine
proteases and strong H-bonds
272
10.15
Marcus theory and proton transfer in carbonic
anhydrase
273
Chapter 11 I Ions and counterions
276
11.1
The Poisson-Boltzmann equation and the
Debye length
277
11.2
Activity coefficient of
anion
279
11.3
Ionization of proteins
283
CONTENTS
11.4
Gouy-Chapman theory and membrane
surface charge
285
11.5
Stern s improvements of Gouy-Chapman theory
288
11.6
Surface charge and channel conductance
291
11.7
Surface charge and voltage gating
293
11.8
Electrophoretic mobility
294
11.9
Polyelectrolyte solutions I.
Debye-Hückel
screening
297
11.10
Polyelectrolyte solutions II. Counterion-condensation
300
11.11 DNA
melting
302
Chapter 1
2
I Fluctuations
307
12.1
Deviations from the mean
307
12.2
Number fluctuations and the
Poisson
distribution
309
12.3
The statistics of light detection by the eye
311
12.4
Equipartition of energy
313
12.5
Energy fluctuations in
a
macromolecule
315
12.6
Fluctuations in protein ionization
317
12.7
Fluctuations in a two-state system
319
12.8
Single-channel current
320
12.9
The correlation function of a two-state system
322
12.10
The Wiener-Khintchine theorem
324
12.11
Channel noise
327
12.12
Circuit noise
329
12.13
Fluorescence correlation spectroscopy
332
12.14
Friction and the fluctuation-dissipation theorem
336
Chapter 1
3
I Ion permeation and membrane potential
339
13.1
Nernst potentials
339
13.2
Donnan
potentials
341
13.3
Membrane potentials of cells
343
13.3.1
Neurons
345
13.3.2
Vertebrate skeletal muscle
345
13.4
A membrane permeable to Na+ and K+
347
13.5
Membrane potentials of neurons again
350
13.6
The Ussing flux ratio and active transport
351
13.7
The Goldman-Hodgkin-Katz voltage equation
352
13.8
Membrane pumps and potentials
354
13.9
Transporters and potentials
355
13.10
The Goldman-Hodgkin-Katz current equation
357
13.11
Divalent ions
360
13.12
Surface charge and membrane potentials
361
13.13
Rate theory and membrane potentials
362
Chapter 1
4
I Ion permeation and channel structure
367
14.1
Permeation without channels
367
14.2
The Ohmic channel
370
CONTENTS
14.3 Energy
barriers and channel properties
371
14.4
Eisenman selectivity sequences
374
14.5
Forces inside an ion channel
376
14.6
Gramicidin A
378
14.7
Rate theory for multibarrier channels
380
14.8
Single-ion channels
384
14.9
Single-file channels
390
14.10
The KcsA channel
394
Chapter 1
5
I Cable theory
400
15.1
Current through membranes and cytoplasm
401
15.2
The cable equation
403
15.3
Steady state in a finite cable
406
15.4
Voltage steps in a finite cable
408
15.5
Current steps in a finite cable
411
15.6
Branches and equivalent cylinder
representations
412
15.6.1
Steady state
413
15.6.2
Time constants
415
15.7
Cable analysis of a neuron
418
15.8
Synaptic integration in dendrites: analytical
models
422
15.8.1
Impulse responses
423
15.8.2
Realistic synaptic inputs
425
15.9
Compartmental models and cable theory
428
15.10
Synaptic integration in dendrites: compartmental
models
430
Chapter
16
Action potentials
434
16.1
The action potential
434
16.2
The voltage clamp and the properties of Na+ and K+
channels
439
16.3
The Hodgkin-Huxley equations
442
16.4
Current-voltage curves and thresholds
447
16.5
Propagation
450
16.6 Myelin
453
16.7
Axon geometry and conduction
455
16.8
Channel diversity
457
16.9
Repetitive activity and the A-current
458
16.10
Oscillations
461
16.11
Dendritic integration
466
Appendix
1
Expansions and series
470
Al.l Taylor series
470
Al
.2
The binomial expansion
471
A1.3 Geometric series
471
CONTENTS
Appendix
2
I Matrix algebra
472
A2.1 Linear transforms
472
A2.2 Determinants
473
A2.3 Eigenvalues, eigenvectors, and diagonalization
474
Appendix
3
I Fourier analysis
477
Appendix
4
I Gaussian integrals
481
Appendix
5
I Hyperbolic functions
483
Appendix
6
I Polar and spherical coordinates
484
References
486
Index
504
|
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| illustrated | Illustrated |
| indexdate | 2024-07-10T00:15:18Z |
| institution | BVB |
| isbn | 9780521624411 9780521624701 |
| language | English |
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| physical | XIII, 512 S. Ill., graph. Darst. |
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| spelling | Jackson, Meyer B. Verfasser (DE-588)155093851 aut Molecular and cellular biophysics Meyer B. Jackson 1. publ., transferred to digital printing, with corrections Cambridge [u.a.] Cambridge Univ. Press 2010 XIII, 512 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Zelle (DE-588)4067537-3 gnd rswk-swf Molekulare Biophysik (DE-588)4170391-1 gnd rswk-swf 1\p (DE-588)4123623-3 Lehrbuch gnd-content Zelle (DE-588)4067537-3 s Molekulare Biophysik (DE-588)4170391-1 s 2\p DE-604 Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024829980&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Jackson, Meyer B. Molecular and cellular biophysics Zelle (DE-588)4067537-3 gnd Molekulare Biophysik (DE-588)4170391-1 gnd |
| subject_GND | (DE-588)4067537-3 (DE-588)4170391-1 (DE-588)4123623-3 |
| title | Molecular and cellular biophysics |
| title_auth | Molecular and cellular biophysics |
| title_exact_search | Molecular and cellular biophysics |
| title_full | Molecular and cellular biophysics Meyer B. Jackson |
| title_fullStr | Molecular and cellular biophysics Meyer B. Jackson |
| title_full_unstemmed | Molecular and cellular biophysics Meyer B. Jackson |
| title_short | Molecular and cellular biophysics |
| title_sort | molecular and cellular biophysics |
| topic | Zelle (DE-588)4067537-3 gnd Molekulare Biophysik (DE-588)4170391-1 gnd |
| topic_facet | Zelle Molekulare Biophysik Lehrbuch |
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