View Index as PDF (184KB)
Cambridge University Press
052162441X - Molecular and Cellular Biophysics - by Meyer B. Jackson
Index
Index
Page numbers in italics refer to figures. Page numbers in bold denotes entries in tables.
absorbing boundary conditions 148, 184, 198, 208, 213, 406
accommodation 449
acetylcholine 118, 119, 205
binding 120, 192
charges 34, 34
acetylcholine receptor 34, 132, 133, 133, 192, 234, 241, 362, 374
channel structural parameters and conductances 371
ligand association rate 204
acetylcholinesterase 34, 205–206, 206
ligand association rate 204
acid–base catalysis 268–270
β–galactosidase 270–271, 271
general–acid catalysts 269, 270, 271
general–base catalysts 269, 269
acidic phosphate groups in nucleic acids 53, 302
action potentials 434
axon geometry and conduction 455–457, 456
channel diversity 457–458
current–voltage curves and thresholds 447–450, 448
definition 434–439, 435, 437, 438
dendritic integration 466–468, 467
Hodgkin–Huxley equations 442–446, 444, 447
myelin 453, 453–455
oscillations 461–466
propagation 450–453, 452
repetitive activity and the A–current 458–461, 459, 460
voltage clamp 439, 439–441, 440
activation energies 169–170, 264, 274
activation of ion channels 442
active transport across membranes 351–352, 386
activity coefficient for ions 279, 279–283, 353
definition 280
infinite dilution 281, 281
A-current 458–461, 459, 460, 468
additivity 128, 129
adenine–thymine base pairs, hydrogen bonding 52
ADP 130
alanine (ala) 8, 38, 81, 85, 119
helix continuation parameter 81
alcohols 48
alkaline phosphatase 211
allosteric enzymes 130–132, 257–258
allosteric interactions 111
allosteric transition 112
binding and response 115–116
binding site interactions 121, 121–122
energy balance in one–site model 116–117, 117
G-protein coupled receptors 117–121, 120
hemoglobin 126, 126–127
ligand-gated channels 132–133, 133
macroscopic and microscopic additivity 128–130
Monod–Wyman–Changeux (MWC) model 123–126
energetics 127, 127–128, 128
enzymes 257
one binding site and one allosteric interaction 112–115, 113
phosphofructokinase 130–132, 131, 132
subunit–subunit interactions 134, 134–136
Szabo–Karplus (SK) model 137–140, 139
α-helices 49, 73, 85
capping 81
mathematical analysis 74
proteins 49, 49, 50
stability 73
amino acids
helix continuation parameters 81
side chains 268
Anisidoris snail 459, 461
arginine 17, 18, 119, 283
arginine (arg), helix continuation parameter 81
Arrhenius equation 169
Arrhenius plot 170
asparagine (asn), helix continuation parameter 81
aspartate 8, 42, 119, 206, 272
aspartic acid (asp), helix continuation parameter 81
ATP 130
axial resistivity 401
axons
geometry and conduction 455–457, 456
reflections 457
speed and size 452
supernormal 449
varicosities 456, 456, 457
bacteriorhodopsin 208
barnacle muscle fibers 462, 464
barnase 86, 189, 189, 190, 192
β–sheets in proteins 49, 68–71, 70, 189
binding energy in enzymes 258–259
binomial distribution 154, 156, 243, 309, 320
binomial expansion 124, 138, 155, 471
Bohr effect 127, 140
Boltzmann constant 4
Boltzmann distribution 2, 4, 5, 17, 56, 161, 182, 260, 277, 288, 307, 313, 362, 378
activation energies 169
reaction coordinate 179
Boltzmann equation 17, 22, 293, 443, 462
Boltzmann weight 2, 32, 57, 74, 96
bond vibrations 3
frequency 44
kinetic energy 3
normal modes 46, 102, 103
Born energy 28
Briggs–Haldane mechanism 254
Brønsted equation 174, 270
Brønsted slopes 268–270
Brownian motion 142, 283, 336
buffers 269, 269
burst analysis 232, 232
n-butane 56–58, 57
cable equation 403, 403–406, 454
cable length constant (λ) 405
cable theory 400
analysis of neurons 418, 418–422, 420, 421
branches and equivalent cylinder representation 412–413, 413
steady-state 413–415, 415
time constants 415–418
cable parameters 406
compartmental models 428, 428–431, 450, 467
current steps in a finite cable 411–412
current through membranes and cytoplasm 401, 401–403
steady-state in a finite cable 406–407, 408
synaptic integration in dendrites
analytical models 422–423, 423
compartmental models 430–433, 431, 432
impulse responses 423–425, 424
realistic synaptic inputs 425–428, 427
calcium chloride, activity coefficient 281, 281
calcium ion channels 207, 208, 392, 458, 462
calmodulin, ligand association rate 204
capacitance
circuit 329
ionic layers 290
carbamylcholine 118, 119
carbon–carbon bonds 44
force constant 261
carbonic anhydrase 177, 273–275, 274, 355
carboxypeptidase 268
catalytic efficiency of enzymes 253
cation–π interactions 33, 33–35, 47
central-limit theorem 65, 156
channel noise 186, 321, 323, 327–328, 328
channel structure 367
Eisenman selectivity sequences 374–376, 375, 398
energy barriers and channel properties 371–374, 372
gramicidin A 370, 378–380, 384, 393
KcsA channel 71, 394, 394–399, 396
Ohmic channels 370, 370–371, 372, 376, 384
rate theory for multibarrier channels 380, 380–384, 383
single–file channels 371, 390, 390–394, 397
single–ion channels 384–390
structural parameters and conductances 371
characteristic equation of a matrix 223, 242, 475
characteristic ratio 62, 63
charge–dipole interactions 31, 31–32
choline 291, 441
chymotrypsin 248, 250, 256, 258, 259, 272
hydrolysis rates 250
ligand association rate 204
chymotrypsin inhibitor-2 190, 191, 192
circuit noise 329, 329–331
mean-square voltage 329
classical configuration integral 3, 46, 301
closed-time distribution 185, 232, 233, 236, 237, 240, 241
coils, random 72, 73, 106, 107, 163–164
frictional coefficients 163
molecular behavior 68
statistics 60, 60–62
stretching 67–68
collision frequency 198, 200
compartmental models 428, 428–430
synaptic integration in dendrites 430–433, 431, 432, 450, 467
concerted binding 91–93
configurational entropy 71, 72, 107
configurational free energy 94, 106–107, 107, 129
configurational partition functions 58–60
conservation of total number of moles 227, 228
loss of 237–240, 240
constant-field equation 353, 360
extended form 361
cooperative units 11, 16, 79, 123, 303
cooperativity within systems
allostoric transitions 123, 130
helix–coil transitions 53, 78, 79, 79
hydrogen bonds 41, 43
molecular associations 91
concerted binding 91–93
nearest–neighbor interactions 94
sequential binding 93–94
protein folding 72, 86–87
thermal transitions 11–12
voltage-induced transitions 19–21, 20
correlation function 322–328, 331–338
Coulomb’s law 25
contribution to potential energy 280
Coulomb potential 25–27, 31, 276, 277, 279–282, 298, 300, 302, 375
Coulombic interactions 32, 34, 177, 206, 398
counterions see ions and counterions
cratic contribution 100
creatine kinase 334, 335, 335
critical assessment of protein structure prediction (CASP) 52
cysteine (cys), helix continuation parameter 81
cytoplasm 401, 401–403
resistance 401, 429
viscosity 335, 406
de Broglie wavelength, thermal 99, 179
Debye length 277–278, 287, 289
Debye–Hückel limiting law 281, 282
dilute solutions 282
exact at infinite dilution 283
ionic atmospheres 281, 282
Debye–Hückel screening 297–305
degeneracy 57, 75, 84, 138
delta function 144, 423, 479
denaturants of proteins 11, 13, 48, 187–192
dendrites 419
action potentials 466–468, 467
synaptic integration
analytical models 422–423, 423
compartmental models 430–433, 431, 432
impulse responses 423–425, 424
realistic synaptic inputs 425–428, 427
desensitization 133
detailed balance 116
kinetics of multi-state systems 228
loss of 237–240, 240
rate processes 170–182
dielectric constant 25, 30, 31, 35, 36, 38, 41, 47, 51, 272, 276, 287, 363, 368, 376, 402, 406
diffusion 142
diffusion equation 66
from microscopic theory 159–160
diffusion-limited associations 197–200, 198
diffusion-limited dissociations 200–201
friction 160–162, 336
Gaussian distribution 156–159, 157
lateral diffusion in membranes 164–165
macromolecules, diffusion constants 163–164, 164
deviation from Stokes–Einstein relation 163
macroscopic diffusion and Fick’s laws 142–143
solving the diffusion equation 143–144
diffusion across an interface 146–148, 147, 148
diffusion with boundary conditions 148–150, 149
one-dimensional diffusion from a point 144–146, 145
three-dimensional diffusion from a point 146
steady-state 150–151
long pipe 151
porous membrane 153–154
small hole 152, 152–153
Stoke’s law 162, 162–163
dimensionality, reduction in 107–108, 108, 212–214
dipicrylamine 369, 369
dipole–dipole interactions 32, 49, 398
dipole moment 26, 31, 31, 32, 35, 49, 395, 396
dipoles
induced dipoles 32–33
interactions with charges 31, 31–32
dispersion force (London force) 35, 39, 43, 52
lipid bilayers 54
DNA 52–53, 62
binding 94, 112, 214
electrostatic repulsion 298, 298
flexibility parameters 63
formation of circular form from linear form 67
melting 302–305, 305
random coil behavior 68
Donnan potentials 341–343, 342, 344, 346
effective segment length of macromolecules 62–63
eigenvalues 46, 223, 474–476
multisubunit kinetics 244
eigenvectors 223, 224, 474–476
three-state model 225
Einstein’s equation for diffusion and friction 161, 267, 347
Eisenman theory of selectivity 374–376, 375, 376, 398
elastase 248, 250
electrogenic membrane pumps 354, 355
electroneutrality 288, 342, 343, 346
electrophoresis 294–297, 295
mobility of ions 295
sheer force 295
velocity of ions 294
electrostatic self-energy 27–29
electrostatic stress 267
elementary weight 57
partition function 58
enthalpy 6, 37, 41
Coulomb’s law 26
hydration 28, 28
ions in water 27
thermal denaturation of proteins 9–12, 10, 72, 87
entropy 6
of electrostatic interactions 26
ions in water 27
protein denaturation 71–73
unfolding entropy 72
rotational entropy 263–264
translational entropy 260, 260–263, 263
enzyme catalysis 248
acid–base catalysis 268–270
β-galactosidase 270–271, 271
allosteric enzymes 257–258
friction in an enzyme-substrate complex 267–268
hydrolysis rates 250
Kramers rate theory 259–260
Michaelis–Menten kinetics 251–254
pre-steady-state kinetics 256–257
proton transfer in carbonic anhydrase 273–275, 274
proximity and translational entropy 260, 260–263, 263
rotational entropy 263–264
serine proteases 272–273
steady-state approximations 254–256
transition state complementarity 264–267, 266
utilization of binding energy 258–259
equipartition of energy 23, 104, 313–317, 329
equivalent cylinder representation 412–413, 413
steady-state 413–415, 415
time constants 415–418
Euler’s formula 479
excluded volume effect 43, 63, 64, 70, 72, 281
theta solvents 65
exponential relaxations 167–169, 169
extended constant-field equation 361
eye, light detection 311–313, 312, 313
Eyring theory 179–180
Fick’s laws 142–143
first law 142
second law 143
fluctuations 307
channel noise 327, 328
circuit noise 329, 329–331
deviations from the mean 307–308
energy fluctuations in macromolecules 315–317
equipartition of energy 313–315
fluorescence correlation spectroscopy 164, 332, 332
friction and the fluctuation-dissipation theorem 336, 338
Poisson distribution 309, 309–311, 310
protein ionization 317–319
single-channel current 320–322, 321
statistics of light detection by the eye 311–313, 312, 313
two-state systems 319–320
correlation function 322–324
Wiener–Khintchine theorem 324–327, 331
fluorescence correlation spectroscopy 164, 332, 332, 335
fluorescence recovery after photobleaching (FRAP) 164, 165
fluorescent proteins 334, 335
flux 198, 200, 347
Ussing flux ratio 351–352, 390
definition 352
folding of proteins 46, 82–86
cooperativity 86–87
good-folding amino acid sequences 84
hydrophobic interactions 47, 48
native state 46, 71, 82, 85, 85
jigsaw puzzle picture 86
molten-globule 82
oil droplet picture 86
time taken 72
Fourier analysis 477, 477–480, 478
Fourier integral 324, 423
Fourier transform 144, 149, 150, 324, 325, 408, 410, 423
additive noise 324, 325
fluctuations 324, 326
inverse 327
Lorentzian 328
free energy
change in 5
electrostatic 15
pressure-induced transitions 12
protein ionization 284
thermal denaturation of proteins 6
configurational free energy 94, 106–107, 107
global states of proteins 2, 3, 4
interactions 21
linear analysis 192
linear relations 172–175, 173, 175
Marcus relation 177–178, 178
molar free energy 5
standard state 95
rotational free energy 101–102, 263
translational free energy 98–101, 260–263
change in 101
translation contribution to ΔG° 99, 100
vibrational free energy 102–104
change in 104
vibrational contribution 102
freely jointed chains 60, 60
freely rotating chains 61
friction 160–162
electrophoretic mobility 294
enzyme–substrate complexes 267–268
fluctuation–dissipation theorem 336, 338
frictional coefficients 163
Stoke’s law 162, 162–163
fructose-1,6-diphosphate 130
fructose-6-phosphate 130, 131
fura-2 196, 197
GABA 183, 236, 374
β–galactosidase 270, 271
gas constant 4
gating current 18, 18–19
gating particle 442
gauche conformation of n–butane 56, 57, 57
Gaussian distribution
polymers 65
random walks 156–159, 157
Gaussian integrals 481–482
geometric series 471
Gibbs–Helmholtz equation 10
global states of proteins 1, 4
allosteric transitions 112, 113, 117, 121, 174
compliance 21–23, 22
definition 2–4
equilibrium between two global states 4–5
free energy 2, 3, 4
partition function 3
transitions 12–14
transitions induced by denaturants 13
transitions induced by temperature 5–7, 6
transitions induced by voltage 14, 14–17
cooperativity 19–21, 20
steepness factor 16, 16
transition voltage 16, 16
glutamate 85, 206, 270–271, 271, 283, 292, 355
glutamic acid (glu), helix continuation parameter 81
glutamine 17, 18, 85
glutamine (gln), helix continuation parameter 81
glycine (gly) 38, 81, 85, 394
helix continuation parameter 81
glycine receptors 374
Goldman–Hodgkin–Katz current equation 348, 357–360, 359, 361, 362, 363, 364, 372, 434
Goldman–Hodgkin–Katz voltage equation 349, 350, 352–354, 354, 357, 360, 387
good-folding amino acid sequences 84
Gouy–Chapman equation 287
Gouy–Chapman theory 285–288, 294, 296–297, 302
Stern’s improvements 288–291
G–protein coupled receptors 117–121, 120, 122
gramicidin A 374, 378–380, 393
channel structural parameters and conductances 371
green fluorescent protein (GFP) 70, 71
guanine–cytosine basepairs, hydrogen bonding 52
harmonic oscillators 21, 44, 100, 103, 104
harmonic potentials 22, 44–46
heat capacity 37, 41, 315, 316
helix–coil transition/theory 53, 60, 73–74, 74, 87, 94, 303
helical propensities 80–82
mathematical analysis 74–78
mean number of helical residues 76
results 78, 78–79
Helmholtz–Smoluchowski equation 296
hemoglobin 70, 70, 137–140, 164, 267, 319
allosteric interactions 126, 126–127
iron–heme binding sites 140
linear free energy relation 174, 174
oxygen binding 92
pH sensitivity 140
Hill coefficient 92, 93, 94, 125–126
sequential binding 93
Hill equation 92, 92, 126, 126, 135, 136
Hill plot 92
hippocampal neuron 406, 430, 431
histidine (his) 249–251, 266, 272, 272–275
helix continuation parameter 81
Hodgkin–Huxley equations 442–446, 444, 447
Hodgkin–Keynes model 390, 392
horseradish peroxidase 206–207
ligand association rate 204
H–P (hydrophobic–polar amino acids) lattice model 83
modeling 83, 83
oil droplet picture 86
sequences 84
good–folding 84
hydration force 39
hydrogen bonds 39–43
energies 42
enzyme–substrate 41, 42
energies 42
force constant 261
nucleic acids 52
adenine–thymine base pairs 52
double-helix formation 52
guanine–cytosine base pairs 52
proteins 48, 49, 83
α–helices 49, 49, 50
β–sheets 49
stretching force constant 45
strong bonds 272–273
histidine–aspartate 272
pK of histidine 272, 273
water 41, 82
hydrophobic forces 36–39, 38, 48, 54, 85, 105–106
protein folding 47, 72, 83–86, 190
hydrophobic matching 53
ideal polymer chains 64
central-limit theorem 65
ideal solutions
deviation from 279
infinite dilution 281
inactivation of ion channels 442
insulin 103, 104
image forces 29, 29–31, 30, 38, 283, 363, 368–371, 377, 377, 379, 395
internal motions in proteins 267
inverse Fourier transform 480
ion hydration energy 28, 28
ion size 376
ion hydration shell 281
ion permeation 339, 368 see also channel structure
Donnan potentials 341–343, 342
forces within ion channels 376, 376–378, 377
Nernst potentials 339–341, 340
permeation without channels 367–369, 369
ionic atmosphere 279, 282
Debye–Hückel limiting law 281
ionic double layer 287
ions and counterions 276–277
activity coefficient 279, 279–283, 353
contribution of screening to potential energy 280
counterion condensation 300–302
Debye–Hückel screening 297–305
DNA melting 302–305, 305
electrophoretic mobility 294–297, 295
velocity 294
ionization of proteins 283–285
membrane surface charge 285–288, 361–362
Stern’s improvements of Gouy–Chapman theory 288–291
Poisson–Boltzmann equation and Debye length 277–278
surface charge and channel conductance 291–293
surface charge and voltage gating 293–294, 294
isoleucine (ile), helix continuation parameter 8, 9, 81
jigsaw puzzle picture for protein folding 86
Johnson noise 331
K system of enzymes 257, 258
KcsA channel 71, 71, 394, 394–399, 396
kinetics of associations 194
bimolecular associations 194–195
binding to DNA 214
binding to membrane receptors 208–211, 209
diffusion-limited associations 197–200, 198
diffusion-limited dissociations 200–201
protein–ligand association rates 203–205, 204
acetylcholinesterase 205–206, 206
evolution of speed 205
horseradish peroxidase 206–207
proton transfer 207–208
rates 207
reduction in dimensionality 212–214
site binding 201–203, 202
small perturbations 195–196, 197
kinetics of multi-state models 216
general solution to multi-state systems 221–225
general treatment of single-channel kinetics 234–236, 236
initial conditions 219–220, 220
loss of stationarity, conservation and detailed balance 237–240
multisubunit kinetics 242–244, 243
random walks and stretched kinetics 244–246, 246
relation between single-channel and macroscopic kinetics 236–237
separation of time scales 220–221
single-channel kinetics 232, 232
single-channel correlations 240–242, 241
stationarity, conservation and detailed balance 226–228
three-state model 216–219
matrix notation 225
single-channel kinetics 229–232, 231
Kirchoff’s law 404
Koshland–Nemethy–Filmer (KNF) model 134, 134–136
Kramers’ theory 180–183
enzymes 259–260, 267–268
ion channels 445
β-lactamase, ligand association rate 204
Langevin equation 336, 397
Laplacian differential operator 143, 146, 285, 485
Lennard–Jones potential 43, 44, 51, 95
leucine 38, 85, 86
leucine (leu), helix continuation parameter 81
Levinthal’s paradox 73
ligand-gated channels 132–133, 133
ligands 202, 203
frequency of binding to receptors 211
protein–ligand association rates 203–205, 204
acetylcholinesterase 205–206, 206
evolution of speed 205
horseradish peroxidase 206–207
reduction in dimensionality 212–214
light detection by the eye 311–313, 312, 313
like–dissolves–like rule 36
Linderstrøm–Lang model of protein ionization 283
linear transformations of matrices 472–473
linkage 122
lipid bilayers 14, 23, 30, 39, 53–54, 54, 108, 164–165, 357, 363, 367–369
dispersion force (London force) 36, 54
hydration forces 39
melting 54
lobster axon 406
lock-and-key stereospecific interactions 43
London force see dispersion force
loop formation 66–67
Lorentzian 328
lysine 18, 85, 250, 283
lysine (lys), helix continuation parameter 81
lysozyme 70, 71, 156, 264
diffusion constant 156, 164
unfolding by thermal denaturation 7–9, 8, 12
melting curves 8, 9
macromolecules, conformations of 56
backbone rotations in proteins 68–71, 69
n–butane 56–58
trans and gauche conformations 56, 57, 57
configurational partition functions and polymer chains 58–60
effective segment length 62–63
energy fluctuations 315–317
entropy of protein denaturation 71–73
flexibility parameters for chain molecules 63
helix continuation parameters for amino acids 81
helix–coil theory 78, 78–79
helical propensities 80–82
helix–coil transition 73–74, 74
mathematical analysis 74–78
loop formation 66–67
nonideal polymer chains and theta solvents 63–65
probability distributions 65–66
protein folding 82–86
cooperativity within 86–87
random coil behavior of molecules 68
statistics of random coils 60–62
stretching of random coils 67–68
macroscopic additivity 128–130
Marcus theory 177–178, 178
enzyme catalysis 273–275, 274
Markov processes 160, 184
matrix algebra
determinants 473–474
eigenvalues, eigenvectors and diagonalization 46, 77, 225, 474–476
linear transformations 472–473
positive semidefinite 45
Maxwell time constant 402, 403
mean capture time 213
mean number of helical residues 76
mean-square displacement 23, 145, 155, 160, 314
mean-square end-to-end length 61
membrane capacitance 402, 405, 428, 429, 452, 456
membrane conductance 21, 348, 370, 400, 429, 440
membrane potentials 339, 343
cells 343–344
muscle, skeletal 345–346
neurons 345, 345, 350–351
divalent ions 360–361
Goldman–Hodgkin–Katz current equation 357–360, 359, 360–363, 364
Goldman–Hodgkin–Katz voltage equation 350, 352–354, 354, 360
membrane pumps 354–355
membrane transporters 355, 358
permeability to sodium and potassium ions 347, 347–349
rate theory 362–365, 363
surface charge 361–362
Ussing flux ratio and active transport 351–352
membrane time constant 405
membranes
binding 108–109, 109
current flow 401, 401–403
lateral diffusion 164–165
protein associations 107–108, 108
proteins 53–54, 54
hydrophobic matching 53
pumps 354–355
receptor binding 208–211, 209
resistance 401
surface charge 285–288, 361–362
Stern’s improvements of Gouy–Chapman theory 288–291
transmembrane voltage 14, 14
transporters 355, 358
methionine (met), helix continuation parameter 81
Michaelis–Menten equation 91, 252, 253
enzyme catalysis 251
microscopic additivity 128–130
microstates of proteins 2, 3
entropy 3
partition function 2, 3
thermal denaturation 6, 6
minimum potential energy conformation of polypeptides 70, 71
mitochondria 355
molecular associations 89
association equilibrium in solution 89–91, 90
binding to membranes 108–109, 109
configurational free energy 94, 106–107, 107
contact formation 95–96
cooperativity 91
concerted binding 91–93
nearest-neighbor interactions 94
sequential binding 93–94
protein association in membranes 107–108, 108
rotational free energy 101–102
solvation effects 105–106
statistical mechanics of association 96–98
thermodynamics of associations 94–95
translational free energy 98–101
change in 101
translation contribution to Δ□ 99, 100
vibrational free energy 102–104
change in 104
vibrational contribution 102
molecular crowding 165
molecular forces 25
bond flexing and harmonic potentials 44–46
cation–π interactions 33, 33–35, 47
charge–dipole interactions 31–32
Coulomb potential 25–27
dispersive forces 35–36
electrostatic self-energy 27–29
hydration forces 39
hydrogen bonds 39–43
hydrophobic forces 36–39, 38
image energy 29–31
induced dipoles 32–33
protein force fields 50–52
stabilizing forces in nucleic acids 52–53
stabilizing forces in proteins 46–50
steric repulsions 43
molten-globule native state 82
Monod–Wyman–Changeux (MWC) model 123–126, 126, 284
energetics 127, 127–128, 128
enzymes 257
hemoglobin 126, 139–140
phosphofructokinase 130–132
ligand-gatol channels 133
Morris–Lecar model 462, 464
muscle, membrane potentials 345–346
myelin 453, 453–455
native states of proteins 46, 71, 82, 85, 85
jigsaw puzzle picture 86
molten-globule 82
oil droplet picture 86
Neher–Steinbach model 234
Nernst equation 340, 356
Nernst potentials 339–341, 340, 344, 344, 356, 357, 364
Nernst–Planck equation 162
NEURON computer program 430, 467
neurons see also axons; dendrites
cable analysis 418, 418–422, 420, 421
compartmental model 428, 428
membrane potentials 345, 345, 350–351
neurotransmitters 34, 89, 118, 184, 205, 235, 351, 355, 393, 423, 457
neutrophils 355
Newton’s equation of motion 51, 397
nodes of Ranvier 453
nonideal behavior of ionic solutions 279, 280, 300, 353–354
nonideal polymer chains 63–65
normal modes of vibration 46, 102, 103
nucleic acids
acidic phosphate groups 53
stabilizing forces 52–53
hydrogen bonds 52
nullclines 464, 465
Nyquist’s theorem 331
Ohmic channels 370, 370–371, 372, 372, 376, 384
smallest channels 371
Ohm’s law 359, 403, 404
oil droplet picture for protein folding 86
open-time distribution 184, 185, 229, 231, 234, 235, 236, 238, 240, 323
orotidine monophosphate decarboxylase 266
ouabain 355
Overton theory 367
oxycarbenium intermediate 264
pancreatic trypsin inhibitor 267
Parseval’s theorem 326
partition coefficient
ion permeation 368
inorganic ions 368
partition function 58
association mechanics 96
N residue chain 76
polymers and monomers 59
protein global states 3
protein microstates 2, 3
thermodynamic stability 3
sum over elementary weights 58
translational partition function 99
passive voltage changes 400
pathway counting 240–242, 241, 387–388
Pauli exclusion principle 43
permeability ratio 350, 352–353, 360, 362, 387, 387–388, 389, 436
persistence length 53, 63, 298
phenylalanine 34, 38, 42, 42, 119, 205
phenylalanine (phe), helix continuation parameter 81
phosphofructokinase 130–132, 131, 132
photoreceptor cells 312, 313
pi-electrons, interactions with cations 33, 33–35, 34, 47
Poisson distribution 309, 309–311, 310
definition 309
fluctuations in molecule number 311, 333
photon absorption 312
RMS deviations 311
Poisson equation 26, 277, 296, 402
Poisson–Boltzmann equation 277–278, 283, 292, 293
linearized form 279, 282, 283
membranes 285, 286
uniformly charged cylinder 297
polar and spherical coordinates 484, 484–485
polarizability of molecules 33, 35
poly–l–alanine, flexibility parameters 63
polyelectrolyte solutions
counterion condensation 300–302
Debye–Hückel screening 297–305
polyethylene 59, 62
flexibility parameters 63
polymer chains
configurational partition functions 58–60
nonideal 63–65
polypeptide backbone of proteins 68, 69
minimum potential energy conformation 70, 71
rotations 69
poly proline 70, 70, 72
positive semidefinite matrices 45
potassium ion channels 136, 291, 292, 292, 294, 437, 439, 439–441, 440, 463
power spectrum 326, 328, 328
proline 81, 250, 265
proline (pro), helix continuation parameter 81
proline racemase 265, 265
protein engineering 192
proteins
allosteric proteins 115
α-helices 49, 49, 50
associations in membranes 107–108, 108
backbone rotations 68–71, 69
β-sheets 49
conformational states 1
denaturation by other variables 12–14
denaturants 13
denaturation by temperature 5–7, 6
cooperativity 11–12
entropy 71–73
lysozyme unfolding 7–9
melting curves 8, 8, 9
number of global transitions 11
rate 188
steepness and enthalpy 9–11, 10
thermal unfolding 106
transition temperature (T□) 6
energy fluctuations 317
fluorescence 334, 335
folding 46, 82–86
cooperativity 86–87
good-folding amino acid sequences 84
hydrophobic interactions 47, 48
jigsaw puzzle picture 86
native state 46, 71, 82, 85, 85
oil droplet picture 86
time taken 72
force fields 50–52
global states 1, 4
compliance 21–23, 22
definition 2–4
equilibrium between two global states 4–5
free energy 2, 3, 4
microstates 2, 3, 6
partition function 2, 3
transitions induced by temperature 5–7
transitions induced by voltage 14, 14–17, 16, 16, 19–21, 20
global transitions 1–2
ionization 283–285
fluctuations 317–319
membrane proteins 53–54, 54
hydrophobic matching 53
predicting structure 51
critical assessment of protein structure prediction (CASP) 52
protein–ligand association rates 203–205, 204
acetylcholinesterase 205–206
evolution of speed 205
horseradish peroxidase 206–207
random coil behavior 68
stabilizing forces 46–50
electrostatic contributions 47
hydrogen bonds 48, 49
voltage-gated channels 17–18, 18
gating current 18, 18–19
S4 amino acid segment 17, 18
proton transfer 207–208
rates 207
quantum effects on bonds 3, 314
quantum mechanics 40, 99–101, 179, 264
Rall branching rules 412, 417, 418
Rall model for neurons 418, 418, 420, 421, 421, 422
Ramachandran plots 69, 70
random walks 154–156
binding to membrane receptors 210, 210
Gaussian distribution 156–159, 157
kinetics of multi-states 244–246, 246
rate processes 167
activation energies 169–170
diffusion over a barrier 180–183
exponential relaxations 167–169, 169
Eyring theory 179–180
ion movements within ion channels 377
linear free energy relations 172–175, 173, 174, 175
Marcus free energy relation 177–178, 178
membrane potentials 362–365, 363
multibarrier channels 380, 380–384, 383
reaction coordinate and detailed balance 170–182, 171, 172
reaction coordinate for global transitions 186–193, 187
single-channel kinetics 183, 183–186, 185
voltage-dependent rate constants 175–176, 176, 177
reaction coordinate 170–182, 171, 172, 173, 204, 249, 258–262, 260, 267–268, 274
global transitions 186–193, 187
rectification 373, 374
red blood cells 355
reflecting boundary conditions 150, 213, 407, 411
refractive index 35
relaxed (R) state 112, 113, 117
hemoglobin 126
repetitive activity 458–461, 459, 460
resting potential of cells 343
retina 312
rhodopsin 312
ribonuclease A 107
root-mean-square (rms) end-to-end distance 64
root-mean-square (rms) length 58
root-mean-square (rms) velocity of a molecule 156, 336
rotational entropy 263–264
rotational free energy 101–102
rotational isomer model 61, 62
rubber and elastic molecules 13, 68
S4 amino acid segment in voltage-gated channels 17, 18
saddle points 186, 187
Saffman–Delbrück equation 165
saltatory conduction 454
selectivity filters 374, 395, 398
self-energy (Born encag) 27–31, 30, 177, 280, 283
sequential binding 93–94
serine (ser) 12, 81, 248, 272, 272
helix continuation parameter 81
serine proteases 248–251, 249, 260, 272–273
hydroxyl group 272
serotonin 393
sheer force 295
simple elastic spring 68
single-channel current and conductance 132, 183, 232, 320–322, 321, 370, 378, 390, 443
single-file channels 371, 390, 390–394
single-ion channels 384–390, 385, 387
sink of diffusion 151
sodium chloride 276, 278
activity coefficient 281, 281
osmolarity of solutions 279
sodium ion channels 293, 436, 437, 439, 439–441, 440
activation 442
solvation effects on molecular associations 105–106
solvents 47, 64, 368
source of diffusion 151
space constant (λ) 405
spectral density 326
S-peptide 107
spherical and polar coordinates 484, 484–485
squid giant axon 406, 439, 439, 440, 443, 444, 446
firing 458, 459
frequency response 458
speed and size 452
stability 226
stabilizing forces in proteins 46–50
stacking interaction 52
double-helix formation 52
standard state, molar free energy 95
state counting 234–236, 236
stationarity 226, 228
loss of 237–240, 240
statistics
light detection by the eye 311–313, 312, 313
random coils 60, 60–62
steady-state diffusion 151
long pipe 151
porous membrane 153–154
small hole 152, 152–153
steepness factor 16, 16
steric repulsions 43
Stern layer 289, 289, 290
Stern’s improvements of Gouy–Chapman theory 288–291
Stirling’s approximation 157
Stoke’s law 162, 162–163, 165, 295, 297
Stokes–Einstein relation 163, 199, 203, 335
stretched kinetics 244–246, 246
supernormal axons 449
superoxide dismutase 206
ligand association rate 204
surface potential 287, 290, 292, 293, 294, 361–362
synapses 184, 468
intergration in dendrites
analytical models 422–423, 423
compartmental models 430–433, 431, 432
impulse responses 423–425, 424
realistic synaptic inputs 425–428, 427
synaptic current 186
Szabo–Karplus (SK) model 123, 126, 137–140, 139
Tanford βT value 188
Taylor series 470, 470
tense (T) state 112, 113, 117
hemoglobin 126
thermal de Broglie wavelength 99, 179
thermodynamics in molecular associations 94–95
theta solvents 65
threonine (thr) 7–9, 12, 81, 119, 266, 394
helix continuation parameter 81
threonine–valine–glycine– tyrosine–glycine (TVGYG) sequence 394, 395, 398
threshold stimulus 436
trans conformation of n–butane 56, 57, 57
transition states 169
complimentarity 264–267, 266
transition temperature (T□) 6
DNA melting 302–305
melting curves 8
steepness and enthalpy 9–12, 10
transition voltage 16, 16
translational entropy 260, 260–263, 263
translational free energy 98–101
change in 101
translation contribution to ΔG° 99, 100
translational partition function 99
transmembrane voltage 14, 14, 339
transmission coefficient 180
transverse resistivity 402
triose phosphate isomerase 204
trypsin 248, 250
hydrolysis rates 250
tryptophan 34, 47, 205, 250
tryptophan (trp), helix continuation parameter 81
tubulin 334, 335, 335
turnover number of enzymes 252
tyrosine 34, 41, 42, 119, 205, 266, 267, 394
tyrosine (tyr), helix continuation parameter 81
tyrosyl–tRNA synthase 41, 42, 265, 266
unfolding of proteins 6, 12, 106
denaturants 13
entropy 72
lysozyme 7–9
melting curves 8, 8, 9
rate 188
Ussing flux ratio 351–352, 390
definition 352
V system of enzymes 257, 258
valine (val) 8, 38, 81, 394
helix continuation parameter 81
van’t Hoff enthalpy 10
van’t Hoff equation 10
varicosities on axons 456, 456, 457
vibrational energy of bonds 3
frequency of vibration 44
kinetic energy 3
normal modes 46, 102, 103
vibrational free energy 102–104, 129
voltage clamp 439, 439–441, 440
voltage–dependent rate constants 175–176, 176, 177
voltage–gated channels 17–18, 18, 293–294, 294, 439–450, 457–458
dendritic 466–468
gating current 18, 18–19
S4 amino acid segment 17, 18
water
dielectric constant 26
temperature dependence 27
enthalpy of solvated ions 27
entropy of solvated ions 27
hydration energy 28, 28
ion size 376
hydration forces 39
hydrogen bonds 41, 82
hydrophobic force 37, 37, 38
wave equation 451
Wiener–Khintchine theorem 324, 331
zeta–potential 296
© Cambridge University Press
Printer friendly version
Email a colleague