Index. α fluctuation, 183, 184, 186, 187, 211, 212, 228

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1 Index α fluctuation, 183, 184, 186, 187, 211, 212, 228 α relaxation, see relaxation, conformational α-helix, 28, 33, 65 69, 71, 75, 76, 203, 247 β fluctuation, 183, β pleated sheet, 28, 33, 69, 72, 75, 76, 78, 79 β relaxation, see relaxation, conformational absorption, 315 gamma-ray, 399 optical, 363, 367 radiation, 315, 316 X-ray edge, 344, 353, 354 acid, 257 charge, 257 ph, 258 adiabaticity Kramers curve, 151 reaction, 131, 146, 147, 149, 150 transition, 149 tunneling, 144 amino acid, 19, 20, 24 building blocks of protein, 19 charges, 259 composition and sequence, 24 side chain, spatial structure, 65 UV absorption spectra, 367, 368 amphipathic, 53 anticodon, 51 apomyoglobin, 121, 371 Arrhenius behavior, 122, 139, 152 equation, 126 law, 160, 162, 164 motion, 128, 139 plot, 121, 126, 162, 163, 184, 225 relation, 101, 128, 150, 163 transition, 125, 138, 140 atomic orbital, 279, 285, 298, 325, 326 base, 257 charge, 257 Bjerrum model, 332 Bloch equation, 418, 423 Bohr, A, 32 Bohr, C, 32, 89 effect, 32, 89 Bohr, N, 32 magnetic moment, 418 orbit, 239, 280, 328 radius, 202, 327 bonding and antibonding, 286, 298 orbital, 286, 287, 289, 293, 299, 305, 326, 332, 366 Boson, 143 peak, 164 Bragg, 341 angle, 349, 402 law, 348, 354 Brownian motion, 132, 273 passage, 135 H. Frauenfelder, The Physics of Proteins, Biological and Medical Physics, Biomedical Engineering, DOI / , c Springer Science+Business Media, LLC 2010

2 444 Index random walk, 165, 190 chlorophyll, 29, 80, 301 chromophore, 108, 109, 189, 241, 364, codon, 50, 51 conformational substate, see substate, conformational Coulomb interaction, 202, 327, 335, 368 covalent bond, 213, 214, 246, , 335, 406, 408 crystal diffraction, 350 CS, see substate, conformational Davydov soliton, , 204 Debye, 103, 161, 178, 246, 311, 330 Debye-Waller factor, , 108, 393, 402, 417, 427, 431 mode, 145 solid, 402 spectrum, 311 delocalization, 201, 202, , 326, 335 density matrix or matrices, , 427 differential scanning calorimetry, DSC, 220, 222 diffusion, 55, 104, 181 high-damping limit, 135 ligand diffusion, 180 linear coefficient, D, 55, 57, 273 protein diffusion, 57 rotational coefficient, D r, 55, 57 Smoluchowski equation, 181 spectral diffusion, SD, 121, 122, 165, 190 dipole-dipole coupling, 327, 329, 427 interaction, 89, 250, 399, 408, 430 dispersion force, 327 dissociation coefficient, 85, 259 energy, 378 double helix, 39, EF, see fluctuation, equilibrium Einstein, 159, 175, 178, 273, 311, 316 coefficient, 316 energy, 311 solid, 401 spectrum, 311 EL, see energy landscape elecric dipole, 326 electric dipole, 318 electric monopole, 396, 397, 405 electric quadrupole, 318, 394, 396 electronic transition, 204, 310, 363, 364, 366, 368 electrostatic force, 243, interaction, 253, 335, 396, 413 emission, 315 Boson, 143 fluorescence, 220, gamma ray, induced, 316 phonon, 143 phosphorescence, 367 radiation, 315 recoilless, 401, 404 spontaneous, 315, 316, 318 wave, 179 wavelength, 221 energy landscape, EL, 14, 15, 55, 95, 97 99, , 121, 122, 157, 158, 165, 173, 175, 178, 180, 181, 183, 184, , 377 free, 199, 217, 218, 224, 226, 227, 229, 230, 417, 431, 432 potential, 217, 224 enthalpy, 136, 213, 214, 265, 266, 275, 276, 334 activation, 101, 130 distribution or spectrum, 102, 229 protein folding, 218, 219, 222, 223, 229 entropy, 95, 98, 119, 120, 129, 136, 138, 151, 159, 199, 253, , 268, , 275, 276, activation, 136 bond, 332 configurational, 275 membrane, 56 Onsager, 332 protein folding, 216, 218, 219, 221, 223, 224, 227, 229, 254 residual, 332, 336, 337 thermal, 275

3 Index 445 equilibrium motion, 176 EXAFS, 343, 344 extinction coefficient or sensitivity, 365, 372 Eyring relation, 128, 130 FEL, see free-electron laser FIM, see functionally important motion fine structure, 413 fluctuation, 95, 97, 105, 113, 122, 131, 160, 184, , 252, conformational, 121, 122, 125, 181, 186 equilibrium, 97, 161, 178, 273, 275 frequency, 176 primary, see α fluctuation protein, 184 rate coefficient, 274 secondary, see β fluctuation thermal, 160, 180, 183 fluctuation-dissipation theorem, 97, 132, 160, 161, 178, 180, 273, 274 fluorescence, 108, 220, 221, 225, 366, 367, 370, maximum wavelength, 371, 372 quantum yield, 371 quenching, 371 Fourier transform, 104, 347, 348, 352, 420, 429 free induction decay, FT-FID, 423 infrared spectroscopy, FTIR, 114, 214, 382, 384 Franck-Condon principle, 364 free-electron laser, FEL, 205, 356, 358, 359 IR, FELIX, 205 X-ray, LCLs, XFEL, SCSS, 359 friction, coefficient, , 137, 150, 151 Kramers relation, 136, 151 transmission coefficient, 133, 135, 136, 151 FT-FID, see Fourier transform FTIR, see Fourier transform functionally important motion, FIM, 97, 273, 275 Gibbs energy, 55, 120, 134, 136, 219, 221, 223, 253, 254, 265, 266, 275, 276 glass, 13 15, 97, 109, 117, 119, 152, , proton glass, 337 temperature, 121 transition, 159 globin, 28 Hb, see hemoglobin heat capacity, 159, 219, 272 argon, 325 benzene, 325 excess, 222, 223 folded protein, 218, sodium, 325 water, 325 heme, 28, 29, 31, 32, 142, , 213, 300, 304, 311, 370, 371, 388 group, 28 32, 145, 148, 213, 241, 299, 300, 367, 368, 371, 388 iron, 100, 114, , 179, 180, 185, 186, 188, ligand, 102, 213, 214, 305, 368 orbital, 369 pocket, 100, 102, 116, 117, 146, 180, 211, 215, 230, 371 protein, 28, 29, 100, 102, 114, 125, 131, 137, 138, 144, 146, 173, 212, 214, 312, 388, 389 hemoglobin, Hb, 27, 29, 32, 83 90, 102, 139, 173, 210, 273, 301, 341, 389 Bohr effect, 32, 89 Perutz, 88, 341 ph effect, 89 structure, 88 Henderson-Hasselbalch equation, 259 Hill, 86 coefficient, 88 equation, 89 plot, 86, 87 hole burning, , 121, 165, 189, 190, 336 homework, 209 myoglobin, 210 neuroglobin, 212 protein folding, 216 protein unfolding, 216

4 446 Index solvent dynamics, 228 Zwanzig model, 226 Hund s rule, 280 hybridization, 283, , 298, 332, 334 hydration, 30, 42, 95, 175, 177, 182, , 212, 272 hydrogen bond, 13, 23, 33, 38, 42, 43, 66, 67, 69 72, 75, 203, 243, , 324, 327, , 387 hydrophilic, 42, 53, 55 hydrophobic effect, 253, 333, 334, 371 base, 42 force, 243 lipid membrane, 53, 55 nonpolar residue, 23 hyperfine interaction, 393, 408 ice, 332, 333, ferroelectric, 330 ice Ih, 337 model, 333, 337 imperfections, 105, 275 infrared, IR, band or spectrum, 116, 118, 140, 202, 204, 206, 211, 214, 336, 382 absorption, 336, 382 internal energy, 222, 264, 266, 267 isomer shift, 405, 406 isothermal, 131, 132, 272 isotope, 116, , 395 effect, 139, 140, 144 isoviscosity, 131, 132, 137 Jablonski diagram, 366 Johnson noise, 273 Karplus relation, 428 Kendrew, 341 Kramers, 131 adiabatic curve, 133, 136, 151 equation, 131, 135, 149 rate coefficient, 133, 137 theory, Lamb-Mössbauer factor, , 402 Landau-Zener, 149 coefficient, 150 factor, 150 parameter, 151 region, 149, 150 Larmor precession, latent heat argon, 325 benzene, 325 crystallization, 334 evaporation or vaporization, 324, 325, 328 fusion, 324, 325 sodium, 325 water, 324, 325 lattice disorder, 104, 105, 275 Laue, von, 341, 348, 350, 354, 356 diffraction equation, , 354 technique, 356, 439 line width, 317 gamma ray, 400, 402, 405 hole burning, 190 NMR, 418, 422, 423, 432 radiation decay, 317 lipid, 53, 55 bilayer, 55, 56 low-temperature dynamics, 189, 191 glass, 164 lysozme structure, 433 Mössbauer effect, 105, 178, , 393, 399 Gaussian, 108, 164, 189, 271, 357 line shape, 108, 109, 186, 317, 404, 432 Lorentzian, 108, 317, 404 nuclear isotopes, 405 scattering, 402 spectrum, , Voigtian, 108 magnetic dipole, 318, 396, 428 magnetic orbit-orbit interaction, 280 Maxwell relation, 120, 164, 183, Mb, see myoglobin membrane, 53 57, 136 metalloporphyrin, 29 metalloprotein, 406, 407 methane structure, 292 molecular orbital, 279, 284, 286, 287, 289, , 366, 367

5 Index 447 myoglobin, Mb, 27, 30, 32, 63, 83, 100, 102, 107, 179, 181, 183, 184, 187, 204, 273, 341, 407 absorption spectrum, 204, 305 structure, 341 neuroglobin, Ngb, 212 neutron diffraction, 437 neutron scattering, 164, 186, 437 Ngb, see neuroglobin nonadiabatic reaction, 147 transition, 146, 150, 151 nonequilibrium motion, 97, 176 nuclear magnetic resonance, NMR, 359, 393, 399, 407, , 427, 429, 430 spectroscopy, 108, 426 spectrum, 432 transition, 418 nucleic acid, 37, 202, 369, 372 Nyquist theorem, 273 peptide bond, 20, 66, 248, 296, 297, 299, 367 phase, related to angles coherence, in, 202, 203, 422 coherence, in46, 423 dephase, 422, 424, 426 difference, shift, 161, 200, 201, 348, diffraction, 345, 353, 439 fluoremetry, 373 fluorometry, 372 Fourier transform, , 439 NMR, phase, related to transitions condensed, 128, 326, 335 diagram, 55 gas, 125, 130, 226 glass, 117 kinetic, 213, 214, 226 transition, 7, 56, 118, 337, 338 phonon, 7, 109, 142, 143, 275, 276, 311, 370, 385, 401 phonon transition, 143 Pin WW domain, 225, 228, 229 pk, 259 polywater, 324 power law, 101, 109, 191, 205 protein folding, 75, 78, 185 proteinquake, quantum dynamics, 199 unfolding, 272 proteinquake, see protein protoheme IX, 300, 301, 367 protoporphyrin, 29, 300, 301 Rabi oscillation, 421 Ramachandran map, 66, 68 plot, 66 Raman scattering, 144, 164, anti-stokes lines, 385, 388 frequency shift, 387 resonance, 388, 389 Stokes lines, 385, 386, 388, 389 Rayleigh scattering, 385, 388, 402 relaxation of spins in NMR longitudinal relaxation time T 1, 418, 419, 422, 426, 428, 432, 433 transverse spin dephasing time, T 2, 419, 422, 424, 426, 432 relaxation, conformational, 105, 224 dielectric rate or spectrum, 164, 183, 187, 188 equilibrium, 176 nonequilibrium, 177, 178, 180, 183 processes, , 164, 177, 178, 180, 209 Debye, 162 Ferry, 163, 164 Johari-Goldstein, 164 paraelastic, 144 pathway, 211 primary, , 177, 189, 228 secondary, , 178, 187, 189 rate, 144, 176, 180 folding, 229 unfolding, 229 water, 229 solvent, 366 time distribution, 15, 175, 178 vibrational, 366 Resonance Raman scattering, 388 scattering

6 448 Index amplitude, 346, 348, 350, 438, 439 cross section, 346, 437, 438 Schrödinger equation, 148, 243, 267, 279, 292, 303, 336, 378 selection rule, 318, 319, 378, 408 self-trapped state, 199, 200, 203, 204, 206 SL, see structure landscape slaving, solid, 13, 14 solvent dynamics, 228 Soret band, 140, 303, 368, 388 specific heat, 159, 164, 175, 272 crystals, 159, 164, 178 glasses, 164 solids, 159 water, 324, 325 spherical harmonics, 279, spin echo, spin glass, spin-orbit interaction, 280 spin-spin interaction, 280, 418, 427 Stokes law, 132, 133 structure landscape, SL, 181, 182 substate conformational, CS, 16, 95, 97 99, 102, , 109, 110, 145, 146, 175, 180, 181, 209, 214, 216, 218, 226, 229, 311, 377, 431 few-level, 121, 122 statistical, 114, 115, 121, 158 taxonomic, , 120, 121, 158, 181, 214, 215 Tier 0, 114, 115, 118, 181 Tier 1, 114, 121, 158, 164, 181, 182, 189, 190 Tier 2, 114, 121, 158, 181, 182, 189, 190 sum rule, 318 Thomas-Reiche-Kuhn sum rule, 319 transition energy diagram, 366 transition rate, 318 transition state theory, TST, 128, 132, 133, 135, 136, 151 TST, see transition state theory tunneling, 7, 122, 125, 128, , 142, 144, 252, 335, 336 UV-visible spectrum, 363, 364 van der Waals, 13, 55, 75, vibration, 7, 104, 105, 107, 114, 127, 143, 178, 187, 241, 269, 310, 311, 336, 370, 377, 401, 402 coherent self-trapped, 199, 200, 203, 204, 206 density-of-state or vibrational spectrum, 164, 178, 179, 204, 214, 337, 389 MbCO stretch, 116, 119 myoglobin, 204 NgbCO, 214 oxyhemoglobin, 389 water, 337 frequency, , 386 amide A band, 380, 381 amide I band, 200, 203, 204, 380, 381, 387 amide II band, 204, 380, 381, 387 CO stretch, 141, 214, 380, 381 normal mode, 178, 200, 269, 379, 382, 387, 401 phonon, 143, 367, 370, 401 quantum number, 378 transition of levels, 310, 363, 364, 366, 370, 421 viscosity, , 146, 151, 159, 160, 162, 164, 183, 184 vitamin B 12, 301 water, condensed, 326 dipole moment, 330, 332, 335 hydrogen bond, 333, 335 infrared absorption, 336, 337, 381 structure, 325, 326 X-ray diffraction, 30, 65, 103, 105, 106, 175, 295, 337, 341, 343, 345, 347, 348, 359, 402, 427, 438, 439 X-ray source, 341, 356, 358, 437, 439 Zeeman effect, 407 interaction, 408, 412 splitting, 309, 396, 411 zero field splitting, 413 zero-phonon, 108 Zwanzig model,