Urry D.W. (Ed.) What Sustains Life? : Consilient Mechanisms for Protein-Based Machines and Materials

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616 Index

Drug addiction

intervention, 513, 514-515

model protein control of,

65-66

protein-based material

intervention of, 466

Drug delivery

leu-enkephalin amide, 65

model protein, 62, 65-66

Naltrexone, 65-66

protein-based material, 24

protein-based

polymerolymeric systems,

511-512

transdermal, 519-521

Tt-type protein-based polymer,

510-524, 563

ulcer, pressure formation

prevention and, 522-524

Drug-laden bioelastic patches,

522-524

Dynamic force spectroscopy,

533

Eddington, A.S., 569

Efficiency

chemical energy, 60-61

chemomechanical

transduction, 208-209

consilient mechanism, 204-206

consiUent protein-based

machine, 203-210

electrochemical transduction,

water, 343-344

energy conversions, 204,

220-221,341-344,404

protein-based machine, 228

Elan vital, 541-542

Elastic-contractile model protein

machines

phosphates energized by

synthetic, 49-50

poised, design of, 203

synthetic, 49-50

Elastic-contractile model proteins

elasticity, 124-125

hydrophobic association in

myofibril and, 425-426

ion-pair formation and

hydrophobic association

of, 261-262

Life-sustaining energies

interconverted by, 60, 61

soft tissue reconstruction, 64

P-spiral, 86-87

structure, 84-87, 86

limitations, 50-51

synthesis, 84-87

thermally driven contraction

for. 111

transition, 67n23

p-turn, 86

Elastic-contractile protein

material, 473

Elastic force

development

energy transduction and,

432-433

hydrophobic association

coupling with, 331,

336-337

energy conversion

mechanisms, efficient and,

344

flexible loops as potential

storage of, 439-442

hydrophobic association

development resulting

from, 439^42

Elasticity, 34. See also

Thermoelasticity

biocompatibility and nature of,

130-131

consilient mechanism of,

energy conversion and,

127-128

contractility and, 128-130

elastic-contractile model

proteins, 124-125

entropic, 490-495

ideal

dominantly entropic,

126-127

fraction of, 128

mechanical work and nonideal,

344

model protein, 124-131

nonideal, 344

poly(GVGVP), cross-linked,

126-128

Elastic model proteins

(GVGVP)25i, 31-32

biocompatibility, 23

synthetic, shortening of, 34-35

Elastic protein-based machines

hydrophobic association in

solution and, 149

macroscopic, constructing,

148-149

motion produced by, 147-150

observations, 147-148

solvent entropy changes and

loading on band of, 150

temperature and, 147-148

visual observation of working,

147-160

Elastic protein-based matrices,

519-521

Elastic protein-based polymers,

23,459-460,482,490-497,

507,

561-562

antigenicity, 490-495

biocompatibility, 492, 561-562

chain, stretched, 67nl2

entropic elasticity and

antigenicity of, 490-495

fiber formation of, 496-497

inert space filler, 507

mechanical resonances, low

frequency in, 130,492-494

monocytes, human and

response to, 482

nonantigenic dynamic, 494-495

plastic and, 23

sheet formation of, 491,

495^96

tube formation of, 495, 496

Elastin

amino acid residue repeating

sequences in, 34-35

folding pattern of the

repeating five residue

sequence of, 31

heat converted to motion by

proteins modeled after, 35

hexapeptide repeating

sequences of, 124

Electrical energy

chemical work and conversion

of, 122

contraction driven by, 37

mechanical work produced by,

156

Electrochemical energy, 41

Electrochemical transduction,

122

efficiency of water, 343-344

hydrophobicity increase and,

343-344

phenomena coherence for,

392

Index 617

proton concentration gradient

production and, 549-550

Electromagnetic energy, 157-158

Electromagnetomechanical

transduction, 174-175

Electromechanical transduction,

174

Electrons, 222-223

transfer, 373, 549-550

consilient mechanism,

375-383

cytochrome c oxidase

oxygen reduction steps of,

389

Electron transport chain, 358,

361-394

complex III of, 365-371

complex II of, 365-371

consiUent mechanism and

coupling of, 361-362

AGap

and, 361-362

mitochondria, analogues for,

365-371

protein machines of, 361

ubiquinol production for,

365-371

Electrostatic-induced repulsion,

200,

209-210

Electrostatic repulsion

mechanism, 61

Electrostatics, 346

Elements, 71-72. See also The

Periodic Table of the

Elements; The Periodic

Table of the Elements of

Nature

Elsas,

E, 502, 538

Emphysema, pulmonary, 240

Endorphins, 511

Energies. See also specific

energies

accessing, 1-2, 219-224

conservation, resources

available to consilient

mechanism of, 131-147

consilient mechanism and,

131-147

function of, 219-224

driving contraction, 32

environmental, accessing, 2

Life defining characteristics

and, 28

Life-sustaining, 1-2, 33, 60, 61

model protein, 231-235

model proteins conversion of

living organism-sustaining,

motion production by, 220-224

motion production by, visual

demonstrations of, 32, 33

non-motion work performed

by, 224

order created out of chaos

with model protein-

contributed, 231-235

protein-based machines and

input/output, 161

protein folding, assembling

and functioning sources

of, 34-43

resources, 71,131-146

resources available to

consilient mechanism of

energy conservation,

131-147

solar, 28

standard free, 347-349

Trdivide moving as

measurement of, 112-118

Energy conversions, 28-29. See

also Photosynthesis;

Respiration

amino acid changes and

diverse, 224

ATP hydrolysis bursts of

apolar-polar repulsive free

energy and, 546

ATP synthase, 394-395

biological,

332-341,

354-360

biology efficiency, aqueous

medium of, 341-344

consilient mechanism and

coupling of function

statement of, 166-167

consilient mechanism of,

103-104, 332-341

energy resources for,

131-147

physical basis, 176-195

consilient protein-based

machine, 168-176

diverse, 103-104

efficiency, 204,220-221,

341-344,404

elastic force and efficient

mechanisms for, 344

elasticity consilient mechanism

and,127-128

folding changes, association of

oil-like domains and

protein-catalyzed, 103

functional group couphng and,

160-168

AGHA

as coupling process in,

203-204

AGHA,

consilient mechanism,

169-170

hydrophobic association,

203-204

inverse temperature transition,

543

Life sustaining,

1,43-48,103

living organisms, 28-29

man-made, 28

mechanical, 169

mechanism of,

61,

344

in mitochondria, 16-17

motion production, 48-50,122

muscle contraction, 46-48

non-mechanical work, 122

protein-based machines

consilient, 168-176

three primary classes of,

549-561

protein-based machines as

catalysts for, 60

protein, biology's, 50-51

proteins catalyze, 29

reversible, 170-171

synthetic model protein

machine emulating, 48-50

temperature change and, 29

ATt-mechanism, 41

Energy converting machine

terminology, 168-169

Energy inputs, 206-208

chaos reversed by, 229-231

model protein, 206

order created out of chaos by,

228-235

Energy sources, 34-43

inverse temperature transitions

extract order from, 43

muscle contraction motion,

46^8

protein-based machine,

131-132

protein folding, assembling

and functioning, 34-43

T, changing, 131-132

Engines, 168-169

biology's heat, 542

618 Index

Enkephalins, 511

Entropic elasticity, 490-495

Entropy (disorder), 67nl9

change in, 67n21

elastic-contractile model

protein transition, 67n23

elastic protein-based machine

band loading and changes

in solvent, 150

inverse temperature transitions

extract, from energy

sources, 43

inverse temperature

transitions providing

protein, 39^0

order decrease and increase in,

106

phase transitions and changes

of, 104-105

protein, 39-40

transition increase in, 39

universe of, 28

Enzymatic cycle, 360

Equilibrium, far from, 234

Escherichia coli (E. coli)

biosynthesis of proteins and

sequences for, 30-32

complex II analogue of, 365-368

genetic engineering, 63

structure, 305

transformation, 471

"An Essay on the Principle of

Population" (Malthus),

70-71

Everse, S.J., 291, 292, 326

Evolution, 218-238

genomic, 91

inverse temperature transition,

569-571

natural selection in, 570-571

protein-based machine,

218-237,224-228

protein-based machines basic

sequence, 31

Fo-motor, 16

ATP synthase, 51

consilient mechanism,

hydrophobic and, 395

housing, 398

proton flow and rotation of,

400^02

rotation barrier for, 402-404

rotor, 398, 400,401

stator, 399

Fi-motor, 16-17

ATP synthase, 17-20, 51-52

ATP synthase, and consihent

mechanism, 18-19

ATP synthase, crystal

structure, 404^20

consilient mechanism,

hydrophobic and, 395-398

cusp of insolubility, 18

housing, 398-399

as rotating cusp of insolubility,

three states, in cross section, 17

"waters of Thales" of ATP

synthase, 19-20

Fi-motor ATPase, 400, 423^24

efficacy and cooperatives of,

420-423

hydrophobic elastic consilient

mechanism and Fi-,

423-424

mechanical work efficacy of,

420-422

rotational direction, 405, 420

y-rotor faces, 406^09

stereo top view of, 412, 413

structure, 404-406

subunits, 404-406

temperature raised by, 400

FAD.

See Flavin adenine

dinucleotide

Famihal thalamic dementia, 296

Fatal famihal insomnia (FFI), 296

mutation causative for, 301,

302

Fat structure, 77-79

Fatty acid structure, 77

Feline spongiform

encephalopathy (FSE),

296

FFI.

See Fatal familial insomnia

Fiber propagation, 300

Fibrin, 293-294

Fibrin clot, 284-294

cross-linking to form hard, 294

Fibrinogen

crystal structure, 284

hydrophobic association,

290-293

hydrophobicity plots of,

288-290

primary structure, 284

structure, 284-288

subunit structure, 284

thrombin activation of,

290-293

a-fibrinogen,

288-289

p-fibrinogen, 288-290

y-fibrinogen, 288-289

Filament assembly, 52-53

Fillingame, R.H., 399, 400,453

Flavin adenine dinucleotide

(FAD)

AGHA

and

reduction

oxidized, 142

reductase reduction of,

365-371

Flory, RX, 546, 571

Folding

ATP-mediated, 308, 309

hydrophobic, 29, 30,112

inverse temperature

transitions, assembly

transition and

hydrophobic, 112

proteins, 34^3

temperature, chemicals for, 42

FSE. See Feline spongiform

encephalopathy

Functional groups

consilient mechanism and

coupling of, 164-167

coupling, 48,160-168

energy conversions and

coupling of, 160-168

AGHA

and state change of,

141-143

AGHA

coupling of, 164-167

hydrophobicity change due to

action of, 165-167

hydrophobicity increase and,

187-191

model protein machines and

coupling of, 48

model protein reduction

attached, motion, 158-159

redox, 136

states,

161-162

AGap (apolar-polar repulsive free

energy of hydration), 123,

192-195,

240

ATPase and, 351-353

as biology's rival to

magnetism, 542-545

Index 619

carboxyl ionization and, 339

charged side chain pattern

orientations and, 397-398

dielectric constant v., and ion

pairing/pKa shifts,

344-346

electron transport chain and,

361-362

fiber production and, 563-564

AGHA

coherence with,

337-338

hydrophobic associations,

297-298

ion pairing and, 344-346, 360

mechanisms, 342

pharmaceuticals controlled

release and, 563

y-phosphate production of,

416-419

pKa shifts and, 344-346

proton ingress controlled by,

384-386

y-rotor, 419-420

P-subunit and y-rotor, 419-420

Gaub,

H.E., 214, 215, 526, 527,

530,

537, 539, 576,

594-596, 608

Genetic code, 224-226

biased, 570-571

consilient mechanism and

relationship to, 226-227

Genetic engineering

E. coli, 63

insulin, 84

model protein, 63

Genome, human

determination of, 90-91

as "periodic table of life," 90

Genomics,

90-91,

Gerstmann-Straussler-Scheinker

disease (GSS), 296

prion protein with related

mutations causative in,

301-302

AGHA

(change in Gibbs free

energy for hydrophobic

association), 240

AGHA

(changing of free energy),

240

bound biologically functional

groups state change by,

141-143

calculating, 138

change estimate, 314

consilient mechanisms, energy

conversions with, 169-170

energy conversion coupling

process and, 203-204

energy conversions by

consilient mechanism,

169-170

estimated values, 138-139

FAD,

oxidized reduction and,

142

functional group coupling by,

164-167

IsGap

coherence with, 337-338

hydrophobic association,

137-146

ion pairing between chains,

effect calculated by, 141

NAD,

oxidized reduction and,

142

phosphorylation and, 142-143,

350

T, change and, 143-146

vinegar-like side chain

functional state change

and, 141

Gibbs free energy, 112. See also

AGHA

allosteric effects Hill plot

delineation of, 193-194

charged species increase in,

340,

341

^Gap.

192-193

hydrophobic association,

137-140

Globin chains

association, 250,251

charged and oil-like residue

distribution in, 251, 252

Glycolysis cycle, 356

Gotte, L., 214

GroES capping, 315, 318-319

GSS.

See Gerstmann-Straussler-

Scheinker disease

(GVGVP)25i, 31-32

Harris and Rice treatment

cooperativity, 200

Heart attacks

cusp of insolubility, 284

insolubility, excess and, 240

Heat

ionization and transition of,

184-185

motion and conversion of, 35

rigor induced by, 244-245

transition, 184-185

Heme binding site, 253-254

Heme groups. See also o}^^

(a^P^) interheme

crevasse

alp^

271-274

o}^\

211-21A

pla^

269-271,

272

hemoglobin, 267-269

myoglobin, 267-269

oxygen binding and

structure/disposition of,

266-271

prospective, 266-267

structure/disposition of,

266-271

Hemoglobin, 249-254

A, phase diagrams, 281,

282-283

consilient mechanism and

oxygen transport

temperature effect

diagnostic of, 254

consilient mechanism as

source of sigmoid oxygen

binding of, 278

consilient mechanism

demonstrated by

structures of, 263-283

cooperativity, positive and

subunit interactions in,

253

deoxygenated states of,

253-254

hemes in, 267-269

binding site geometry and,

253-254

Hill plot, 8, 22

hydrophobic association and

fundamental functional

unit of, 260

myoglobin oxygen binding

proteins and, 249-250, 251

oxygenated states of, 253-254

oxygen binding and,

265-271,

278

analogy to, 255, 256

consilient mechanism and,

256-257

properties, 250, 253

oxygen transport by, 9, 21,

249-263

620

Index

Hemoglobin (cont.)

phase diagrams, 281,282-283

phenomena, molecular basis

for coherence of, 265-266

positive cooperativity in, by

consilient mechanism, 278

R state, 257-258

sigmoid oxygen binding of, 278

structural changes due to

oxygen binding of,

265-271

structures, 263-283

T state, 257-258,265

aqueous core of, 265

Hemoglobin S, 279-282

hydrophobic association and

tetrameters of, 279-281

persistence, 281-282

phase diagrams, 281,282-283

Hemophilia

cusp of insolubility and, 284

solubility, excess and, 240

solubility-insolubility

boundary, 3

Henderson-Hasselbalch

equation, 196-197

cooperativity introduced into,

198-200

titration curve comparison to,

197-198

Hill coefficients, 207-208

Hill plots, 8-9

Gibbs free energy allosteric

effects delineated by,

193-194

hemoglobin, 22

myoglobin, 22

steepness quantified using,

8-9

Himmel, D.M., 431,434-438,

440-445,447

Histidine, imidazole side chain,

392-394

Hoban, L.D., 499, 538

Hugel,T.,214,215,530,537,

594-596, 608

Hunte, C, 372, 374, 375, 379, 380,

384,385,

448,450

Hydration. See also

AGap,

Hydrophobic hydration

cusp of insolubihty lowered by,

41^2

ions,

dissolving and, 359

oil-like group, 41^2,109-112

Hydration competition, 177-179

apolar-polar, 201

cooperativity, positive and,

338-339

cusp of insolubility, movable

and, 18

fundamental process as,

184-191

hydrophobic-polar, 338

observation, 177-179

oil-like and vinegar like group,

6-10,18,123-124

pentagonally arranged water

and,179-181

pKa shifted state and, 9-10,

123

positive cooperativity results

from, 10

Hydrocarbon units (oil-like

groups), 2-3

ATP-produced repulsion

between charged groups

and, 11

charged group competition for

water with, 6-10,18,

123-124

charged groups and, 11

control association of, 22-23

dissociation of, 6

hydration around, 41-42,

109-112

hydrophobic hydration

disappearance and, 119

hydrophobic replacing and,

122

lowered cusp of insolubility

and increased hydration

around, 41^2

motion produced by

separation from water of,

pentagonal arrangement of

water around, 38-39

phase separation, 6

re-association of, 6

separation from water, 6, 30

solubility, 2-3

water around, process

involving, 109-112

water balance and, 6,11

Hydrogen (H), 29, 72,125

Hydrophobic assembly, 29, 30

Hydrophobic association,

195-196

allosteric proteins and,

243-244

amino acid structure and, 125,

126

amino-terminal domain and

lever arm head, 438,439,

440,441,442

dephsophorylation-initiated,

248-249

elastic-contractile model

proteins, 261-262,425^26

elastic force development and,

439^42

coupling of, 331, 336-337

elastic protein-based machine

solution and, 149

energy conversion, 203-204

fibrin, human fragment double

D,293-294

fibrinogen, 290-293

free energy change for,

137-146

AGap,

297-298

AGHA,

137-146

Gibbs free energy for, 137-140

hemoglobin fundamental

functional unit and, 260

hemoglobin S tetrameters and,

279-281

hydrophobic hydration amount

on complementary

surfaces and, 339-341

interconnecting chain

segments stretched by, 546

intermolecular, 53

intramolecular, 53

inverse temperature transition,

249,297-298,425-426

ion pair formation in elastic-

contractile model

proteins, 261-262

muscle contraction and,

245-249,248-249

muscle contraction by inverse

temperature transition,

249,425^26

myofibril, 425-426

myoglobin-like protein,

249-254

phosphorylation effect on,

530-532

phosphorylation initiated

dimerization by, 53,

Index 621

protein machine function and,

202

at Qo site, 382

rigor states and, 243-245,425

RIP tip, 362

thermodynamic basis for

water, 310-312

transition, 170

Hydrophobic dissociation,

195-196

amino-terminal domain and

lever arm head, 438, 439,

440,

441,

442

consiUent mechanism

relationship with, 202

cusp of insolubility positioning

by, and hemoglobin

transport of oxygen,

249-263

hemoglobin transport of

oxygen and, 249-263

hydrophobic hydration amount

on complementary

surfaces and, 339-341

pKa shifts after, 195

thermodynamic basis for

water, 310-312

Hydrophobic domains

association/dissociation and

pairs of spatially

assembled, 242-244

ATP,

bound repulsion and,

312-314

charges buried as ion pairs

within, 312

cooperativity, positive and,

254-257

hydrophobic hydration

disappearance and,

242-243

T-R state transition and, 261

Hydrophobic effect, 122-124

amino acid residues and, 333

comprehensive, 332-341

inverse temperature

transitions, 334

Hydrophobic face, 415,416

Hydrophobic folding, 29, 30

Hydrophobic (oil-like) groups

polar group hydration

competition with, 338

water abutting, 38, 39

Hydrophobic hydration, 109,

122-123,130

changes in, 118-119

charged groups and, 119

charged species and, 340, 341

complementary surface

amount of, 339-341

destruction, 349-350

disappearance of, 119,

242-243

hydrophobic domains and

disappearance of,

242-243

identification, 177-179

insolubility and disappearance

of, 119, 242-243

measurement, 177-179

oil-like group increase and

disappearance of, 119

solubility and, 119,181-182,

242-243

thermodynamic properties of,

112

Tt value determined by,

182-184

Hydrophobic-induced repulsion,

200

Hydrophobicity, 134

carboxyl ionization and,

254-256

cooperativity and interfaces of,

257,260, 261

electrochemical transduction

efficiency and increased,

343-344

functional group action and

change in,165-167

functional group composition

and increasing, 191

functional group stepwise

replacement and

increasing, 187-190

increased, 187-190,

300-301,

343-344

ion pairing and model protein,

182,183

oil-like residue replacement

and increased, 300-301

pKa shifts and, 187-191

plots,

258-261

fibrinogen, 288-290

refolding, chaperonin-directed,

308-314

subunit interfaces and, 258-261

unfolding, chaperonin-

directed, 308-314

Hydrophobicity scale

amino acid residue, 132-136

Trbased, 132-137,146-147

Hydrophobic moieties, 349

Hydrophobic residues, 190

Hydrophobic rotors, 396

Hydroxylation, prolyl, 321-322

Insolubility, 2. See also Cusp of

insolubility; Cusp of

insolubility, movable;

Solubility-insolubility

boundary

disease and, 239, 240

excursions too far into, 3,239,

241

hydrocarbon unit, 2-3

hydrophobic domain,

181-182

hydrophobic hydration

disappearance and, 119,

242-243

medical problem of protein,

295-304

molecular chaperones and,

304-320

prion protein-induced, 240

protein, 295-304

protein-based biological

systems presenting excess

of, 239-240

temperature interval, 2-3

Trdivide between solubility

and,109,112-113

water, 11

Insulin. See also Proinsulin

discovery, 77

genetic engineering of, 84

synthesis, 82-84, 93nl4

Integral membrane proteins, 79

a^P^ (a^p^) interheme crevasse,

271-274,275

Inverse temperature transitions,

37-38,43,

85,482-483

denaturation, cold of proteins

and,107-108

endothermic/exothermic

components of, 335-336

energy conversions by means

of, 543

energy source order extracted

by, 43

evolution by, 569-571

622 Index

Inverse temperature transitions

(cont)

genetic code's bias for use by,

570

hydrophobic association, 249,

297-298,

425^26

hydrophobic consiUent

mechanism and, 545

hydrophobic effect, 334

hydrophobic folding and

assembly transition,

112

inverted phase transitional

behavior of, 108-109

model protein, 108

muscle contraction and model

protein contraction with,

424-426

muscle contraction by

hydrophobic association,

249,425-426

phase diagram, 108-119

phase separation

characterizations, 105

protein-based machine

consequences and,

59-62

protein-based machines and

endothermic/exothermic

components of, 335-336

protein entropy and, 39^0

protein negative entropy

provided by, 39^0

thermodynamics, second law

and, 543-545

universal arrow of time

reversal and evolution by,

569-571

vital force and, 542-545

Ionian Enchantment, 550

Ionian Enlightenment, 70

Ionization

carboxyl, 254-256

AGap

and, 339

heat transition and, 184-185

Ion pairing, 359-360

calculating effect of, 141

contraction driven by, 156

elastic-contractile model

protein hydrophobic

association, 261-262

AGap

and, 344-346, 360

AGHA

and calculating effect of,

141

insolubilization of fiber

formation enhanced by

low, 302

low dielectric constant v. AGap

and,344-346

model protein chain, 262

model protein hydrophobicity

and, 182,183

protein-based polymer and

formation of, 344-345

Trdivide moving with pairing

of, 117

Ions

binding of calcium, 447-448

calcium, 425, 429, 430, 446^48

dissolving of, 359

formation, 359-360

hydration and dissolving of,

359

hydrophobic consilient

mechanism integration of

calcium, 446-448

hydrophobic consilient

mechanism powerstroke

triggered by calcium,

447-448

muscle contraction and

calcium, 247,425, 429,

430

Tf-based hydrophobicity scale

and negative/positive,

135-136

Isomers, optical, 77

Isometric contraction, 344

Kemppainen, B.W., 521-523,

539

Kendrew, 252

Key molecular players

model proteins and

mechanical work

performed by, 45-46

photosynthesis and charge

change of, 45

respiration and charge change

of, 45

Kinase activities

nanosensor-detected, 528-532

tumor tissue diagnostics assay

of, 529-530

Kinases assays, 532, 565-566

Krebs cycle, 356

Kuru, 296

Lange, C, 372, 379, 380, 448, 450,

451

Lanolin synthesis, 81

Laws of nature, 72

Laws of physics, 542

Lecithin

membrane containing, 79

structure, 78

Lenaz, G., 450

Leslie, A.G.W., 452,453

Leu-enkephalin amide

drug delivery, 65

release, zero order of

positively charged,

512-514

Life.

See also "Second secret of

life";

"What Sustains

Life?"

consilient mechanism and

sustaining, 2-4

energies as characteristics

defining, 28

energies sustaining, 1-2, 60,

energy conversions sustaining,

1,43^8,103

motion as index of, 32-34

protein-based machines and

sustaining, 548-561

protein-based machines of,

94-101

vital force sustaining,

548-561

Ligands

binding, 307-308

capping, 307-308

polarity of, evaluation,

412^15

Light energy

chemical energy converted

from, 44

motion produced by, 223-224

Living organisms

ATP and construction/

maintenance of, 350-351

as chemical factories, 91-92

products and components of,

70-93

Lower animals, vertebrate

difference from, 90

Lung diseases, environmentally

induced, 322-323

Lysozyme amyloidosis, 304

Index 623

Macromolecules, 543

Macrophages, 322-323

Mad cow disease

amyloid deposits, 297

insolubility , excess and, 240

solubility-insolubility

boundary, 3

Magnetism, 542

MALDI-TOF. See Matrix-assisted

laser desorption

ionization-imt-oi-^i^i

Malthus, Thomas Robert, 70-71

Martz, E., 325, 371, 430

Mass spectra, 485-488

Matrix-assisted laser desorption

/on/zflrion-time-of-flight

(MALDI-TOF), 487-488

Meaningful answers, obtaining,

71-72

Mechanical energy, 32,169

Mechanical work

ATP performance of, 555-561

chemical energy-produced,

151-156

contractile machines, 4

electrical energy-produced, 156

electromagnetic energy-

produced, 157-158

energy conversions not

involved in, 122

Fi-ATPase efficacy for,

420-422

hydrophobic consiUent

mechanism and, 555-556

isometric contraction, 344

key molecular players, 45-46

model protein, 45^6

nonideal elasticity and, 344

pressure-volume energy

production of, 156-157

thermal energy-produced,

150-151

Mechanisms, efficient, 61-62

Mechanist

challenge, 236

vitalist v., 235-237

Mechanochemical transduction,

172,173

cellular, 498,499

molecular machines efficient

for water, 342-343

pH dependence of length and,

342-343

Mechanoelectrochemical

transduction, 174

Mechanoelectromagnetic

transduction, 175

Medical devices

biology's own mechanisms/

devices used by, 562-564

coatings, 525

consiUent mechanism

approach to, 562

protein-based materials for,

24-25

Membranes. See also Cell

membranes; Integral

membrane proteins;

Mitochondrial membrane

lecithin in, 79

micelles, 78

structure, 77-79

thylakoid, protein-based

machines in, 80

Menz, R.L., 397, 404, 412^14,

419-422, 452, 453

Messenger RNA (mRNA), 98

Metabolism, 28

Micelles, 78

Mitochondria

complex II, 365-371

complex III, 365-371

electron transport chain,

analogues, 365-371

energy conversion in, 16-17

Mitochondrial membrane, inner

protein-based machines for,

proton release/uptake into,

363-365

proton translocation across,

549

reactions in, 357-359

Mitochondrion

oxidative phosphorylation in,

356-359

structure, 356-357

Modal protein v, 9,10

Model protein machines

function coupling and, 48

motion produced by, 50

photosynthesis, respiration,

and motion energy

conversions emulated

from, 48-50

progression to biology's

machines, 50-59

protons pumped on reduction

by, 48^9

synthetic, 48-50

Model proteins. See also

Designed model proteins;

Elastic-contractile model

proteins

biodegradable plastics, 62, 66

contraction with, 32

de /tovo-designed, 84, 455

drug addiction control with,

65-66

drug delivery, 62, 65-66

elasticity, 124-131

energies sustaining living

organisms converted with,

energy, 231-235

inputs, 206

families of, 22

genetic engineering, 63

hydrophobicity, 182,183

increased temperature and,

108-110

insoluble, 108,109

inverse temperature

transitions, 108, A2A-A26

ion pairing and hydrophobicity

of, 182,183

ion pairing between chains of,

262

key molecular players perform

mechanical work in,

45-46

mechanical work performed

by, 45^6

medical applications, 62

as molecular engines and

motors, 160

molecular structure, 124-131

muscle contraction and,

424-426

order created out of chaos

with energy contributed

by, 231-235

order, increased of, 108-110

pKa shifts and, 192-195

stretching, internal chain

motion decrease and, 126,

127

tissue reconstruction, 23-24,

62,

63-65

titrable functional group, acid

as energy input, 206

624 Index

Model proteins (cont.)

transitions in water, 104-108,

106

Model protein studies

contraction, 32

energy conversions in

mitochondria as

interpreted from, 16

muscle contraction as inferred

from, 15-16

Molecular chaperones, 304-320

Molecular dynamics, 545

Molecular machines, 170,

171-175

mechanochemical transduction

in water and efficient,

342-343

mutations for creating new

and more efficient,

227-228

protein-based polymer

function as, 124

second kind, 175-176

Molecules

carbon-containing, 74-75

mirror images, 74-76

Monoclonal antibodies, 480-481

Monocytes, human, 482

Monod, J.

allosteric effects discovered by,

21-22

"second secret of life," 7, 9-11,

21-22

On Symmetry and Function in

Biological Systems, 1

Monomers, 458

concatenation of, 471

genes/sequence, 471

protein-based polymer

biosynthesis and, 470-471

Motility, 90-91

Motion, 28

carboxylate protonation and

production of, 158,159

chemical energy production of,

220-222

consilient protein-based

machines production of,

158-160

elastic protein-based machine

production of, 147-150

electron production of,

222-223

energy conversions, 48-50,122

energy production of, visual

demonstrations, 32, 33

heat converted to, 35

as index of Life, 32-34

light energy production of,

223-224

light use and production of,

160

model protein machines,

synthetic production of, 50

muscle contraction efficient

production of, 424

oxidized functional group

attached to the model

protein reduction and

production of, 158-159

polymer phase separation and,

104

pressure change and

production of, 159, 222

production, 50,119-122,

147-150,158-160, 220,

424

salt added to model protein

and production of, 158,

159

salt conversion efficiency into,

220-221

synthetic model protein

machine emulating energy

conversions of, 48-50

temperature production of,

119-122,158,159

thermal energy production of,

220

treadmilling in formation and

maintenance of actin and

microtubular tracts for, 53

Motors, 168-169. See also Rotary

motors

linear, 3-4

rotary, 4

Muscle contraction, 14-16, 34

calcium ion activation of, 247,

425

calcium ion release and, 429,

430

clam-shaped globular protein

and, 57, 58

dephosphorylation and, 425

energy-converting events of,

46-48

energy sources for motion of,

46-48

hydrophobic association in,

245-249,425^26

hydrophobic associations

initiated

dephosphorylation and,

248-249

inverse temperature transition

contraction of model

proteins and, 424-426

inverse temperature transition

of hydrophobic

association, 249,425-426

isometric, 15

isotonic, 15

model protein, 424-426

study of, 15-16

molecular level, 426-430

motion efficiently produced by,

424

myosin II motor, 428-430,

557-561

myosin II motor, an ATPase

representative, 424-448

pH activation of, 247,425

shortening, 14

sliding filament of, 425-428,

557-561

structural description, 14

stretch activation of, 248,425

stretching, exothermic and, 246

striated muscle structure of,

425^28

temperature raising and,

246-247

thermal activation of, 246-247,

425

Myocardial infarction, 3

Myofibril, 425^26

Myoglobin

deoxygenated states of,

253-254

heme binding site geometry

and, 253-254

heme in, 267-269

hemoglobin oxygen binding

proteins and, 249-250, 251

Hill plot, 8,22

hydrophobic association of

proteins like, 249-254

oxygenated states of, 253-254

oxygen binding by, 9,250, 253

Myosin filament

actin binding site use on cross-

bridge of, 440,443^44

Index

625

cross-bridge, 440,443^44

cross-bridge in YZ plane

perpendicular to, 429,

433^41

Myosin II motor

ATPase of, 351

chemomechanical

transduction, 555-561

consilient mechanisms in,

430-446

cross-bridge, 430-432

crystal structure analysis and,

430-446

muscle contraction, 428-430

muscle contraction, an

ATPase representative,

424^48

Myosin motor domain

Dictostelium discoidium, 11-12

sculpted appearance of, 13

stereo view, 13

NAD.

See Nicotinamide adenine

dinucleotide

NADH oxidation, 362-365

Naltrexone drug delivery, 65-66

Nanoparticles, 519

Nanosensors

bioelastic, 565

design, 26, 528-529

kinase activities detected by,

528-532

kinase assay bioelastic,

565-566

mechanical resonance use by,

532-533,534

Natural selection, 570-571

Negative cooperativity, 197

The New Organon or True

Directions Concerning the

Interpretation of Nature

(Bacon), 571

Niacin structure, 82

Nicotinamide adenine

dinucleotide (NAD), 142

Nicotinamide, lysine-attached,

222

Nicotinic acid structure, 82

Nitrogen (N), 29,72

NTP.

See Nucleoside

triphosphate

Nuclear magnetic resonance

(NMR), 484^87

Nucleic acids

bases pairing for, 87

protein sequence translation

from sequences of, 1

sequences, 1

stoichiometry, 87

structures, 87-90

sugar-phosphate backbone of,

syntheses, 87-90

Nucleoside triphosphate (NTP),

Oil-like character

changing, 162-164

temperature and, 162,163

transition zone, 162-164,167

Oil-like groups. See

Hydrocarbon units;

Hydrophobic groups

apolar,

135,201,

214n39, 415,

416

associated, 3-4

cusp of insolubihty lowered by,

41-42

dissociated, 3-4

hydrophobicity scale for

measuring character,

134

vinegar-Uke groups' co-

existance with, 176

water surrounding, disorder of,

544-545

Oil-like side chains, 341

Oil structure, 77-79

On Symmetry and Function in

Biological Systems

(Monod), 7

Opoid peptides, 511

Opposing resonance, 347-348

Order Out of Chaos: Man's New

Dialogue with Nature

(Prigogine, Stengers),

228-229,234, 235, 569

Organic chemistry, 92n8

Ovalbumin loading curves,

518-519

Oxidation

elastic fiber elastic recoil loss

and, 322

glucose, 355-356

intermediary metabolism

glucose, 356

macrophage oxidative attack

on foreign substances,

322-323

NADH, 362-365

products of glucose, 356

Tt effects on, 136

ubiquinol, 373-375

Oxidative phosphorylation, 354

in mitochondrion, 356-359

protein motor of, 394-424

Oxidative stress, 320

Oxygen (O), 29, 72

binding, 9, 250, 253, 256, 257,

265-271,

278

cooperativity, positive and

binding analogues of,

254-257

cytochrome c oxidase

reduction of, 387-391

heme group binding to,

266-271

hemoglobin binding of,

256-257,

265-271,

278

analogy to, 255, 256

consilient mechanism and,

256-257

hemoglobin transport of, 9, 21,

249-263

myoglobin binding of, 9, 250,

253

reduction, 387-391

sigmoid, binding, 278

tertiary structure and binding

of, 261

Oxyhemoglobin

crystal structure, 265-266

deoxyhemoglobin external

differences from,

265-266

R state, 241,258

T-R state transition in, 258

Palma, M.U., 282, 283, 324, 325

Palma-Vittorelh, M.B., 324

PaoU, M., 325

Pasteur, L.

molecules with mirror images

and,74-75

science, basic and apphed,

456^57

Pauling electronegativity scale,

412-415

Pentapeptide, 124