Index to subjects

Index to subjects Volume 1 Number 4 August 1991

(z-helix structure, of bacteriorhodopsin, 534 ofreaction centres, 506 ABC transporters, 590 Absorption spectrum, retinal, 577 Acetylcholine receptors, muscarinic, 575, 648 nicotinic, 569 Acetylcholinesterase, 523, 525 Acriflavine, 593 Adhesives, proteinaceous, 640 ADP/ATP carrier, mitochondrial, 506, 507 Aerolysin, 539 Affinity selection, 621 Aida, 634-635 Alanine-scanning mutagenesis, 606 Alcohol dehydrogenase, Saccharomyces cerevisiae, 618 Algorithms, for engineering of metalloproteins, 633 for sequence-symmetry minimization, 653-655, 656 for substrate specificity, 619 Alzheimer's disease, 565 Amaranthus hybridus, 549 Amino acid residues, in de novo proteins, 630-631 Amino acid sequences, of P-type pumps, 555 of transport proteins, 590, 593 Antibiotic, transport proteins, 593-594 Antibodies, catalytic, 626-628 chimeric, 624 cloning` 608 engineered, 624-628 functional domains, 624 monoclonal, 624 specificity, 626 therapeutic power, 626 Apocytochrome c, mitochondrial, S07 Apolipoproteins, domain structure, 510-511 high-resolution structure, 511 Arabidopsis thaliana, glucose transporter, 595 Arabinose, binding protein, Escherichia coli, 619 transporter, Escherichia co/i, 595 Assembly, of electron transfer chain, 564 Asymmetry, of electron transfer pathway, 547-548 ATP, production, in Halobacteria, 534 synthase, interaction with cardiolipin, 507 ATPases, 555, 558 Autophosphorylation, 585 Azurin, site-directed mutants, 612 B-sheets,

of recombinant proteins, 639 sandwiches, 634 B-structure, of antibody light chains, 626 of apolipoprotein, 510 of membrane proteins, 539 of porins, 539, 540, 542 ~0~-structures, design of, 634 Bacteria, photosynthetic, 546-548 Bacteriochlorophylls, 546 Bacteriopheophytins, 546 Bacteriorhodopsin, 534-537 function, 535-537 structure, 506, 540 structure-function relationships, 534 Base pairs, complementary, 655 Bek protein, 584 Beta vulgaris, sucrose transporter, 595 Betabellin, 634 Bicarbonate, as cofactor in photosynthesis, 549 Binding, non-specific, to lipid surfaces, 644 sites, in de novo protein, 632-633 Biosensor, microphysiometer, 647-651 Biosynthesis, of GPI anchors, 525 of respiratory chain, 562 Biotin, 644-645 Bond angles, in engineered proteins, 614

Caenorhabditis elegans, 584 Calcium, binding, by protein kinase C, 519-520 channel, voltage-sensitive, 571 Carboxylate, transport proteins, 593-594 Cardiolipin, 507 Catalysis, by antibodies, 626-628 Catecholamine receptors, 575 Caveolae, 527 Cell, biology, of GPI-anchored proteins, 525-527 growth, humoral factors in, 582 polarity, 526 triggering, by receptor ligands, 648 Channels, ion specific, 569-573 ligand-gated, 569-571 voltage-controlled, 541,542 voltage-gated, 571-573 Chaperonins, 542 Chenopodium rubrum, glucose transporter, 595 Chlamydomonas reinhardtii, 546 Chloride, channel, voltage-sensitive, 573 Cholera toxin, 642, 644, 651 Cholesterol,

(~) Current Biology Lid ISSN 0959-440X

Index to subjects esterification, 510 transport, 513--514 Chymohelizyme, 633 Citrate transporter, 593, 594 Cloning, of antibodies, 608 Close-packed arrays, of protein molecules, 644 Co-crystallization, 541 Cofactors, in photosynthesis, 549 Coiled coil structure, 632 Computer-aided, protein engineering, 619-620, 633 Concanavalin A, 527 Connectedness, of a DNA structure, 655 Connexin, 539 Cooper-Hagerman, electrophoresis, 657 Crosslinking, of periodic polypeptides, 640 Crystal transfer, from lipid layers, 643 Crystallization, of ATPase, 555, 557-558 of epidermal growth factor receptor, 585 Crystallographic studies, of lipid phases, 501 CSF (colony-stimulating factor), receptor, 582, 584 Cubic, domains, of ternary systems, 503 phases, lipid, 501-503 Cyanobacterium, Synechocystis 6803, 546 Cyclophilin, 575 Cysteine, residues, in de novo proteins, 631, 632, 633 substitution, 607 Cytochalasin B, 592, 595, 596, 597 Cytochrome, oxidase, interaction with cardiolipin, 507 Cytochrome b, 563 Cytochrome c, oxidase, 562, 563 peroxidase, 613 phenylalanine residue, 612 Cytokine, receptors, 582-586 DAG (diacylglycerol), 516-518 Decay accelerating factor, 525, 528 Deletion-mutagenesis, 606 Desensitization, 578 Design, of altered specificity, 618 DI, polypeptide, 551-552

Dictyostelium discoideum, 564 Diels-Alder reactions, catalysed by antibodies, 626 Differential scanning calorimetry, of apolipoprotein, 511 Differentiation, humoral factors in, 582 Diffusion coefficients, 502 Dihydrofolate reductase, 613 Dihydropyridine receptor, 572 Disease, defects of electron transfer chain in, 564-565 and GPI anchors, 528 parasitic, 528 DNA, branched, 653-658 junctions, four-arm, 657

immobile, 653-658 partially mobile, 653 three-arm, 657 mitochondrial, 562 objects, construction of, 655, 657-658 as drug delivery systems, 657 as scaffolding medium, 653 structural engineering, 653-658 Domains, antigen-binding, 626 of apolipoproteins, 510-511 functional, of antibodies, 624 identification, 606 Down-regulation, 578 Drug-delivery systems, 657 Drugs, intercalative, 657 Dye, Stains-All, 657 Effector pathways, 648 Efflux proteins, 593 EGF receptor, 584, 585 Eicosanoids, 516 Elastin, 640 Electron, diffraction, of phosphoporin crystals, 540 microscopy, of bacteriorhodopsin, 534 of insulin receptor, 585 of lipid cubic phases, 502 of P-type pumps, 555 of porins, 539-540 of streptavidin, 645 of two-dimensional protein crystals, 642 transfer, kinetics, 612 regulation, 564 transfer chain, mitochondrial, 562-565 photosynthetic, 546 transfer mechanism, 612 transfer pathway, asymmetry, 547 transfer proteins, isoforms, 564 Electrophoresis, Cooper-Hagerman, 657 Energetics, of enzyme reactions, 612 of enzyme-substrate interactions, 617 Enerb:~/ metabolism, 647 Engineering see protein engineering Enzyme-substrate interactions, energetics, 617 Enzymes, catalytic mechanism, 611-614 chimeric, 618 function, design de novo, 633 redesign, computer-based, 619-620 redox, 612 substrate specificity, engineered, 617--622 Epo (erthyropoietin), receptor, 582, 584 Erb proteins, 584

Escherichia coli, porins, 539

Index to subjects transport proteins, 593-596 Ethidium, 593 Expression, of de novo proteins, 631,632 of periodic proteins, 639--640 of protein variants, 607 of recombinant proteins, 607 FcyRIII receptor, 527-528 Felix, 632 Ferritin, 644 FGF (fibroblast growth factor), receptor, 584 Fibroin, silk, 638 Fingerclasp, 634-635 Fish, electric, 569 Fluorescence, anisotropy, 507 energy transfer experiments, 577 recovery, 502, 526 Folate, receptor, 527 Folding, of ATPase, 558 of de novo proteins, 631, 632, 635 of electron transfer proteins, 563 of porins, 542 of recombinant proteins, 639 of rhodopsin, 576 Forskolin, 592, 595, 597, 651 Fourier-transformed infrared spectroscopy, 536 Freeze-fracture electron microscopy, 502 Frozen-hydrated microscopy, of ATPase crystals, 557, 559 Fucose/H + transporter, 593 Fusion proteins, 607 G proteins, 575 GABA (y-aminobutyric acid), receptor, 571 c~-Galactose, 523 Galactose, binding by mutant enzyme, 619 transporter, 594 13-Galactosidase, E. coli, 612 Genetic approaches, to engineering specificity, 620-622 Geometry, of engineered proteins, 614 of lipid cubic phases, 503 GH (growth hormone), receptor, 582 Glucose, transporter, 590, 594, 595, 597 Glutamate, receptor, 571 Glutathione, reductase, 618 Glycine, receptor, 571 residues, in de novo proteins, 631 Glycophorin, 507 Glycosyl-phosphatidylinositol, 523-528 GM1 ganglioside, 644 Gouy-Chapman-Stern theory, 519 Gp130 glycoprotein, 583 GPI, anchors, 523-528 glycosyl residue, 523 signal peptide, 525

Grendel, 634 Growth factor, receptors, 582-586 Growth hormone, receptors, 606 screening for, 621 H-2D antigen, 527 Haeomoglobinuria, 528 Halobacteria, 534, 537 Halorhodopsin, 537 HDL (high-density lipoproteins), 513-414 Helical bundles, 632 Helichrome, 633 Hexose/H + transporter, Chlorella kessleri, 595 Histidine, residues, in de novo proteins, 633 Holliday junction, 653-658, 657 Homolog-scanning mutagenesis, 606 Hormone-receptor interactions, 585 Hormones, lipid, 516--520 Hybridoma technology, 624 Hydrophobic interactions, with membrane lipids, 506, 507 Hydrophobicity analysis, of transport proteins, 593 IFN (interferon), receptor, 582 IGF-1, receptor, 584 IL(interleukin), receptor, 582 Infinite period minimal surfaces (IPMS), 502 Inhibitors, peptidase, 626 for sugar transport proteins, 596-597 Insulin, receptor, 584, 648 quaternary structure, 585 resistance, 584 Internalization, 578 Ion, channels, 569-573 synthetic, 633-634 pumps, P-type, 555-559 Iron, non-heme, 546, 562 Isoforms, of electron transfer proteins, 564 Jl, junction complex, 655 Junctions, immobile, in DNA, 653--658 Kallikrein, 634 Kearns-Sayre syndrome, 565 KGF (keratinocyte growth factor), 584 KgtP transport protein, 593, 594 Kinetics, of bacteriorhodopsin photocycle, 537 of electron transfer, 612 of fluorescence recovery, 502 of metarhodopsin formation, 508 of photosynthesis, 547 of sugar transport, 595 Labelling reagents, for sugar transport proteins, 596-597 I~-Lactamase, Bacillus subtilis, 612 Lactate dehydrogenase, B. stearothermophilus, 618 Lactose, transporters, 593-596 Langmuir-Blodgett technique, 643

Index to subjects LAPS (light-addressable potentiometric sensor), 647 LDL (low-density lipoproteins), 510-513 Leather, 635 Leishmania,

GPI anchors, 528 membrane transport protein, 590 Leucine zipper, 512, 594-595, 632 Ligands, binding by receptors, 577, 582, 585, 651 cell triggering by, 648 lipid-based, 644 , screening for, 651 Light-harvesting protein, 539, 540 Lipid anchors, on membrane proteins, 523-528 Lipid-protein interactions, model systems, 506-509 Lipids, crystallization of proteins on, 541, 642-645 cubic phases, 501-503 diversity, 516 as hormones and second messengers, 516-520 as modulators, 508, 517-518 physical properties, 501, 507, 518, 643 selectivity towards, 506-507 transport, 510 Lipophosphoglycan, 528 Lipopolysaccharides, 541 Lipoprotein, receptors, 510-514 Listeria, 528 Luciferase, 613 Lymphokine, receptors, 582 Macrocycle, DNA structures, 656 Madin-Darby canine kidney cells, 525 Maltoporin, 540, 541 Maltose transporter, yeast, 594 Manganese cluster, in PSII, 550-551 0[-Mannose, 523, 525 Materials applications, of protein engineering, 638-640 MELAS (mitochondrial myopathy, encephalomyopathy, lactic acidosis and stroke-like episodes), 565 Melibiose transporter, 593, 596 Membrane proteins, t-structure, 539 design, 633-634 interactions with lipids, 506 lipid anchors, 523-528 Membranes, cubic phases in, 501 dynamic state, 520 structure, 506 Mercuric reductase, 613 MERRF (myoclonus epilepsy with ragged red fibres), 565 Metabolic rate, cellular, 647 Metal, binding sites, engineering of, 633 Metalloproteins, engineered, 633 Metarhodopsin, 508 Microphysiometer, biosensor, 647-651 Mitochondria, dysfunction, 564-565 electron transfer chain, 562-565 Mixed micelle system, 518

Mobility, of membrane phospholipids, 518-519 of proteins, 526-527 Model systems, for lipid-protein interactions, 506-509 Modelling` of de novo proteins, 630 Modification site, 611 Molecular, biology, and protein engineering, 605-608 dynamics methods, 631 Molten globules, in de novo protein, 632 Monte Carlo methods, 631 Muscarinic acetylcholine receptor, 648 Mutagenesis, of transport proteins, 595 Mutation, point, 605 random, 606 site-directed, of mercuric reductase, 613 of photosynthetic reaction centres, 546-552 in protein engineering, 617 Myelin, proteolipids, 507 NADH-ubiquinone reductase, 562 Neisseria meningitidis, 542

Neutron, diffraction studies, of bacteriorhodopsin, 535 scattering experiments, on lipid cubic phases, 501 NGF (nerve growth factor), receptor, 583 Nucleic acids, secondary structure prediction, 655 structural design, 653 Octarellin, 634 Oncogenes, 584 Osmoporin, 541, 542 PA (phosphatidic acid), 516 Paracoccus denitrificans, 562

Parkinson's disease, 565 Paroxysmal nocturnal haeomoglobinuria, 528 Pattern recognition, in crystallography, 501 PCR (polymerase chain reaction), 605 PDGF (platelet-derived growth factor), receptor, 584 PE (phosphatidylethanolamine), 643 Peptidase, inhibitors, 626 PG (phosphatidylglycerol), 519 PH-20 glycoprotein, 526 Phage, display, 620 filamentous, 607, 620 Pharmacological studies, of second-messenger pathways, 651 Phase diagrams, of lipid-containing systems, 502-503 Phorbol-ester binding, 517-518 Phospholipases, 523 Phospholipids, effect on protein kinase C, 517, 519 in lipid anchors, 525 precursors, 516 Phosphoporin, 540, 541 Phosphorylation, of receptors, 578 Phosphotransferases, 590 Photobleaching, 502, 526

Index to subjects Photoreactions, primary, 546-548 Photosynthesis, cofactors, 546, 549 kinetics, 547 reaction centres, 546-552 Photosystem II, 546, 548, 550 PI (phosphatidylinositol), 519 Plasmodium, 528 Platelet-activating factor, 516 Pleiotropic response, 582 Polymer chemistry, 638 Porins, eukaryotic, 541 folding, 542 matrix, 540, 541, 542 oligomeric state, 541 three-dimensional structure, 539-542 topology, 541 Porphyrins, binding of, 657 Potassium, channel, voltage-sensitive, 572 PRO (prolactin), receptor, 582 Proline, residues, in de novo proteins, 630 Prolyl isomerase, 575-576 Propidium, 657 Protease, (x-lytic, 619 Protein, delivery system, 525-527 design, de novo, 630-635 dynamics, and catalytic function, 613 engineering, of antibodies, 624-628 for materials applications, 638-640 molecular biology methods, 605-608 in study of enzyme catalysis, 611-614 function, modulated by lipids, 508 kinase, cAMP-dependent, 618 kinase C, 578 as model system, 516-518 mobility, 526-527 pump, 534-537 silk-like see SLP Protein~rotein interactions, 606 Proteins, adhesive, 640 chimeric, 606 crystallization on lipid layers, 642-645 de novo, structure determination, 631 matrix, 638 modification, 611 engineering, for enzyme substrate specificity, 617-622 periodic, 638-640 purity, important in crystallization, 644 transport, 590-597 two-dimensional crystals, 642-645 Proteolipids, myelin, 507 Proton, conduction pathway, of bacteriorhodopsin, 535-537 pumping, 535, 562 Protonation reactions, 548 PS (phosphatidylserine), 517-519 Purple,.

bacteria, 546-552 membrane, 534-535 Putidaredoxin, 612 Qa-2 antigen, 527 QacA transport protein, 593 Quadrilateral, DNA structures, 656 Quinones, 546, 547, 548 Radio-imaging, of tumors, 626 Raman spectroscopy, 535 Reaction centres, bacterial, 506, 508, 539, 541 photosynthetic, 546-552 Receptor-substrate interactions, 585 Receptors, agonist binding, 648, 651 assembly and structure, 575-576 crystallization, 585 cytoplasmic surface, 577-578, 583 dimerization, 585 ligand binding, 585 microphysiometer studies, 647-651 for modified LDL, 512-513 mutant, 584 orphan, 651 phosphorylation, 578 for plasma lipoproteins, 510-514 regulation, 578 self-phosphorylation, 585 seven-helix, 575-578, 606 Recombinant DNA methods, 611 Redox, enzymes, 612 Regulation, by receptors, 578 of electron transfer, 564 Residues, functional, identification, 606 Retinal, 534, 535, 536, 577 Retinitis pigmentosa, 576 Rhamnose/H + transporter, 593 Rhodobacter, capsulatus, 539 spheroides, 506, 546 Rhodopseudomonas viridis, 506, 508, 546 Rhodopsin, 507, 508, 575, 576, 578 Drosophila, 575 Ribulosebisphosphate carboxylase, 607 engineered, 617 Ricinus, sucrose transporter, 595 RNA polymerase, binding to lipid layer, 644 Root-cell membranes, structural .study, 502 Saccharomyces cerevisiae, efflux protein, 593 sugar transport proteins, 594 Sarcoplasmic reticulum, ATPase crystals in, 557 X-ray studies, 558 Scenedesmus obliquus, 552 SCF (stem cell factor) receptor, 584 Schiff base, 534-536, 577 Scrapie prion protein, 523

Index to subjects Screening, for altered enzymes, 620 in vivo, 607 Second messengers, lipid, 516-520 pathways, 648, 651 Self-ditfusion measurements, 502 Sequence homology, of sugar transport proteins, 591 Sequence-symmetry minimization, 653-656 Seven-helix, receptors, 575-578 Shpilka, 634 Side-chain, conformation space, 619 Signal, generation and termination, 585 peptide, GPI, 525 transduction, 584, 585 Signalling, transmembrane, 527, 582-586 Silk, fibroin, 638 spider dragline, 639-640 SLP (silk-like protein), 638 Sodium, channel, voltage-sensitive, 571 Space-filling, by polyhedra, 503 Speciticity, engineering, genetic approaches, 620-622 protein engineering for, 617-622 Spectroscopic probes, for active sites, 614 Sphingolipids, 516 Spleen focus-forming virus, 584 Staphylococcus aureus transport protein, 593 Stoichiometry, of membrane protein interactions, 506 of PKC-PS interaction, 518 of porin-lipopolysaccharide interaction, 541 Streptavidin, 643-645 Streptomyces coelicolor, efflux protein, 593 Structure, determination methods, 540 of electron transfer chain, 562-563 of P-type ion pumps, 555-559 Structure-function relationships, of bacteriorhodopsin, 534 of enzymes, 611 of PKC, 517 of porins, 542 in protein engineering, 617 study of, 535 Substrate, specificity, engineered, 617-622 Substrates, for sugar transport proteins, 592 Subtilisin, 612 Succinate-ubiquinone reductase, 562 Sucrose/H + transporters, in plants, 595 Sugar, transport proteins, 590-597 Suppressor strains, 607 Synechocystis 6803, cyanobacterium, 546, 552

Taq polymerase, inaccuracy, 605, 608 Ternary systems, cubic domains, 503 Tetracycline transporter, 593 Thermodynamics, of bacteriorhodopsin photocycle, 536-537 Thrombin, 634 Thy-1, 523, 525-527 TNF (tumor necrosis factor), receptor, 582, 583 Toxoplasma, 528 Transducin, 578 Transferrin receptor, 507 Transmembrane, domains, of sugar transpo.rt proteins, 590-594 helices, of ATPase, 558-559 signalling receptors, 582-586 Transport, cholesterol, 513-514 function, of lipoproteins, 510 transmembrane, 527 Transport proteins, amino acid sequences, 590 antibiotic, 593-594 carboxylate, 593-594 glucose, 590 mutagenesis, 595 three-dimensional structure, 597 Triglyceride hydrolysis, 510 Tropoelastin, 640 Tropomyosin, 632 Trypanosomes, African, 523-528 Trypsin, screening for, 620 Tryptophan, residues, in de novo proteins, 631,632 Tumors, radio-imaging, 626 Tyrosine kinase, receptors, 584-585 Ubiquinol cytochrome c reductase, 562 Ultracentrifugation, preparative, of HDL, 513 VLDL (very-low-density lipoproteins), 510 VSG (variant surface glycoprotein), 523, 525, 528 VSV G protein, 527 Water, protein-associated, 535 X-ray studies, of apolipoprotein, 512 of bacterial reaction centres, 506 of membrane proteins, 546 of porins, 540 of sarcoplasmic reticulum, 558 Xenopus, oocytes, mutant acetylcholine receptors, 569, 571 Xylose/H + transporter, 596 Yeast, sugar transport proteins, 594-595 Zea mays, glucose transporter, 595 Zinc-binding site, engineered, 633