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Index to subjects volume 2 number 1 February 1992

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List of journals scanned The Index Medicus abbreviation is in parentheses Accounts of Chemical Research (Acc Chem Res) Acta Chemica Scandinavica (Acta Chem Scand) Acta Crystallographica Section A (Acta Crystallogr [A]) Acta Crystallographica Section B (Acta Crystallogr [B]) Advances in Lipid Research (Adv Lipid Res) Advances in Protein Chemistry (Adv Protein Chem) Analytical Biochemistry (Anal Biochem) Annual Review of Biochemistry (Annu Rev Biochem) Annual Review of Biophysics and Biophysical Chemistry (Annu Rev Biophys Biophys Chem) Archives of Biochemistry and Biophysics (Arch Biochem Biophys) Biochemical and Biophysical Research Communications (Biochem Biophys Res Commun) Biochemical Journal (Biochem J) Biochemistry and Cell Biology (Biochem Cell Biol) Biochemistry (Washington) (Biochemistry) Biochemistry -- USSR (Eng transl) (Biochemistry [Engl Tr]) Biochimica et Biophysica Acta - - Bioenergetics (Biochim giophys Acta) Biochimica et Biophysica Acta - - Biomembranes (Biochim Biophys Acta) Biochimica et Biophysica Acta -- Lipids and Lipid Metabolism (Biochim Biophys Acta) Biochimica et Biophysica Acta --Protein Structure and Molecular Enzymology (Biochim Biophys Acta) Biochimie (Biochimie) Biofizika (Biofizika) Biological Chemistry Hoppe-Seyler (Biol Chem Hoppe Seyler) Biophysical Chemistry (Biophys Chem) Biophysical Journal (Biophys J) Biopolymers (Biopolymers) Biotechnology (Biotechnology) Carbohydrate Polymers (Carbohydr Polymers) Carbohydrate Research (Carbohydr Res) Cell (Cell) Chemistry and Physics of Lipids (Chem Phys Lipids) Cold Spring Harbor Symposia on Quantitative Biology (Cold Spring Harb Symp Quant Biol) Comparative Biochemistry and Physiology B - - Comparativ~ Biochemistry (Comp Biochem Physiol [B]) DNA and Cell Biology (DNA Cell Biol) EMBO Journal (EMBO J) European Biophysics Journal (Eur Biophys J) European Journal of Biochemistry (Eur J Biochem) FEBS Letters (FEBSLett) Indian Journal of Biochemistry and Biophysics (Indian J Biochem Biophys) International Journal of Peptide and Protein Research (lnt J Pept Protein Res) Journal of Applied Crystallography (J Appl Crystallogr) Journal of Biochemical and Biophysical Methods (J Biochem Biophys Methods) Journal of Biochemistry (Tokyo) (J Biochem (Tokyo)) Journal of Biological Chemistry (J Biol Chem) Journal of Biomolecular Structure and Dynamics (J Biomol Struct Dyn) Journal of Carbohydrate Chemistry (J Carbohydr Chem) Journal of Cell Biology (J Cell Biol) Journal of Computer-Aided Molecular Design (J Comput Aided Mol Des) Journal of Crystal Growth (J Crystal Growth) Journal of Enzyme Inhibition (J Enz Inhib) Journal of Lipid Research (J Lipid Res) Journal of Magnetic Resonance (J Magn Reson) Journal of Membrane Biology (J Membr Biol) Journal of Microscopy (J Microsc) ournal of Molecular Biology (J Mol Biol) ournat of Molecular Evolution (J Mol Evol) ournal of Molecular Structure (J Mol Struct) ournal of Protein Chemistry (J Protein Chem) ournal of Structural Biology (J Struct Biol) ournal of the American Chemical Society (J Am Chem Soc) ournal of Theoretical Biology (J Theor Biol) ournal of Virology (J Virol) Macromolecules (Macromolecules) Methods in Enzymology (Methods Enzymol) Molecular and Cellular Biology (Mol Cell Biol) Molecular Evolution (Mol Evol) Nature (Nature) Nucleic Acids Research (Nucleic Acids Res) Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences (Philos Trans R Soc Lond [Biol]) Proceedings of the Japan Academy Series B - - Physical and Biological Sciences (Proc Jpn Acad [13]) Proceedings of the National Academy of Sciences of the United States of America (Proc Natl Acad Sci USA) Proceedings of the Royal Society of London. Series B: Biological Sciences (Proc R Soc Lond [Biol]) Progress in Biophysics and Molecular Biology (Prog Biophys Mol Biol) Progress in Lipid Research (Prog Lipid Res) Protein Engineering (Protein Eng) Proteins - - Structure Function and Genetics (Proteins) Quarterly Reviews of Biophysics (Q Rev Biophys) Review of Scientific Instruments (Rev Sci Instrum) Science (Science) Trends in Biochemical Sciences (Trends Biochem Sci) Trends in Biotechnology (Trends Biotechnol) Ultramicroscopy (Ultramicroscopy) Virology (Virology) ~) Current Biology Ltd ISSN 0959-440X
Transcript

List of journals scanned The Index Medicus abbrev iat ion is in parentheses

Accounts of Chemical Research (Acc Chem Res) Acta Chemica Scandinavica (Acta Chem Scand) Acta Crystallographica Section A (Acta Crystallogr [A]) Acta Crystallographica Section B (Acta Crystallogr [B]) Advances in Lipid Research (Adv Lipid Res) Advances in Protein Chemistry (Adv Protein Chem) Analytical Biochemistry (Anal Biochem) Annual Review of Biochemistry (Annu Rev Biochem) Annual Review of Biophysics and Biophysical Chemistry (Annu

Rev Biophys Biophys Chem) Archives of Biochemistry and Biophysics (Arch Biochem

Biophys) Biochemical and Biophysical Research Communications

(Biochem Biophys Res Commun) Biochemical Journal (Biochem J) Biochemistry and Cell Biology (Biochem Cell Biol) Biochemistry (Washington) (Biochemistry) Biochemistry - - USSR (Eng transl) (Biochemistry [Engl Tr]) Biochimica et Biophysica Acta - - Bioenergetics (Biochim

giophys Acta) Biochimica et Biophysica Acta - - Biomembranes (Biochim

Biophys Acta) Biochimica et Biophysica Acta - - Lipids and Lipid Metabolism

(Biochim Biophys Acta) Biochimica et Biophysica Acta --Protein Structure and

Molecular Enzymology (Biochim Biophys Acta) Biochimie (Biochimie) Biofizika (Biofizika) Biological Chemistry Hoppe-Seyler (Biol Chem

Hoppe Seyler) Biophysical Chemistry (Biophys Chem) Biophysical Journal (Biophys J) Biopolymers (Biopolymers) Biotechnology (Biotechnology) Carbohydrate Polymers (Carbohydr Polymers) Carbohydrate Research (Carbohydr Res) Cell (Cell) Chemistry and Physics of Lipids (Chem Phys Lipids) Cold Spring Harbor Symposia on Quantitative Biology (Cold

Spring Harb Symp Quant Biol) Comparative Biochemistry and Physiology B - - Comparativ~

Biochemistry (Comp Biochem Physiol [B]) DNA and Cell Biology (DNA Cell Biol) EMBO Journal (EMBO J) European Biophysics Journal (Eur Biophys J) European Journal of Biochemistry (Eur J Biochem) FEBS Letters (FEBS Lett) Indian Journal of Biochemistry and Biophysics (Indian J Biochem

Biophys) International Journal of Peptide and Protein Research (lnt J Pept

Protein Res)

Journal of Applied Crystallography (J Appl Crystallogr) Journal of Biochemical and Biophysical Methods (J Biochem

Biophys Methods) Journal of Biochemistry (Tokyo) (J Biochem (Tokyo)) Journal of Biological Chemistry (J Biol Chem) Journal of Biomolecular Structure and Dynamics (J Biomol

Struct Dyn) Journal of Carbohydrate Chemistry (J Carbohydr Chem) Journal of Cell Biology (J Cell Biol) Journal of Computer-Aided Molecular Design (J Comput Aided

Mol Des) Journal of Crystal Growth (J Crystal Growth) Journal of Enzyme Inhibition (J Enz Inhib) Journal of Lipid Research (J Lipid Res) Journal of Magnetic Resonance (J Magn Reson) Journal of Membrane Biology (J Membr Biol) Journal of Microscopy (J Microsc) ournal of Molecular Biology (J Mol Biol) ournat of Molecular Evolution (J Mol Evol) ournal of Molecular Structure (J Mol Struct) ournal of Protein Chemistry (J Protein Chem) ournal of Structural Biology (J Struct Biol) ournal of the American Chemical Society (J Am Chem Soc) ournal of Theoretical Biology (J Theor Biol) ournal of Virology (J Virol)

Macromolecules (Macromolecules) Methods in Enzymology (Methods Enzymol) Molecular and Cellular Biology (Mol Cell Biol) Molecular Evolution (Mol Evol) Nature (Nature) Nucleic Acids Research (Nucleic Acids Res) Philosophical Transactions of the Royal Society of London.

Series B: Biological Sciences (Philos Trans R Soc Lond [Biol]) Proceedings of the Japan Academy Series B - - Physical and

Biological Sciences (Proc Jpn Acad [13]) Proceedings of the National Academy of Sciences of the

United States of America (Proc Natl Acad Sci USA) Proceedings of the Royal Society of London. Series B: Biological

Sciences (Proc R Soc Lond [Biol]) Progress in Biophysics and Molecular Biology (Prog Biophys

Mol Biol) Progress in Lipid Research (Prog Lipid Res) Protein Engineering (Protein Eng) Proteins - - Structure Function and Genetics (Proteins) Quarterly Reviews of Biophysics (Q Rev Biophys) Review of Scientific Instruments (Rev Sci Instrum) Science (Science) Trends in Biochemical Sciences (Trends Biochem Sci) Trends in Biotechnology (Trends Biotechnol) Ultramicroscopy (Ultramicroscopy) Virology (Virology)

~) Current Biology Ltd ISSN 0959-440X

Index to subjects Volume 2 Number 1 February 1992

Accessory proteins, in protein folding, 26-31 Acetylation, of histones, 81 Acidic residues, in nucleases, 86, 96 Actin, 31, 64 Activation, allosteric, 98 Active sites

of aminoacyl tRNA synthetases, 140 of nucleases, 95-96

Adenovirus, ssDNA binding proteins, 127 Adenylate kinases, 62, 63 Aggregation, of proteins, 23, 29 Algorithms

for RNA secondary structure, 131 for side-chain conformations, 48

(z-helices, 1, 13, 17 ~-stru ctu re

of leucine zipper, 116 of tRNA synthetases, 138-139 of ubiquitin, 8 of zinc fingers, 109

Amino acid residues, helix-forming properties, 13, 17, 49 Amino acid sequence, of nucleotide-binding proteins, 61 Aminoacyl-tRNA synthetases, 138-141 Antennapedia homeodomains, 100, 105 Antibody domains, 5~54 Antibody-antigen complexes, 52 Anticodon loop, of tRNA, 65 AP-1, 116, 117, 119 Apomyoglobin, 8, 41 Arginine residues, in zinc fingers, 111 Aromatic residues, stacking with DNA bases, 124 Aspartate aminotransferase, 23 Aspartyl-tRNA synthetases, E. coli, 138-140 ATF/CREB, 116, 120 ATP, binding, 64 ATPase, 30-31, 63

Bacillus cereus, phospholipase C, 86 Bacillus stearothermophilus, tyrosyl tRNA synthetase, 138 Bacillus thuringiensis, protoxin, 7 BamHI endonuclease, 93, 96 Barnase, 2, 48, 85-86 Base pair unstacking, 98 Bean pod mottle virus, 145, 146 B-structure

of capsid proteins, 133, 146 of cyclophilin, 27 of FMN-binding enzymes, 65 formation, 1, 21 of nucleotide-binding proteins, 61 of ribonucleoprotein, 134 stability, 13 of tRNA synthetases, 138--139 of troponin C, 57 of ubiquitin, 8 of zinc fingers, 58, 109

Bicoid, 105 Binding

of calcium, 4 editorial overview, 1-4 energetics, 38, 94 of magnesium ions, 36 of metal ions by proteins, 57-59 of single-stranded DNA, 124-127

Biochemical studies of aminoacyl-tRNA synthetases, 140 of endonucleases, 94 in mapping of protein~DNA contacts, 105

Brome mosaic virus, 144 Buried charges, 41, 47, 85 bZip family, 116--121

c-Fos, 120 C/EBP, 116, 117, 120 Calbindin, 54, 57-58 Calcium binding, 4, 52, 54, 57-58 Calmodulin, 54, 55, 58 Capsid proteins, 133, 143-148 Catabolic gene activator protein, E. coli, 73-74, 100 CELF, 117 Chain fold, of nucleotide-binding proteins, 61-63 Chaperonins, 28-30 Chemical shift data, for repressor--operator complexes, 102 CheY, 62 Chromatin, 78 Chymotrypsin inhibitor, 48 Circular dichroism studies

of bZip proteins, 118 of denatured proteins, 7 of DNA, 71 of gene 5 protein, 126 of peptides, 17

Circular dichroism studies, of folding intermediates, 21 Cis-trans isomerization, of peptide bonds, 2, 21, 22 Citrate synthase, 29 Co-solvents, 36, 37 Coiled-coil structure, 10, 116-119 Computer simulations, of protein folding, 9 Conformation space, of polypeptide chain, 6 Copolymers, random, 13-14, 16 Cornoviruses, 144-145 Coulomb equation, 16 Cowpea chlorotic mottle virus, 144 Cowpea mosaic virus, 145 Cro repressor, 72-7.3, 95, 101-103 Crosslinking experiments, 80 CRP, 117-118 yII-Crystallin, 23 Cyclosporin A-cyclophilin, 3, 27, 52, 53 Cysteinyl tRNA sythetase, 141 Cystic fibrosis gene product, 63 Cytochrome c, 8, 30, 47

Current Biology Ltd ISSN 0959-440X

Index to subjects

Databases, protein, 93 Debye-Huckel equation, 16 Denaturation

energetics, 6 methods, 8, 9, 10, 41

Denatured states, compact, 7-9 Dihydrofolate reductase, 22, 28, 55 Dimerization, of leucine zippers, 117-119 Disulphide bonds, 2, 22 DNA

A and B, 71-72 bending, 74-75, 100, 103 binding, 58, 86 binding by ~L repressor, 102-103 binding by leucine zipper, ~119 cleavage by restriction endonucleases, 93 conformation, 71-75 deformation, 72, 95, 98 major and minor grooves, 71-73, 78, 80, 93, 94, 103, 110, 112, 119, 131 recognition

by glucocorticoid receptor, 112 by helix-turn-helix motif, 100-105

replication, in retroviruses, 86 single-stranded, 124-127, 147 supercoiling, 74, 79

DNA viruses, 145-147 DNA-protein interaction, 98 DNA-binding proteins, 10, 58 DNA/RNA hybrid binding, 86 DnaK protein, 30 DNase I, 74, 89-90 Domains, folding, 23 Down syndrome, 81 Dynein, 63

E. coli aminoacyl tRNA synthetase, 138-141 catabolic gene activator protein, 73-74, 100 chaperonins, 29 DNA polymerase I 3',5'-exonuclease, 87 recA protein, 126 SecB, 30 tryptophan synthetase, 8

E-F hand, calcium binding sites, 4 EcoRI and EcoRV, 93-98 Electron microscopy

of chaperonins, 29 of DNA, 74

Electrostatic effects in denatured states, 9 in folding, 3 on protein stability, 40-43 in,side-chain interactions, 16

Elongation factor Tu, 62 Endonucleases, 88-89, 96 Energetics

of base pair unstacking, 98 of binding, 38 of denaturation, 6, 40 of endonucleases, 95 of helix formation, 13-15, 16, 18

of ionization, 42 of protein stabilization, 35, 46 of three-component interactions, 37-38 of unfolding, 42

Engrailed homeodomains, ~100, 105 Enzyme-substrate binding, 85 Ethylation protection studies, of ribonucleoprotein, 134 Exclusion, preferential, 35-36, 37

Factor IX, 54 FAD, binding to proteins, 61 Fd phage, proteins, 124-126, 147 Ferredoxins, 54-55 Fis, 74, 103, 105 FKBP, 27 Flavocytochrome b2, 65 Flavodoxin, 53, 62, 65 Fluorescence studies

of folding, 9 of gene 5 protein, 126

FMN, binding, 53, 65 Fokl, 93 Folding

accessory proteins, 26-31 domains, 9, 23 in vitro and in vivo, 9, 23, 28 intermediates, 1, 21, 22 mechanism, 21-24 of mutant protein, 24 overview, 1-4 pathways, 1-2, 9, 22 time scale, 21

Footprinting, 103, 112, 132 Fos, 119 Fos-Jun, 117, 118 Fructose-l,6-bisphosphatase, 64

G proteins, 62 gag proteins, 109 GAL4, 112 GCN4, 116, 117 Gel-exclusion chromatography, 9 Gel-filtration chromatography, 28 Gel-shift method, 95 Gene 32 protein, of T4 phage, 124, 126, 133 Gene 5 protein, of fd phage, 124 Genetic studies, in mapping of protein-DNA contacts, 105 Glucocorticoid receptor, 59, 109, 111-112, 120 0c-Glucosidase, 28 Glutamate residues

in Klenow fragment, 87 in T4 lysozyme, 46

Glutaminyl tRNA synthetase, E.coli, 138, 139 Glutathione reductase, 62 Glycolate oxidase, 65 GroE proteins see also chaperonins, 3, 9, 24 Growth hormones, refolding, 23 Guanylate kinase, 62 Guest-host methods, 13-14, 16

H-ras-p21, 62 Heat-shock proteins, 30, 64

Helix-loop-helix, 57 Helix-turn-helix, 73, 74, 100-105 Helix-coil equilibrium parameters, 14, 15, 17-18 Helix-forming properties, of amino acid residues, 13, 49 Hexokinase, 64 High-mobility-group proteins, 78, 81 Histidine residues

in active sites of AspRS, 140 in HIV ribonuclease H, 86 nuclear polarization experiments, 7

Histones, 78-81 HIV

gag proteins, 109 protein-nucleic acid interactions, 143 Rev protein, 132 Tat protein, 132 ribonuclease H, 86

Homeodomain recognition, 100, 105 HPLC methods, for folding intermediates, 22 Hydrogen bonding

non-Watson-Crick, 102, 139 in polypeptide backbone, 17 in protein stability, 41

Hydrogen exchange studies in antigen binding, 54 of apomyoglobin, 41 in denatured proteins, 8, 9 of folding, 21 of leucine zipper, 118 in native state proteins, 7 of protein stability, 40

Hydrophobic effects in preferential exclusion, 36 in side-chain interactions, 16

Hydrophobic interior, of proteins, 30, 41, 46--48

IB/EBP, 117-118 Ike protein, 125 IL6DBP, 117-118, 120 Inhibitor-I, 2 Insertions and deletions, tolerance to, 46, 85 Interferon, expression in E. coli, 23 Ion-pair interactions, 118 Iron-sulfur proteins, 54-55 Isotope enrichment techniques, 52, 53

Kinetics of endonucleases, 94-95 of protein folding, 1-2

Klenow fragment, 87 K m and kca t values, of endonucleases, 94

L1-L69, 73 LAC9, 112 Lac, promoter, 74 Lac, repressor and operator, 102 ~-Lactalbumin, 2, 8, 9, 30 pre-~-Lactamase, 28 Lactate dehydrogenase, 9 ~-Lactoglobulin, 36 Lambda repressor, 100--105, 117 Langmuir isotherm, 38

Index Io subjects

LAP, 117-118 Leucine zippers, 49, 116-121 Ligand binding, 2, 3-4, 27, 52-55, 96 Linderstrom-Lang model, 41, 43 Lysozyme

denatured, 7 folding, 9, 21 hydrophobic interior, 30, 46, 48 transition state, 2

Lysyl tRNA synthetase, yeast, 140 Lytechinus variegatus, 5S RNA gene, 79

M13 phage, 147 M-values, 47 Magnesium, and nucleases, 93, 96 Magnesium ions, in salting-out, 36 Magnesium-ATP, 29 MAK33, 8 Malate dehydrogenase, Halobactefium maris-mortui, 37 Male-associated protein ZFY, 110 Mammalian, ssDNA-binding proteins, 127 Mat~2, yeast transcription factor, 100 Metal ions, binding by proteins, 57-59, 96 Methionyl tRNA synthetase, E. co/i, 138, 139, 140-141 2-Methyl-2,4-pentanediol, 35, 36 MetJ repressor, 72 Microsomal triglyceride transfer protein, 27 Molecular chaperones, 3, 9, 23-24, 28-31 Molecular dynamics simulations, of peptides, 21 Moloney murine leukaemia virus, 86 Molten globules, 1, 3, 7-9, 28 Mononucleotides, binding, 63-65 Monte Carlo methods, 42 Mutagenesis studies

of brome mosaic virus, 144 of calcium-binding sites, 59 of DNA binding, 124 of DNase I, 89 of fd gene 5 protein, 125 in folding, 3, 13, 22 of Fos, 119 of gene 5 protein, 126 of phosphoglycerate kinase, 23 of protein stabilization, 41 of RNase T1, 85 of tRNA synthetases, 141

Mutational studies of apomyoglobin, 8 of nucleases, 95, 96 of protein stability, 2, 13, 46-49

Myoglobin, 8 Myosin, 63

NAD and NADP, binding to proteins, 61 NMR studies

of apomyoglobin, 41 of barnase, 85 of calcium-binding proteins, 54 of capsid proteins, 144 of chaperonins, 28 of fd gene 5 protein, 125 of folding, 21

Index to subjects

of glucocorticoid receptor, 111 of leucine zipper, 118 of ligand binding, 3, 52-55 of molten globules, 8 of oestrogen receptor, 111 of peptides, 17 of Pfl gene 5 protein, 125 of repressor-operator complexes, 102 of rhodanese-groEL, 9 of RNA, 131 of RNP, 133 of staphylococcal nuclease, 85 of ubiquitin, 8 of unfolded proteins, 6-7 of zinc fingers, 109, 110

Non-Watson-Crick bonding, 102, 139 Nuclear hormone receptors, 109, 111 Nuclear Overhauser effects

of barnase, 86 of bound water, 54 of dentured proteins, 9 of ferredoxin, 54-55 in ligand binding, 52 of native proteins, 7 for repressor-operator complexes, 102 in short peptides, 17 of staphylococcal nuclease, 84-85 of zinc fingers, 110

Nuclear polarization experiments, 7 Nucleases, structure and function, 84-90 Nucleosomes, 74, 79 Nucleotides, binding by proteins, 61-65

Oestrogen receptor, 109, 111 Osmolytes, natural, 37 Ovomucoid proteinase inhibitor, 110

P1 nuclease, 86-87, 88 Packing, in protein interior, 47-48 PAGE, 28 Partition functions, for homo- and heteropolymers, 18 Parvovirus, 145-146 Penicillium citrinum, P1 nuclease, 86-87 Peptides

binding to calmodulin, 55 helical content, 14

Peptidyl prolyl isomerases, 26-28 Pfl phage, gene 5 protein, 125 Phage

capsid protein, 133 Cro repressor, 72-73 endonuclease V, 88-89 gene 32 protein, 124, 126, 133 gene 5 protein, 124-126 ~pX174, 146-147 RNA polymerase, 131 with single-stranded DNA, 147 ssDNA-binding proteins, 124-127 tailspike proteins, 23

Phenyl tRNA synthetase, 141 Phosphofructokinase, 64 Phosphoglycerate kinase, 23

Phospholipase C, of Bacillus cereus, 86 pK a, of an ionizable group, 40-42 Plasminogen, 7 Poisson-Boltzmann method, 42 Polar residues, 46, 47 ~" Polyethylene glycol, 36 Polypeptides, viral, 144-145 Positioning contacts, in DNA recognition, 101 Post-translational modification, 120 Potentiometric titration, 13-14, 42, 43 Precipitation, of soluble proteins, 35 Proline residues, in T4 lysozyme, 46 Promoters, 74 Protease inhibitors, 2 Proteases, c~-Iytic, 2 Protein

aggregation, 23 conformation, 1 denatured, 6-10 engineering, 59, 85, 140 folding see folding hydrophobic interior, 47-48 metal-ion binding, 57-59 nucleotide binding, 61-65 stability, 35-38, 40--43, 46-49, 47 surface, 35-36 unfolded, 6-7, 28 viral, 143-148

Protein disulfide isomerase, 26 Protein kinases, 63-64 Protein-ligand interactions, 52 Protein-nucleic acid interactions, 55, 71-75, 78-81, 93, 143-148 Protein-solvent interactions, 36 Protoxin, Bacillus thuringiensis, 7 Pvull, 93

Raman spectroscopy of k repressor, 103 of viral DNA, 147

Random-coil configuration, 6 RecA protein, E. col/, 126 Redox potential, of PDI and thioredoxin, 27 Refolding rate, 4 Regulatory gene expression, 100, 116, 120 Regulatory proteins, medical interest, 63 Repressor--operator complexes, 95, 102 Repressors, 100, 101 102 7~-Resolvase, 62 Restriction endonucleases see endonucleases Retroviruses, DNA replication, 86 Rev protein, HIV, 132 Reverse transcriptase, 86 Rhodan.ese, 9, 23, 28 Rhodanese-GRoE, 24 Ribnucleoprotein domain, structure, 133 Ribonuclease H, 86, 87 Ribonuclease A, 7, 21, 30, 41 Ribonuclease T1, 22, 41, 85 Ribosomal proteins, 133 RNA

binding, 65 circular, 85

enzymatic activity, 131 protein-binding sites, 131 secondary and tertiary structure, 131 transfer, 138-141

RNA plant viruses, 143-144 RNA polymerase, 73, 74, 79, 131 RNA-protein interactions, 131-135 Rossman fold, 138 Rotamase see peptidyl prolyl isomerase Rubisco, 28, 29

S-values, 13-14 Salt bridges, 41, 48 Salting-out see precipitation Scattering techniques, 37 Scissors grip model, 119, 120 SecB, E. co/i, 30 Secondary structure

formation and stability, 13-18 of molten globules, 8 of RNA, 131 in unfolded proteins, 1

Selex method, 132 Serine tRNA synthetase, E. coil, 138 Serpins, 2 Serratia marcescens, endonuclease, 89 Side-chain conformations, of molten globules, 8 Side-chain interactions, 14, 16-17, 49 Signallin~ intercellular, 116 Signature sequences, of aminoacyl tRNAs, t38 Sinai, 93 Small nuclear ribonucleoproteins, 133 Solvent effects, on protein stability, 3, 35-38 Spl, 71 Specificity, in leucine zippers, 116-121 Spectral editing, 52, 53 SSB protein, E. coli, 124 Staphylococcal nuclease, 6, 21, 30, 41, 47, 84-85 Steric exclusion, 36 Steric hindrance, 47 Steroid hormone receptors, 58 Stopped-flow measurements, 21, 22 Structures

of aminoacyl tRNA synthetases, 138, 140-141 of catabolite gene activator protein, 100-101 of endonucleases, 93 of parvovirus, 145-146 of protein-DNA complexes, 71 of protein-ligand complexes, 3 of ribonucleoprotein domain, 133 of ribonuclease H, 86 of staphylococcal nuclease, 84-85 of TBSV, 143 of zinc fingers, 109-112

Substitutions, tolerance to, 46 Substrate analogues, 85 Superosmolytes, 37 Superoxide dismutase, mutant, 48 Surface residues, and protein stability, 48

Tat protein, HIV, 132 Tertiary structure

Index to subjects

of molten globules, 8 of RNA, 131

Tetrahymena thermophila, high-mobility-group proteins, 81 Therapeutic importance, of protein-nucleic acid

interactions, 143 Thermus thermophilus, thermophilic chaperonins, 28 Thioredoxin, 26, 41, 47, $4 Thioredoxin reductase, 61-62 Three-component interactions, 37-38, 48, 72 Time scale, of protein folding, 21 Tobacco mosaic virus, 147 Tomato bushy stunt virus, 143 Total charge effects, 41 Transcription, 80, 131 Transcription activation, 74-75, 120, 124 Transcription factors, 71, 109, 112, 116 Transition state, in unfolding, 2 Transport proteins, superfamily, 63 Trimethylamine dehydrogenase, 65 Troponin C, 57 Trypsin inhibitor (BPTI), 2, 22, 48, 54 Trypsin tRNA synthetase, mammalian, 138 Tryptophan residues

in folding of dihydrofolate reductase, 22 genetic insertion, 9 nuclear polarization experiments, 7 in ribonuclease H, 86

Tryptophan synthetase, E. coil, 8 Turnip crinkle virus, 144 Tyrosine residues

nuclear polarization experiments, 7 in P1 nuclease, 87

Tyrosyl tRNA synthetase, Bacillus stearothermophilus, 138

U1 A, 133 Ubiquitin, NMR studies, 8 Unfolded state, 4 Unfolding, energetics, 42

Valyl tRNA synthetase, E. co/i, 141 Van t'Hoff equation, 37 Viruses

helical, 147 spherical, 143-147

Water, bound, 54 Writhe, of DNA, 74-75

X-ray studies of chromatin, 80 of endonudease V, 88 of fd gene 5 protein, 125 of leucine zipper, 118, 120 of ligand binding, 3 of nuclear hormone receptors, 111-112 of nucleosomes, 79 of ribonudease H, 86 of ribonudeoprotein, 134 of staphylococcal nuclease, 85 of virus particles, 143 of zinc fingers, 109

Xenopus

Index Io subjects

5S RNA gene, 79 transcription factor IliA, 109

Yeast aminoacyl tRNA synthetases, 138-140

transcription factor, Mat~2, 100

Zif268, 71 Zif-DNA complex, 110 Zinc, bindin& 4, 58, 86--87 ~

ssDNA-binding proteins, 127 Zinc fingers, 4, 55, 57, 58, 71, 109-112


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