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  • Biochemistry and Biotechnology  (16,218)
  • Physics  (10,646)
  • Nuclear reactions  (4,460)
  • Capillary electrophoresis
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  • 1
    Electronic Resource
    Electronic Resource
    A study of the pollution of the Aries River (Romania) using capillary electrophoresis as analytical technique (2000)
    Springer
    Environmental geology 39 (2000), S. 1372-1384 
    Details
    ISSN: 1432-0495
    Keywords: Key words Aries River ; Capillary electrophoresis ; Mining effluent ; Romania
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  This paper examines two issues, the extensive pollution occurring in the Aries River, NW Romania, as a result of unchecked discharge of mining effluents into the river system, and the suitability of capillary electrophoresis (CE) as an analytical method for investigations into water chemistry. The results confirm the first objective by providing details on the pollution of the Aries River and its geochemical system and demonstrate the usefulness of CE. In its upper reaches, the river system is characterized by high contents of SO4 2– as a direct result of acid mine effluents and the oxidation of sulphide minerals on mine dumps as well as inflows from settling ponds. Although continuous dilution by natural branch waters and natural water-rock interaction reduces the pollution to some extend, the total level of SO4 2– remains above European averages. The waters of the Aries River, by comparison, contain contents of Cu2+ and Zn2+ up to 100 times higher than those of unpolluted river water.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002540000168
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  • 2
    Electronic Resource
    Electronic Resource
    Time-dependent interactions of platinum(II) complexes with 5′-GMP under simulated physiological conditions studied by capillary electrophoresis (2000)
    Springer
    JBIC 5 (2000), S. 498-504 
    Details
    ISSN: 1432-1327
    Keywords: Key words Cisplatin ; Nucleoside monophosphates ; Capillary electrophoresis ; Platinum complexes ; Matrix-assisted laser-desorption ionization mass spectrometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The binding behaviour as well as the time-dependent reaction of five platinum(II) complexes with 5′-GMP have been investigated by capillary electrophoresis under simulated physiological conditions referred to chloride concentration, pH and temperature. Different amine ligands influenced the binding properties towards 5′-GMP and resulted in different half-times of the overall reaction. Complexes with bidentate ligands reacted faster with the monophosphate compared to complexes with monodentate ligands. Complexes consisting of two monodentate hydroxyethylamine ligands reacted very slowly owing to a competitive intramolecular reaction of the hydroxyethyl residues, which was proven by NMR investigations. Reducing the number of hydroxyethyl residues increased the half-times of the reactions. Moreover, the major adducts formed with 5′-GMP were identified by MALDI-MS analysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050010
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  • 3
    Electronic Resource
    Electronic Resource
    Hemolymph ion composition and volume changes in the supralittoral isopod Ligia pallasii Brandt, during molt (2000)
    Springer
    Journal of comparative physiology 170 (2000), S. 329-336 
    Details
    ISSN: 1432-136X
    Keywords: Key words Calcium ; Capillary electrophoresis ; Hemolymph volume ; Isopod ; Molting
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract We analyzed ion composition and volume of the hemolymph of Ligia pallasii in four different stages of the molt cycle using capillary electrophoresis and 3H-inulin. The main ions in the hemolymph were Na+, K+, Mg2+, Ca2+, and Cl−. The Ca2+concentration increased significantly during the molt by 47% from intermolt to intramolt and by 37% from intermolt to postmolt, probably due to resorption of Ca2+ from the cuticle and sternal CaCO3 deposits. The K+ concentration increased significantly by 20% during molt. The hemolymph volume normalized to the dry mass of the animals decreased by 36% from intermolt to late premolt. This was due to a reduction in the hemolymph volume and to an increase in dry mass of the animals during premolt. A sudden increase in the hemolymph volume occurring between late premolt and intramolt served to expand the cuticle. Since the Na+, K+, Mg2+, and Cl− concentrations did not change significantly from late premolt to intramolt, the increase in hemolymph volume suggests an uptake of seawater rather than freshwater.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003600000108
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  • 4
    Electronic Resource
    Electronic Resource
    Separation of Enantiomers of Drugs by Capillary Electrophoresis with Permethyl-gamma-Cyclodextrin as Chiral Solvating Agent (2000)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 23 (2000), S. 413-429 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; enantiomer separation ; chiral drugs ; TM-γ-cyclodextrin ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---High-throughput screening is a promising new approach in analytical chemistry. Within the framework of an extended screening program (The German-Chinese Drug Screening Program), the enantioseparation of 86 drugs was investigated by capillary zone electrophoresis in the presence of the chiral solvating agent (CSA) octakis-(2,3,6-tri-O-methyl)-γ-cyclodextrin (TM-γ-CD). By this means, 15 drugs could be separated into enantiomeric pairs. Approximate measures for the degree of interaction (migration retardation factor, Rm) and for the degree of enantiomer recognition (migration separation factors, αm) revealed intriguing patterns that were compared with those found for native γ-cyclodextrin (γ-CD). Although there is a distinct influence of the analyte structure on the electrophoretic data, interpretation remains difficult. Most remarkably, permethylation of γ-CD leads neither to a higher affinity nor to better chiral recognition, in contrast to the findings with α-CD.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Simultaneous Determination of Organic Acids in Wine Samples by Capillary Electrophoresis and UV Detection: Optimization with Five Different Background Electrolytes (2000)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 23 (2000), S. 647-652 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; UV detection ; organic acids ; background electrolyte optimization ; wine ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---A simple technique is described for the routine capillary electrophoretic determination of organic acids in wine samples. Several aromatic and non-aromatic compounds, including phthalic acid, benzoic acid, sorbic acid, boric acid, and phosphate, were evaluated as background electrolytes in order to obtain the highest resolution and detection sensivity. Factors that affect capillary electrophoretic separation such as the concentration and pH of the background electrolyte (BGE), the concentration of the electroosmotic flow modifier (EOF), and methanol addition to the electrolyte were investigated systematically. Tartaric, malic, succinic, acetic, and lactic acids were determined simultaneously in approximately six minutes using an electrolyte containing 3 mM phosphate and 0.5 mM myristyltrimethylammonium bromide (MTAB) as electroosmotic flow modifier at pH 6.5. This method is quantitative, with recoveries in the 90-102% range and linear up to 50 mg L-1. The precision is better than 1% and the procedure shows the appropriate sensibility, with detection limits between 0.015 and 0.054 mg L-1. The proposed method was successfully employed for the determination of organic acids in wine samples by direct sample injection after appropriate dilution and filtration.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Optimization analysis by capillary electrophoresis of thiamine in meat: comparison with high perfomance liquid chromatography (1999)
    Springer
    European food research and technology 209 (1999), S. 355-359 
    Details
    ISSN: 1438-2385
    Keywords: Key words Meat ; Thiamine ; Capillary electrophoresis ; High performance liquid chromatography
    Source: Springer Online Journal Archives 1860-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract  A new capillary electrophoresis (CE) method for the analysis of thiamine in meat is proposed. Samples were submitted to acidic and enzymatic hydrolysis and the extracts were purified using ethanol and an ion exchange column. The thiamine content was determined by CE using 100 mM sodium tetraborate, 50 mM sodium phosphate (pH 7.6), 50 mM sodium dodecyl sulphate and 10% isopropyl alcohol as a separation buffer solution. The analysis was carried out at 15 kV and 50  °C in a 70 cm effective length× 75 μm i.d. fused-silica capillary using on-column UV detection at 254 nm and 7 s injection time (27 nl injection volume). The results obtained by CE for thiamine contents in meat were compared to those obtained by HPLC using an ion-pair reverse phase column with post-column derivatization and fluorescence detection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002170050509
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  • 7
    Electronic Resource
    Electronic Resource
    Cisplatin-resistant bladder carcinoma cells: enhanced expression of metallothioneins (1999)
    Springer
    Urological research 27 (1999), S. 157-163 
    Details
    ISSN: 1434-0879
    Keywords: Key words Transitional cell carcinoma ; Cisplatin resistance ; Cross-resistance ; Methotrexate ; Metallothioneins ; Capillary electrophoresis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Cisplatin is one of the most potent cytotoxic drugs and in chemotherapy has ameliorated numerous tumors. Nevertheless, resistance to cisplatin is a problem that is encountered in the chemotherapy of urologic tumors, especially transitional cell carcinomas. In order to improve definition of the mechanisms of cisplatin-resistance we established a series of cisplatin-resistant sublines from the cell line RT 112 in increasing concentrations of cisplatin. The most resistant subline CP3 is approximately 10 times more resistant than the parental line and shows a 10-fold cross-resistance against methotrexate, whereas vinblastine and doxorubicin are equally effective in the parental and sublines. Combined treatment of CP3 cells with cisplatin and buthionine sulfoximine (BSO) does not result in enhanced cell kill, thereby ruling out glutathione as a resistance mechanism. However, in comparison with parental cells, CP3 cells are about 1.5 times more resistant against cadmium. On the protein level, the cisplatin-resistant cells reveal an enhanced expression of metallothionein II (MTII), but not MTI, suggesting that the cisplatin resistance we observed in these sublines is at least partly mediated by MTII. These sublines will in the future serve as valuable tools for the analysis of cisplatin resistance, especially in view of metallothionein-mediated resistance mechanisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002400050103
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  • 8
    Electronic Resource
    Electronic Resource
    Nonaqueous capillary electrophoresis for the analysis of selected tropane alkaloids in a plant extract (1999)
    Springer
    Chromatographia 49 (1999), S. 54-60 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Micellar electrokinetic capillary chromatography ; Nonaqueous media ; Tropane alkaloids ; Hyoscyamine and scopolamine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The potential of nonaqueous capillary electrophoresis has been investigated for the separation of structurally similar tropane alkaloids. The effects of the organic solvent and of electrolyte composition on separation selectivity, migration times, and efficiency are described. The addition of trifluoroacetic acid to the separation buffer was found beneficial for manipulation of the order of migration of the two positional isomers littorine and hyoscyamine. Replicate injections under nonaqueous conditions gave migration time and peak area data of excellent precision. The application of the optimized conditions to the analysis of hyoscyamine and scopolamine in genetically transformed root cultures ofDatura candida x D. aurea is presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467187
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  • 9
    Electronic Resource
    Electronic Resource
    Determination of total iron binding capacity of serum by capillary electrophoresis (1999)
    Springer
    Chromatographia 49 (1999), S. 71-74 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Serum analysis ; Total iron binding capacity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A capillary electrophoresis (CE) technique for determining total iron binding capacity (TIBC) of serum has been developed. The optimum serum pretreatment involves the following major steps: at first, saturate serum transferrin with Fe+3; then, dissociate them completely after removing excess unbound Fe. Finally, complex the released iron with phenanthroline, a chromophore, to make suitable for the CE analysis. Ammonium acetate (pH=5.0) was used as CE background electrolyte solution. In this system, a good linear correlation coefficient was maintained over the range 0.5≈10 μM (r=0.9979,n=12). Seven adult serum samples were studied and the TIBC parameters measured. In the present system, 10≈30 μL serum is sufficient for determination. The study shows that the CE technique described is a powerful method for rapid, efficient, sensitive and reliable analysis and hence particularly suitable for clinical application.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467190
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  • 10
    Electronic Resource
    Electronic Resource
    Nonaqueous capillary electrophoresis for the analysis of labile pharmaceutical compounds (1999)
    Springer
    Chromatographia 49 (1999), S. S7 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Nonaqueous electrolytes ; N-Methylformamide ; UV-detection ; Pyridinyl-methyl-sulfinyl-benzimidazoles
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A screening method using nonaqueous capillary electrophoresis (NACE) has been developed for purity analysis of pyridinyl-methyl-sulfinyl-benzimidazoles (PMSB). Eight different polar organic solvents were tested as background electrolytes.N-Methylformamide (NMF) was found to have the best properties in respect of both electrophoretic behavior and high solubility of five different model compounds. Optimization of the CE separation with regard to the effects of addition of various electrolyte modifiers is reported. An additional feature of amide solvents, rarely utilized in CE, is their intrinsic basic nature; this is of particular interest for analysis of compounds such as the PMSB, the degradation of which is acid-catalyzed. It is shown here that these compounds are stable at room temperature for weeks in NMF solution. Results from quantitative application of the NACE method were highly precise (typically 1.8%RSD for normalized peak area); linearity was good and detection limit in drug purity determination was low (∼0.05 area % relative to the drug compound).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02468970
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  • 11
    Electronic Resource
    Electronic Resource
    Head-column field-amplified sample stacking in binary-system capillary electrophoresis: The need for the water plug (1999)
    Springer
    Chromatographia 49 (1999), S. S12 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Field-amplified sample stacking ; Water plug ; Drugs in biological fluids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Strategies to improve the sensitivity of drug monitoring in microliter amounts of biological fluids by capillary electrokinetic methods are currently being explored in our laboratory. Head-column field-amplified sample stacking is the most effective method of sensitivity enhancement—this approach is robust and highly reproducible when applied correctly. For analysis of opioids as standards or in plasma extracts by binary capillary electrophoresis with ethylene glycol, the data presented in this work unambiguously demonstrate that the water plug initially inserted at the column inlet is essential for establishing a steady current during separation, and thus the highest reproducibility. Internal calibration shows thatRSD imprecision values otherwise up to approximately 30% are reduced to values significantly below 10%. The water plug also results in higher detector responses at elevated solute levels (≥100 ng mL−1) and leads to increased sensitivity when the sample (standards and extracts of body fluids) is dissolved in water. The water plug does not, however, furnish higher sensitivity in the analysis of opioids as standards or in plasma extracts that are prepared in the optimized sample solvent or buffer. The optimum length of the water plug cannot, furthermore, be obtained merely by dipping the capillary inlet into water (insertion of water by capillary action). The water zone obtained in this way must be elongated by approximately 0.6 mm by deliberate hydrodynamic introduction of additional water from a different vial. These head-column field-amplified sample-stacking conditions are shown in operation on two different commercial instruments. As an illustration, data are presented depicting the analysis of dihydrocodeine and nordihydrocodeine in plasma and urine specimens of individuals to which dihydrocodeine was administered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02468971
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  • 12
    Electronic Resource
    Electronic Resource
    Capillary gel electrophoresis of nucleic acids in pluronic F127 copolymer liquid crystals (1999)
    Springer
    Chromatographia 49 (1999), S. S65 
    Details
    ISSN: 1612-1112
    Keywords: Review ; Capillary electrophoresis ; DNA ; Oligonucleotides ; Pluronic polymers ; Liquid crystals ; Micelles
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The liquid crystalline gel phases of solutions of Pluronic F127, a triblock copolymer, were recently introduced as an alternative to disordered solutions of random coil polymers as replaceable media for capillary gel electrophoresis (CGE). Pluronic F127, from BASF, is a copolymer of poly(ethylene oxide) and poly(propylene oxide) with the approximate formula (EO)106 (PO)70 (EO)106. Polymer chains aggregate into spherical micelles in aqueous solutions, with poly(propylene oxide) chains creating a hydrophobic core surrounded by brushes of hydrated poly(ethylene oxide) tails. Crowding at high concentrations promotes ordering of micelles. Solutions in the range of about 14–24 % polymer are self-supporting, gel-like cubic liquid crystals at 25–30°C, but when cooled they become low viscosity liquids that are easily loaded into capillaries. This article reviews applications of Pluronic F127 media for capillary gel electrophoresis separations of nucleic acids of several types including oligonucleotides, double stranded DNA fragments, and supercoiled plasmid DNAs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02468978
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  • 13
    Electronic Resource
    Electronic Resource
    Peptide characterization by CE-ESI-MS with orthogonal spray (1999)
    Springer
    Chromatographia 49 (1999), S. S73 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Electrospray-ionization ; Mass spectrometry ; Orthogonal spray ; Peptides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Capillary electrophoresis (CE) with tandem UV and MS detection is increasingly being used for the analysis of complex mixtures. Here the analysis of peptides by CE-ESI-MS with a fully automated system is described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02468979
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  • 14
    Electronic Resource
    Electronic Resource
    Separation of the enantiomers of four chiral drugs by neutral cyclodextrin-mediated capillary zone electrophoresis (1999)
    Springer
    Chromatographia 49 (1999), S. 411-414 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Chiral separation ; Neutral cyclodextrins ; Clorprenaline and other chiral drugs
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Neutral cyclodextrin (CD)-modified capillary zone electrophoresis (CZE) has been applied to the chiral separation of four basic drugs— clorprenaline, benzhexol, esmolol and terazosin. Selector screening and concentration optimization experiments were performed. The resolution was 3.9 for clorprenaline, 2.3 for benzhexol, 3.1 for esmolol and 1.2 for terazosin when the running electrolyte was 60 mM hydroxypropyl-β-CD, 15 mM heptakis (2,3,6-Tri-O-methyl)-β-CD, 60 mM γ-CD and 60 mM heptakis (2,6-di-O-methyl)-β-CD, respectively, in 50 mM, pH 2.5 sodium phosphate buffer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467615
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  • 15
    Electronic Resource
    Electronic Resource
    Characterization of the transmembrane serine receptor by capillary zone electrophoresis (1999)
    Springer
    Chromatographia 49 (1999), S. 28-34 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Membrane proteins ; Serine receptor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Capillary zone electrophoresis (CZE) was applied to the characterization of the transmembrane serine receptor in biosynthetic samples. The serine receptor, otherwise known as Tsr (taxis to serine and repellents), is a ∼ 60,000 Dalton intrinsic membrane protein whose periplasmic domain (ligand binding domain) reversibly binds the amino acid serine. In general, the electrophoresis of intrinsic membrane proteins is difficult due to severe solubility problems and adsorption which occurs during the electrophoretic run. This is due to the tendency of these types of proteins to undergo aggregation, self-aggregation and precipitation in aqueous environments. The addition of percentage levels of the surfactant, sodium dodecyl sulfate (SDS), to a tetraborate run buffer was shown to be effective both in enhancing the solubility of intact Tsr and in preventing the adsorption of intact Tsr to the fused-silica capillary wall during electrophoretic analysis. Critical separation parameters such as run buffer concentration, surfactant concentration and surfactant type were optimized to give the best separation profiles.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467183
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  • 16
    Electronic Resource
    Electronic Resource
    Evaluation of coelectroosmotic capillary zone electrophoresis for the rapid analysis of twelve aromatic sulphonate compounds (1999)
    Springer
    Chromatographia 49 (1999), S. 261-267 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Coelectroosmotic flow ; Osmotic modifiers ; Aromatic sulphonate compounds ; Organic solvents
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Coelectroosmotic capillary zone electrophoresis (CZE) has been investigated as a means of rapid analysis of twelve aromatic sulphonate compounds. The main factors affecting reversal of electroosmotic flow (EOF)—type of osmotic modifier and concentration-were studied. Two types of osmotic modifier, an alkylammonium salt (cetyltrimethylammonium bromide, CTAB) and a cationic polyelectrolyte (hexadimentrine bromide, HDB) were investigated. The composition of the running buffers was optimized according to the characteristics of each osmotic modifier. A concentration of HDB as low as 0.0001% (w/v) was used successfully to provide a stable and reversed EOF.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467554
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  • 17
    Electronic Resource
    Electronic Resource
    Column wall modifications using polyethylene oxide for capillary electrophoresis of ribonucleotides (1999)
    Springer
    Chromatographia 49 (1999), S. 299-305 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Column technology ; Deactivation ; Polyethyleneoxides ; Ribonucleotides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary In this study, a variety of fused silica capillaries with different combinations and sequences of treatments with HMDS and polyethylene oxide were prepared in order to develop an optimized column modification method for analysis of ribonucleotides. The 12 most common ribonucleotides (UTP, CTP, ATP, GTP, UDP, CDP, ADP, GDP, UMP, CMP, AMP, and GMP) in human cells were used as test solutes. Column performance measurements, including electroosmotic flow (EOF), solute migration speed and retention, column efficiency, peak shape, and resolution were investigated. By analyzing solute migration speed and retention of various hydrophilic/hydrophobic solutes, the column wall effects (EOF and adsorption) can be distinguished. This analysis method can give guidance in optimizing polymer coating properties (hydrophilicity/hydrophobicity) for CE columns. By studying the performance of these columns after various surface treatments, we were able to improve the separation of ribonucleotides from real samples to within 16 minutes with high efficiency and stability (over 300 analyses) using columns first deactivated with hexamethyldisilazane, and then coated with polyethylene oxide.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467560
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  • 18
    Electronic Resource
    Electronic Resource
    Allele typing of short tandem repeats by capillary electrophoresis (1999)
    Springer
    International journal of legal medicine 113 (1999), S. 26-32 
    Details
    ISSN: 1437-1596
    Keywords: Key words STRs ; Capillary electrophoresis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Law
    Notes: Abstract Capillary electrophoresis with laser-induced fluorescence was applied to the analysis of six STRs and the amelogenin sex test with the purpose of verifying accuracy and precision of the sizing method with the GS500 internal standard. Sequenced dye-labeled, PCR-amplified alleles from amelogenin, HumVWA31, HumTH01, HumF13A01, HumFIBRA, D21S11 and HumCSF1PO loci were run several times on the same capillary and on multiple capillaries and the offset of computer-measured fragment sizes from the expected molecular weights was calculated and analysed. All loci except D21S11 showed a poor degree of accuracy. Precision results from run-to-run and day-to-day injections displayed a maximum standard deviation (SD) 〉 0.15 nt for HumVWA31, HumF13A01, D21S11 and HumFIBRA, although the maximum range of calculated sizes in multiple runs was lower than 1 basepair. No variation in precision was observed according to the quality of the DNA template. Allele typing by comparison with allelic ladders for each locus is recommended.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004140050274
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  • 19
    Electronic Resource
    Electronic Resource
    Experimentation with Chiral CE: The Application of Two Chiral Selectors and Partial Filling with Chiral Selector (1999)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 22 (1999), S. 33-38 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; chiral separation ; negatively charged chiral selectors ; capillary filling methods ; dual systems ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Data on the use of two chiral selectors, namely 18-crown-6 tetracarboxylic acid and a negatively charged cyclodextrin derivative (sulfated-β-cyclodextrin or carboxymethyl-β-cyclodextrin), in the same background electrolyte are presented. The use of such dual systems has a considerable influence on the resolution, as illustrated for the separation of tryptophan derivatives. Reduction of the consumption of chiral selector without significant loss in resolution was obtained by only partly filling the capillary and applying a run buffer without selector. This is illustrated for the chiral separation of tryptophan hydroxamate and the diastereomeric and enantiomeric separation of the dipeptide α/b-AspPhe-OMe.
    Additional Material: 5 Ill.
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  • 20
    Electronic Resource
    Electronic Resource
    Optimization and Parameter Study for Chiral Separation by Capillary Electrophoresis (1999)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 22 (1999), S. 449-453 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; experimental design ; cyclodextrin ; chiral separation ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Orthogonal design and uniform design were used for the optimization of separation of enantiomers using 2,6-di-O-methyl-β-cyclodextrin (DM-β-CD) as a chiral selector by capillary zone electrophoresis. The concentration of DM-β-CD, buffer pH, running voltage, and capillary temperature were selected as variable parameters, their different effects on peak resolution were studied by the design methods. It was concluded that orthogonal design offers a rapid and efficient means for testing the importance of individual parameters and for determining the optimum operating conditions. However, for a large number of both factors and levels, uniform design is more efficient. The effect of addition of methanol and citric acid buffer on the separation of enantiomers was also examined.
    Additional Material: 5 Ill.
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  • 21
    Electronic Resource
    Electronic Resource
    Determination of Dihydroxybenzenes in Plastic Food Packaging Materials and in Food Simulating Liquids Using Capillary Electrophoresis (1999)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 22 (1999), S. 39-42 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; CE ; chemical migration ; food contact plastics ; dihydroxybenzenes ; packaging ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---A capillary electrophoresis method has been developed to determine 1,2-dihydroxybenzene and 1,3-dihydroxybenzene in the food simulants distilled water, 3% acetic acid, 15% ethanol, and olive oil. Both substances, used as monomers and additives to make food packaging plastics, could be analyzed within 15 min. The 1,4-dihydroxybenzene isomer was unretained and eluted with the electroosmotic flow, and so the CE method can give only a semi-quantitative estimate of this isomer if it is present as a migrant. The analytical recovery for the 1,2- and 1,3-isomers from spiked simulants was good at 87% to 98% except for 1,2-dihydroxybenzene which could only be recovered to the extent of 58% from olive oil. Calibration graphs were linear and the limit of detection for each substance was 0.6 mg/kg, which is well below migration limits for these substances. It is concluded that CE offers a rapid and reliable analysis for the control of migration from plastics intended for food contact which employ 1,2-dihydroxybenzene or 1,3-dihydroxybenzene during manufacture, and offers a screening method for 1,4-dihydroxybenzene migration.
    Additional Material: 4 Ill.
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  • 22
    Electronic Resource
    Electronic Resource
    Capillary Electrophoretic Identification of Commercial Gelling Agents (1999)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 22 (1999), S. 79-82 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; thickeners ; monosaccharides ; PMMA capillaries ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Gelling agents based on polysaccharides have become extremely important in the food industry. As more and more products like soups and sauces have become available in lyophilized form, thickeners have to be added to give a controlled consistency to the finished meal. A capillary electrophoretic method has been developed to investigate the monosaccharide composition of hydrolyzed thickeners. 2-Aminoanthracene was used as a derivatization reagent to allow sensitive fluorescence detection. This system was applied to a set of standard thickeners as well as to food samples.
    Additional Material: 5 Ill.
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  • 23
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    Electronic Resource
    At-Line Solid-Phase Extraction Coupled to Capillary Electrophoresis: Determination of Amphoteric Compounds in Biological Samples (1999)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 22 (1999), S. 183-187 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; interfacing ; sample treatment ; serum ; solid-phase extraction ; sulfonamides ; urine ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---No abstract
    Additional Material: 4 Ill.
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  • 24
    Electronic Resource
    Electronic Resource
    A Fast and Reliable Method for the Determination of Anionic Impurities and Neutralization Agents in Electrodipcoats Using Capillary Zone Electrophoresis with Conductivity Detection (1999)
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 22 (1999), S. 297-299 
    Details
    ISSN: 0935-6304
    Keywords: Capillary electrophoresis ; conductivity detection ; inorganic anions ; organic acids ; electrodipcoats ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---No abstract
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 25
    Electronic Resource
    Electronic Resource
    Determination of carbon disulphide in air as xanthogenate by ion chromatography and capillary electrophoresis (1999)
    Springer
    Chromatographia 49 (1999), S. 678-680 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Ion chromatography ; Carbon disulphide in air ; Alkyl xanthogenates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A simple and sensitive method is presented for the measurement of carbon disulphide in air without interference from other gaseous sulphides. The procedure is based on the collection of CS2 in an ethanolic solution of KOH, where it is converted to potassium ethyl xanthogenate (PEX). The latter is determined by high-performance ion chromatography (HPIC) and/or capillary zone electrophoresis (CZE). Laboratory and field determination of detection limit, reproducibility and linearity, and specific advantages over other gas chromatographic and wet chemical methods, are discussed. Quantitative measurements of CS2 in air can be performed after sampling for 1 h with limits of detection as low as 15 ppb by HPIC and ca 0.1 ppm by CZE.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02466911
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  • 26
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    Electronic Resource
    Capillary electrophoretic analysis of anions in a multi-anion background electrolyte: Interference of system peaks (1999)
    Springer
    Chromatographia 49 (1999), S. 309-316 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Anions ; System peaks
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary This study deals with the simultaneous analysis of UV-transparent anions by capillary electrophoresis with indirect UV-detection. With a background electrolyte (BGE) based on UV-absorbing chromate and UV-transparent borate, the interference of system peaks with those of sample anions (chloride, sulfate, citrate, phosphate) is shown. The existence of such system peaks, and their position in relation to the peaks of the sample anions, are explained on the basis of the eigenpeak theory proposed by Poppe [1]. With this BGE the system peaks were manifested as a negative peak followed by a positive peak. Their shapes depended on the relative mobilities of the analyte and BGE anions and their areas depended on the amount of sample. The mobility of the system peak depends on the borate/boric acid mobility, which was adjusted by slight variation of the pH close to its pK a-pH is the key factor governing system-peak mobility. When the locations of the system peaks are optimized, the quantification of citrate can be achieved; this was successfully used for determination of anions in milk.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467562
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  • 27
    Electronic Resource
    Electronic Resource
    Capillary electrophoresis study of human serum albumin binding to basic drugs (1999)
    Springer
    Chromatographia 49 (1999), S. 343-346 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Frontal analysis ; Binding constants ; Basic drugs ; Human serum albumin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The applicability of capillary electrophoresis/frontal analysis (CE/FA) for determining the binding constants of the drugs propranolol (PRO) and verapamil (VER) to human serum albumin (HSA) was investigated. After direct hydrodynamic injection of a drug-HAS mixture solution into a coated capillary (32 cm × 50 μm i.d.), the basic drug was eluted as a zonal peak with a plateau region under condition of phosphate buffer (pH 7.4; ionic strength 0.17) at 12 kV positive running voltage. The unbound drug concentrations measured from the plateau peak heights had good correlation coefficients,r〉0.999. Employing the Scatchard plot, the Klotz plot and nonlinear regression, the drug protein binding parameters, the binding constant and the number of binding sites on one protein molecule, were obtained. The binding constant obtained was compared to a reported equilibrium dialysis result and they are basically in good agreement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467568
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  • 28
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    Electronic Resource
    Separation of nucleoside mono-, di- and triphosphates by capillary electrophoresis via cadmium complexation (1999)
    Springer
    Chromatographia 49 (1999), S. 379-384 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Nucleotides ; Cadmium complexation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The CE separation of twelve nucleotides (5′-mono-, di-, triphosphates of adenosine, guanosine, cytidine and uridine) was improved by adding cadmium ion to the ammonium citrate/citric acid buffer (pH 5, ionic strength 100 mM). Cadmium ion acts as a complexing agent for some nucleotides (ATP, CTP, GTP, UTP, GDP). In order to accelerate the separation, the electroosmotic flow was reversed by flushing the fused-silica capillary with 0.2 % aqueous solution of the polycationic surfactant hexadimethrine bromide. A good separation of the twelve nucleotides studied was then achieved on a dynamically coated capillary in less than 5 min by using an ammonium citrate/citric acid buffer (pH 5, ionic strength 100 mM) to which 2 mM cadmium ion has been added. High peak efficiencies were obtained (210 000 theoretical plates) and the resolution between two adjacent peaks was always greater than 1.5.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467610
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  • 29
    Electronic Resource
    Electronic Resource
    Quantitative and selective analysis of lactose by capillary electrophoresis (1999)
    Springer
    Chromatographia 49 (1999), S. 406-410 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Pharmaceutical Analysis ; Lactose
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A CE method has been validated for the analysis of batches of lactose used as a pharmaceutical raw material. This method was shown to be selective for lactose and was found to be quantitative. The separation was achieved due to on-capillary chelation of the lactose with borate ion. The resulting complex was detected at 195nm. An internal standard is employed to improve injection precision and detector linearity. A system peak occurred in the separation and was systematically investigated to show that it was not sample related. The method was validated and successfully submitted to regulatory authorities and is now in routine use in a number of our quality control laboratories.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467614
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  • 30
    Electronic Resource
    Electronic Resource
    Investigation of derivatization of oligosaccharides by means of reductive amination for separation in capillary electrophoresis (1999)
    Springer
    Chromatographia 49 (1999), S. 666-670 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Anion exchange chromatography ; Carbohydrate ; Derivatization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The derivatization process of malto-oligosaccharides by means of reductive amination for the subsequent separation by capillary electrophoresis (CE) is investigated. Aminonaphthalene-disulfonic acid was used as derivatization agent for this purpose. The molecular weight distribution found by CE differed significantly from that measured by anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD). While the proportion of maltodextrins with lower molecular weight was higher in CE than in HPAEC-PAD, the opposite hold for oligomers with higher molecular weights. An investigation of the derivatization process provided strong indications that degradation of higher molecular weight oligomers could be the reason for these differences. The derivatization process was optimized with respect to minimal degradation expressed as the peak area ratio of maltose to maltoheptaose at simultaneously maximal reaction rate expressed as the peak area of maltoheptaose by using a Box-Behnken design. It was found that only a compromise allowed both sufficient reaction turnover and low degradation of the oligomers. This technique could be employed successfully to analyze maltodextrins and oligomannans in coffee.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02466909
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  • 31
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    Electronic Resource
    Recent advances in the clinical applications of capillary electrophoresis (1999)
    Springer
    Chromatographia 49 (1999), S. S79 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Diagnosis of myelomatosis ; Metabolic disorders ; Serum proteins ; CE-MS
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary CE is used both for routine clinical analysis and for specialized clinical investigations. CE analysis of serum proteins is fast and reliable, with immunosubtraction for identification of immunoglobulins. This method was used to show the appearance of a pathological protein many years prior to the diagnosis of myelomatosis. CE with diode array detector and CE-MS were suitable for the diagnosis of a number of metabolic disorders. Online analyte concentrators are sometimes required to enhance the concentration sensitivity of CE.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02468980
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  • 32
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    Electronic Resource
    CE-MS-MS of peptides using a novel orthogonal CE ESI sprayer and ion trap MS (1999)
    Springer
    Chromatographia 49 (1999), S. S87 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Electrospray-ionization ; Ion trap mass spectrometry ; Separation of compounds
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Capillary electrophoresis (CE) coupled with mass spectrometry (MS) has proven a powerful alternative to conventional chromatographic separation techiques. Here the analysis of various compounds with a novel CE ESI sprayer and an ion trap mass analyzer is described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02468983
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  • 33
    Electronic Resource
    Electronic Resource
    Ultrasound in vascular pathologies (1998)
    Springer
    European radiology 8 (1998), S. 849-857 
    Details
    ISSN: 1432-1084
    Keywords: Key words: Ultrasound ; Physics ; Vascular studies ; Vascular pathologies ; Ultrasonic contrast agents ; Clinical applications
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract. The choice of the optimal ultrasonic frequency for vascular studies is determined by the required resolution and penetration. Anatomical real-time two-dimensional imaging and blood flow studies provide complementary information. Intravascular scanning allows high-frequency ultrasound to be used, with correspondingly good spatial resolution. Contrast resolution is degraded by beam side lobes and the limited dynamic range of the ultrasonic pulse. The physics of ultrasonic scattering by blood, pulsed Doppler and duplex scanning and colour flow imaging performances determines the limits of clinical applications. Contrast agents enhance the echogenicity of blood, improving sensitivity and, through second harmonic detection, suppressing solid tissue echoes. Three-dimensional display, with segmentation by the presence of the flow signal, facilitates spatial perception. Clinical applications in vascular pathologies are summarised.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003300050482
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  • 34
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    Electronic Resource
    Sample preparation for photometric determination of histamine in foodstuffs compared with capillary electrophoresis (1998)
    Springer
    Zeitschrift für Lebensmittel-Untersuchung und -Forschung 206 (1998), S. 246-250 
    Details
    ISSN: 1431-4630
    Keywords: Key words Histamine ; Capillary electrophoresis ; Photometric determination ; Liquid liquid extraction ; Solid phase extraction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract  To determine levels of histamine, two methods were used, photometry in conjunction with two sample clean-up procedures, and capillary zone electrophoresis (CZE). The two sample clean-up procedures used were liquid liquid extraction (LLE) with n-butanol and solid phase extraction (SPE). Using CZE, the separation of histamine from the matrix was good. The other method, photometry, represents a classic and simple method, that can be employed for in situ measurement of histamine. We found that it was necessary to clean up the samples prior to photometry; if this was not done, the recorded levels of histamine were higher than those determined by CZE. In order to determine levels of histamine, both of these rapid tests were applied to ten different foodstuffs. The levels of histamine measured using photometry following either LLE or SPE were compared. The results indicated that photometry is a suitable method for the measurement of histamine, although the sample solutions have to be purified by either LLE or SPE. Samples do not need to be cleaned up before CZE because there is no interference between histamine and attendant material. Both sample clean-up procedures were applied to the following foodstuffs: tomatoes, sauerkraut, tuna, leaf spinach, cream spinach, white wine and mackerel. The differences of the measured values vary between 3% and 18% for LLE and 6% and 27% for SPE. For the other foodstuffs, such as beef, beer and non-alcoholic beer, only one sample clean-up procedure is suitable. LLE used for beef and beer leads to differences in measured levels of histamine between 18% and 50%, respectively, whereas SPE used for non-alcoholic beer leads to differences of 20%.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002170050252
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  • 35
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    Electronic Resource
    Mixing in Stars and the Evolution of the 3He Abundance (1998)
    Springer
    Space science reviews 84 (1998), S. 199-206 
    Details
    ISSN: 1572-9672
    Keywords: Nuclear reactions ; Nucleosynthesis ; Abundances ; Stars:Evolution ; Interior ; Rotation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We first recall the observational and theoretical facts that constitute the so-called 3He problem. We then review the chemical anomalies that could be related to the destruction of 3He in red giants stars. We show how a simple consistent mechanism can lead to the destruction of 3He in low mass stars and simultaneously account for the low 12C/13C ratios and low lithium abundances observed in giant stars of different populations. This process should both naturally account for the recent measurements of 3He/H in galactic HII regions and allow for high values of 3He observed in some planetary nebulae. We propose a simple statistical estimation of the fraction of stars that may be affected by this process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1005027519798
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  • 36
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    Electronic Resource
    Capillary zone electrophoretic separation of basic proteins and drugs using guaran as a buffer modifier (1998)
    Springer
    Chromatographia 47 (1998), S. 219-224 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Beta-blockers ; Protein separation ; Drug separation ; Guaran ; Buffer modifier
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Guaran, a neutral polysaccharide, has been used as a buffer modifier to improve the separation of basic proteins and drugs. Migration reproductibility, peak shape and efficiency were improved when 0.1% guaran was added to the buffer. The concentration of guaran, ionic strength, and pH of buffer solution were optimized to obtain the optimum separation of proteins. Possible separation efficiencies of 700,000 plates per meter were obtained for test proteins. The relative standard deviation (% RSD) of the migration time of all test proteins was less than 0.5%. Improved separation of β-blockers was also observed when guaran was added to the buffer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02466585
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  • 37
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    Electronic Resource
    Characterization of humic-like substances in airborne particulate matter by capillary electrophoresis (1998)
    Springer
    Chromatographia 47 (1998), S. 619-624 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Airborne particles ; Humic-like substances
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A considerable fraction of the refractory organic carbon in airborne particulate matter is to be attributed to humic-like substances (HULIS). Such atmospheric HULIS isolated from different air dust samples by a microscale extraction procedure were characterized by capillary electrophoresis (CE). For fractionation of HULIS the working conditions of the CE system were optimized using a borate buffer (pH 8.2), polyacrylamide (PAA) coated, fused-silica capillary and polyethylene glycol as sieving modifier. Using CE under optimized conditions, HULIS produced electropherograms showing well resolved and reproducible signals.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467443
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  • 38
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    Electronic Resource
    Rapid and reproducible capillary electrophoretic separation of double-stranded DNA fragments in a simple methyl cellulosic sieving system (1998)
    Springer
    Chromatographia 47 (1998), S. 125-134 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; DNA fragments ; Cellulose derivatives ; Sieving cellulose matrix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A rapid, robust and reproducible method providing excellent separation performance and simplicity using a 0.5% MC-4000 methyl cellulosic sieving medium in DB-1 coated capillaries has been developed. The method is suitable for qualitative comparison of DNA restriction profiles for fragments in the size range 100–1000 base pairs (bp). Efficiencies up to 8.5 million plates/m (1057 bp fragment) were recorded. Peak resolution of 6 bp (291/297 bp, 335/341 bp) and 4 bp (238/242 bp, 341/345 bp) was achieved. In addition, 1 bp partial resolution of 123/124 bp and 298/297 bp was obtained. Run-to-run (n=15), day-to-day (n=4), and capillary-to-capillary (n=3) variations of 0.1–0.2% RSD, 0.3–0.5% RSD, and 0.1–0.3% RSD, respectively, were observed. The MC-4000 sieving matrix was found to be better than hydroxypropyl methyl cellulose and hydroxypropyl cellulose, in terms of both performance and stability in the DB-1 coated capillaries. The efficiency and resolution in DB-WAX capillaries were inferior to those obtained in DB-1 capillaries. The commercially available DB-1 capillaries were stable for months in the sieving medium at pH 8.3 and could be regenerated to provide high efficiency after accidental current breaks.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02466571
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  • 39
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    Electronic Resource
    Capillary electrophoretic study of the complexation of nucleotides with magnesium and calcium ions (1998)
    Springer
    Chromatographia 48 (1998), S. 739-744 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Nucleotides ; Inorganic cations ; Complexation with Mg and Ca
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The complexation equilibrium between nucleotides (ATP, ADP) and inorganic cations (Mg2+, Ca2+) has been studied by capillary electrophoresis. The equilibrium constant and the stoichiometry of nucleotide-inorganic cation complexes can be deduced from the dependence of the electrophoretic mobility of each nucleotide on the negative logarithm of the inorganic cation concentration. The experimental values of complexation constants determined by CE compare favorably with those in the literature. As expected, Mg2+ forms more stable complexes with ATP (logK=2.30 and 4.10 at pH 5 and 8, respectively) than with ADP (logK=1.92 and 3.15 at pH 5 and 8, respectively). In the pH range 4–8, the stoichiometry of ADP-Mg2+ and ADP-Ca2+ complexes is always 1∶1 whereas that of the complexes between these cations and ATP depends on pH-hence ATP-Mg2+ and ATP-Ca2+ complexes have 1∶1 stoichiometry at pH 5 and 1∶2 at pH 8.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467641
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  • 40
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    Electronic Resource
    Peak recognition imitating human judgement (1998)
    Springer
    Chromatographia 48 (1998), S. 331-346 
    Details
    ISSN: 1612-1112
    Keywords: Peak integration ; Baseline determination ; Quantitation ; Capillary electrophoresis ; Chromatography
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Peak integration is still a major source of error in analytical techniques such as chromatography (LC and GC), aapillary electrophoresis (CE), spectrosocpy, and electrochemistry. If the baseline is complex, e.g. because of matrix effects, or if the peak shape is irregular, e.g. because of peak tailing, the results are often not satisfactory when classical procedures are used. These shortcomings arise because of the stepwise appearance of the chromatogram. An algorithm that copies the human method of considering baseline and peaks as a whole has already been introduced. Here the use of a straight line as a baseline model led to an improvement in several instances. The baseline is, however, usually not exactly straight and rigid. A baseline model with flexible properties is more advantageous. Thus the smoothing cubic spline function is applied in this work. Here the rigidity can be controlled by use of a parameterp k. The prediction interval of the spline is used for iterative distinction between baseline and peak regions. Afterwards straightforward optimization of the peak boundaries is applied. More than 50 series of consecutive injections of the same sample (n=40 on average) were used to test the performance of this procedure. The same raw data have been integrated by means of the algorithm described here and by use of commercially available software. The reproducibility of the main component peak are within the series was taken as a measure of integration quality. Typically the new procedure reducesRSD % by approximately 33% (e.g. from 1.5% to 1.0%). The improvement is even more impressive for difficult samples with complex matrices, e.g. blood plasma or polymer excipients. for such samples improvements of up to a factor of 6 are obtained.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467701
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  • 41
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    Electronic Resource
    Experimental design methodologies to optimize the CE separation of epinephrine enantiomers (1998)
    Springer
    Chromatographia 48 (1998), S. 395-401 
    Details
    ISSN: 1612-1112
    Keywords: Capillary electrophoresis ; Enantiomers ; Epinephrine ; Experimental designs ; Optimization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A capillary electrophoretic method using a chiral selector was optimized by experimental design for the enantioresolution of epinephrine enantiomers. Two β-cyclodextrins derivatives, namely heptakis-2,6-di-O-methyl-β-cyclodextrin and carboxy-methyl-β-cyclodextrin, respectively neutral and charged, were used as chiral selectors employing an uncoated capillary. By using a statistical experimental design in which all factors are varied at the same time, it was possible to optimize the method with regard to the resolution between peaks and the two migration times. A fractional factorial design and a central composite design were used. A compromise between conflicting goals, such as maximization of resolution and minimization of analysis time, was found by means of a desirability function D. Balancing these goals against each other, the most acceptable solution to the problem was found and the optimized method gave a fast separation with complete resolution between the adrenaline enantiomers. The response surfaces obtained confirmed the robustness of the method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02467710
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  • 42
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    Electronic Resource
    Characterization of receptors with a new negative image: Use in molecular docking and lead optimization (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 321-336 
    Details
    ISSN: 0887-3585
    Keywords: surface characterization ; DOCK ; structure-based molecular design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design. Proteins 30:321-336, 1998. © 1998 Wiley-Liss, Inc.
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    Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 352-356 
    Details
    ISSN: 0887-3585
    Keywords: myoglobin ; nitric oxide ; ligand binding ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 Å resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112°. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the Nε atom of histidine64 is located 2.8 Å away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold. Proteins 30:352-356, 1998. © 1998 Wiley-Liss, Inc.
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    A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 372-380 
    Details
    ISSN: 0887-3585
    Keywords: protein modeling ; crystal structure ; conformation change ; prediction ; mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge. The method attempts to allow for natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGK and a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex. Proteins 30:372-380, 1998. © 1998 Wiley-Liss, Inc.
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    Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 388-400 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; free energy perturbation ; thermodynamics integration ; spherical solvent boundary potential ; cell multipole method ; Nosé-Hoover equation ; component analysis ; chymotrypsin inhibitor 2 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nosé-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, ΔΔG. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nosé-Hoover algorithm and Kirkwood reaction field are also discussed. Proteins 30:388-400, 1998. © 1998 Wiley-Liss, Inc.
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    Proteolysis as a probe of thermal unfolding of cytochrome C (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 435-441 
    Details
    ISSN: 0887-3585
    Keywords: cytochrome c ; thermal unfolding ; proteolysis ; proteinase K ; thermolysin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent hydrogen exchange experiments on native cytochrome c implicate a sequential unfolding pathway in contrast to a simple two-state process. We have studied the heat-induced unfolding of this protein by using spectroscopic measurements to detect changes in conformation and proteolytic enzyme digestion to identify regions of the protein that are labile. Several spectroscopic profiles were monitored: CD at 222 nm, a measurement of secondary structure change in the protein, the absorbance at 280 nm, involving the local environment of Trp 59, and absorbance at 420 nm, the Soret band of the heme. The apparent Tm values for these probes differ, consistent with an unfolding pathway containing intermediates. The limited digestion by proteinase K is consistent with population of an intermediate state in unfolding. We find a single strong region of cleavage at low temperature with retention of structure in each fragment. Proteins 30:435-441, 1998. © 1998 Wiley-Liss, Inc.
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    Crystallographic and spectroscopic characterization of a molecular hinge: Conformational changes in bothropstoxin I, a dimeric Lys49-phospholipase A2 homologue (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 442-454 
    Details
    ISSN: 0887-3585
    Keywords: venom toxin ; protein-membrane interaction ; X-ray diffraction ; spectroscopy ; quaternary structural change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bothropstoxin I (BthTX-I) from the venom of Bothrops jararacussuis a myotoxic phospholipase A2 (PLA2) homologue which, although catalytically inactive due to an Asp49→Lys substitution, disrupts the integrity of lipid membranes by a Ca2+-independent mechanism. The crystal structures of two dimeric forms of BthTX-I which diffract X-rays to resolutions of 3.1 and 2.1 Å have been determined. The monomers in both structures are related by an almost perfect twofold axis of rotation and the dimer interfaces are defined by contacts between the N-terminal α-helical regions and the tips of the β-wings of partner monomers. Significant differences in the relative orientation of the monomers in the two crystal forms results in “open” and “closed” dimer conformations. Spectroscopic investigations of BthTX-I in solution have correlated these conformational differences with changes in the intrinsic fluorescence emission of the single tryptophan residues located at the dimer interface. The possible relevance of this structural transition in the Ca2+-independent membrane damaging activity is discussed. Proteins 30:442-454, 1998. © 1998 Wiley-Liss, Inc.
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    Structure-based design of model proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 10-20 
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    ISSN: 0887-3585
    Keywords: protein design ; lattice model ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model. Proteins 31:10-20, 1998. © 1998 Wiley-Liss, Inc.
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    Modelling repressor proteins docking to DNA (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 535-549 
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    ISSN: 0887-3585
    Keywords: docking ; protein-DNA ; prediction ; structure ; base recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The docking of repressor proteins to DNA starting from the unbound protein and model-built DNA coordinates is modeled computationally. The approach was evaluated on eight repressor/DNA complexes that employed different modes for protein/ DNA recognition. The global search is based on a protein-protein docking algorithm that evaluates shape and electrostatic complementarity, which was modified to consider the importance of electrostatic features in DNA-protein recognition. Complexes were then ranked by an empirical score for the observed amino acid /nucleotide pairings (i.e., protein-DNA pair potentials) derived from a database of 20 protein/DNA complexes. A good prediction had at least 65% of the correct contacts modeled. This approach was able to identify a good solution at rank four or better for three out of the eight complexes. Predicted complexes were filtered by a distance constraint based on experimental data defining the DNA footprint. This improved coverage to four out of eight complexes having a good model at rank four or better. The additional use of amino acid mutagenesis and phylogenetic data defining residues on the repressor resulted in between 2 and 27 models that would have to be examined to find a good solution for seven of the eight test systems. This study shows that starting with unbound coordinates one can predict three-dimensional models for protein/DNA complexes that do not involve gross conformational changes on association. Proteins 33:535-549, 1998. © 1998 Wiley-Liss, Inc.
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    Influence of protein structure databases on the predictive power of statistical pair potentials (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 139-149 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; statistical potentials ; protein structure database ; assessing protein models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139-149, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: Conformational influence of an engineered disulfide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 128-138 
    Details
    ISSN: 0887-3585
    Keywords: antibody ; antitumor ; single chain Fv ; variable domains ; X-ray crystallography ; protein structure ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A recombinant Fv construct of the B1 monoclonal antibody that recognizes the LewisY-related carbohydrate epitope on human carcinoma cells has been prepared. The Fv is composed of the polypeptide chains of the VH and VL domains expressed independently and isolated as inclusion bodies. The Fv is prepared by combining and refolding equimolar amounts of guanidine chloride solubilized inclusion bodies. The Fv is stabilized by an engineered interchain disulfide bridge between residues VL100 and VH44. This construct has a similar binding affinity as that of the single-chain construct (Benhar and Pastan, Clin. Cancer Res. 1:1023-1029, 1995). The B1 disulfide-stabilized Fv (B1dsFv) crystallizes in space group P6122 with the unit cell parameters a = b = 80.1 Å, and c = 138.1 Å. The crystal structure of the B1dsFv has been determined at 2.1-Å resolution using the molecular replacement technique. The final structure has a crystallographic R-value of 0.187 with a root mean square deviation in bond distance of 0.014 Å and in bond angle of 2.74°. Comparisons of the B1dsFv structure with known structures of Fv regions of other immunoglobulin fragments shows closely related secondary and tertiary structures. The antigen combining site of B1dsFv is a deep depression 10-Å wide and 17-Å long with the walls of the depression composed of residues, many of which are tyrosines, from complementarity determining regions L1, L3, H1, H2, and H3. Model building studies indicate that the LewisY tetrasaccharide, Fuc-Gal-Nag-Fuc, can be accommodated in the antigen combining site in a manner consistent with the epitope predicted in earlier biochemical studies (Pastan, Lovelace, Gallo, Rutherford, Magnani, and Willingham, Cancer Res. 51:3781-3787, 1991). Thus, the engineered disulfide bridge appears to cause little, if any, distortion in the Fv structure, making it an effective substitute for the B1 Fab. Proteins 31:128-138, 1998. Published 1998 Wiley-Liss, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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    Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 150-159 
    Details
    ISSN: 0887-3585
    Keywords: photosynthetic reaction center ; bacteriorhodopsin ; cytochrome C oxidase ; zipper ; packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Membrane-embedded protein domains frequently exist as α-helical bundles, as exemplified by photosynthetic reaction centers, bacteriorhodopsin, and cytochrome C oxidase. The sidechain packing between their transmembrane helices was investigated by a nearest-neighbor analysis which identified sets of interfacial residues for each analyzed helix-helix interface. For the left-handed helix-helix pairs, the interfacial residues almost exclusively occupy positions a, d, e, or g within a heptad motif (abcdefg) which is repeated two to three times for each interacting helical surface. The connectivity between the interfacial residues of adjacent helices conforms to the knobs-into-holes type of sidechain packing known from soluble coiled coils. These results demonstrate on a quantitative basis that the geometry of sidechain packing is similar for left-handed helix-helix pairs embedded in membranes and coiled coils of soluble proteins. The transmembrane helix-helix interfaces studied are somewhat less compact and regular as compared to soluble coiled coils and tolerate all hydrophobic amino acid types to similar degrees. The results are discussed with respect to previous experimental findings which demonstrate that specific interactions between transmembrane helices are important for membrane protein folding and/or oligomerization. Proteins 31:150-159, 1998. © 1998 Wiley-Liss, Inc.
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    Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 2-33 
    Details
    ISSN: 0887-3585
    Keywords: chevron plot ; energy landscape ; folding funnel ; kinetic trap ; lattice models ; non-Arrhenius behavior ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple-exponential and two-state (single-exponential) kinetics. Experiments show that two-state relaxation times have “chevron plot” dependences on denaturant and non-Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple-exponental behavior, whereas the HP+ model gives more smooth funnels and two-state behavior. Multiple-exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two-state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process. Proteins 30:2-33, 1998. © 1998 Wiley-Liss, Inc.
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    Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 49-60 
    Details
    ISSN: 0887-3585
    Keywords: kohonen network ; mitochondrial processing peptidase (MPP) ; mitochondrial intermediate peptidase (MIP) ; neural network ; protein import ; sequence motif ; mitochondrial targeting ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps. Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs. Neural networks were used to define local sequence features around precursor cleavage sites. Proteins 30:49-60, 1998. © 1998 Wiley-Liss, Inc.
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    Don Caspar, TMV, and protein-protein interactions (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 109-112 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    A hybrid sequence approach to the paracelsus challenge (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 136-143 
    Details
    ISSN: 0887-3585
    Keywords: protein design ; protein structure ; circular dichroism ; trifluoroethanol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Inspired by the Paracelsus Challenge of Rose and Creamer (Proteins 19:1-3, 1994), we have designed a protein sequence that is 50% identical to an all-helical protein but is intended to fold into a largely β-sheet structure. Rather than attempt a de novo design, our strategy was to construct a hybrid sequence based on a helical “parent” protein (434 Cro) and a “target” protein with the desired fold (the B1 domain of protein G). The hybrid sequence (Crotein-G) is 50% identical to 434 Cro but is also 62% identical to the B1 domain of protein G. We also created a variant of Crotein-G (ZCrotein-G) that contains a potential His3Cys1 zinc binding site. At low protein concentrations and in the presence of 20% 2,2,2-trifluoroethanol (TFE) (v/v), the circular dichroism spectra of the designed proteins are distinct from that of 434 Cro and similar to that of the B1 domain of protein G. However, the proteins fail to denature in a cooperative manner. Furthermore, aggregation occurs at moderate protein concentrations or in the absence of TFE. Addition of zinc to ZCrotein-G does not promote structure formation. In summary, 434 Cro has been altered to something that may resemble the B1 domain of protein G, but the protein does not adopt a native structure. Proteins 30:136-143, 1998. © 1998 Wiley-Liss, Inc.
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    Monte Carlo simulation of denaturation of adsorbed proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 168-176 
    Details
    ISSN: 0887-3585
    Keywords: denaturation kinetics ; irreversible conformational changes ; metastable states ; folding temperature ; lattice model ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Denaturation of model proteinlike molecules at the liquid-solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types (A and B) is assumed to be adsorbed in the native folded state (a 3 × 3 × 3 cube) so that one of its sides is in contact with the surface. The details of the denaturation kinetics are found to be slightly dependent on the choice of the side, but the main qualitative conclusions hold for all the sides. In particular, the kinetics obey approximately the conventional first-order law at T 〉 Tc (Tc is the collapse temperature for solution). With decreasing temperature, below Tc but above Tf (Tf is the folding temperature for solution), deviations appear from the first-order kinetics. For the most interesting temperatures, that is, below Tf, the denaturation kinetics are shown to be qualitatively different from the conventional ones. In particular, the denaturation process occurs via several intermediate steps due to trapping in metastable states. Mathematically, this means that (i) the transition to the denatured state of a given molecule is nonexponential, and (ii) the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of values of this rate constant (different values of kr correspond to the transitions to the altered state via different metastable states). Proteins 30:168-176, 1998. © 1998 Wiley-Liss, Inc.
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    Monte Carlo simulation of the kinetics of protein adsorption (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 177-182 
    Details
    ISSN: 0887-3585
    Keywords: adsorption ; irreversible conformational changes ; denaturation rate constant ; kinetic control ; diffusion control ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Adsorption of proteins occurs via diffusion toward the interface, actual adsorption, and subsequent irreversible conformational changes resulting in denaturation of the native protein structure. The conventional kinetic models describing these steps are based on the assumption that the denaturation transitions obey the first-order law with a single value of the denaturation rate constant kr. Meanwhile, recent Monte Carlo simulations indicate that, in general, the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of this rate constant (physically, different values of kr correspond to the transitions to the altered state via different metastable states). We have calculated the kinetics of irreversible adsorption of proteins with and without distribution of the denaturation rate constant kr in the limits when protein diffusion in the solution is, respectively, rapid or slow. In both cases, the adsorption kinetics with distribution of kr are found to be close to those with a single-valued rate constant kr provided that the average value of kr in the former case is equal to kr for the latter case. This conclusion holds even for wide distributions of kr. The consequences of this finding for the fitting of global experimental kinetics on the basis of phenomenological equations are briefly discussed. Proteins 30:177-182, 1998. © 1998 Wiley-Liss, Inc.
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    Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 228-231 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; local vs. non-local interactions ; secondary structure prediction ; fragment matching algorithms ; PDB ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: One of the most important questions in the protein folding problem is whether secondary structures are formed entirely by local interactions. One way to answer this question is to compare identical subsequences of proteins to see if they have identical structures. Such an exercise would also reveal a lower limit on the number of amino acids needed to form unique secondary structures. In this context, we have searched the April 1996 release of the Protein Data Bank for sequentially identical subsequences of proteins and compared their structures. We find that identical octamers can have different conformations. In addition, there are several examples of identical heptamers with different conformations, and the number of identical hexamers with different conformations has increased since the previous PDB releases. These observations imply that secondary structure can be formed entirely by non-local interactions and that an identical match of up to eight amino acids may not imply structural similarity. In addition to the larger context of the protein folding problem, these observations have implications for protein structure prediction methods. Proteins 30:228-231, 1998. © 1998 Wiley-Liss, Inc.
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    Structural modeling of the complex between an acetylcholine receptor-mimicking antibody and its snake toxin antigen (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 249-263 
    Details
    ISSN: 0887-3585
    Keywords: antibody-antigen complex ; snake toxin ; protein docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The antibody Mα2-3 neutralizes the functional, acetylcholine receptor binding activity of its antigen, neurotoxin α, and exhibits several other properties in common with the receptor itself. We present here the results of calculations examining the three-dimensional structure of the toxin α:Mα2-3 complex. The antigen structure, determined by nuclear magnetic resonance spectroscopy,1 was docked to models of the variable fragment of the antibody combining site2 by using a method based on surface complementarity and maximization of buried surface area3,4 while taking into account the possibility of conformational change on complexation. Extensive experimental information on the location of the functional epitope was incorporated into the analysis and used to screen candidate geometries of the complex resulting from the modeling. Eight plausible structures that are in accord with the experimental data were derived. Common structural features of the models are discussed, and residues of the antibody-combining site that are expected to play important roles in complexation are identified. In particular, three epitope residues that, according to mutagenesis experiments, make particularly strong contributions to the binding, interact excentrically and do not make contact with the central loops of the combining site, L3 and H3. Proteins 30:249-263, 1998. © 1998 Wiley-Liss, Inc.
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    Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 287-294 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; side chain contact prediction ; lattice protein models ; CREB-binding protein ; KIX domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 Å. This is to be compared with the estimate of 12.9 Å that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). Proteins 30:287-294, 1998. © 1998 Wiley-Liss, Inc.
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    Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: Strategies and applications (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 74-89 
    Details
    ISSN: 0887-3585
    Keywords: mass spectrometry ; matrix-assisted laser desorption/ionization ; electrospray ; database searching ; gel electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The entire genomic DNA sequences of a number of prokaryotic and eukaryotic species are now available and many more, including the human genome, will be completed in the near future. The state-of-life of a cell at any given time, however, is defined by its protein composition, i.e., its proteome. Gel electrophoresis, mass spectrometry, and bioinformatics will be important tools for protein and proteome analysis in the post-genome era. Protein identification from electrophoretic gels by mass spectrometric peptide mapping or peptide sequencing combined with sequence database searching is established and has been applied to numerous biological systems. We describe current strategies and selected applications in molecular and cell biology. The next challenges are detailed structure/function analyses, which include studying the molecular composition of multiprotein complexes and characterization of secondary modifications of proteins. The advantages and limitations of a number of mass spectrometry-based strategies designed for microcharacterization of low amounts of protein from electrophoretic gels are discussed and illustrated by examples. Proteins Suppl. 2:74-89, 1998. © 1998 Wiley-Liss, Inc.
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    A fusion protein between serum amyloid A and staphylococcal nuclease - synthesis, purification, and structural studies (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 381-387 
    Details
    ISSN: 0887-3585
    Keywords: serum amyloid A ; fluorescence ; circular dichroism ; acute phase ; denaturation ; nuclease ; amyloidosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We developed a recombinant DNA system to overexpress a fusion protein between the small, minimally soluble acute phase serum protein, serum amyloid A (SAA), and the bacterial enzyme staphylococcal nuclease (SN). This fusion protein is very soluble and is immunoreactive to polyclonal anti-SAA antibodies. Tryptophan fluorescence shows smooth denaturation curves for the fusion protein in guanidinium HCl or potassium thiocyanate. Fluorescence also indicates that only a single tryptophan residue (of the four present) is accessible to iodide quenching and, presumably, is exposed on the surface of the fusion protein. Circular dichroism (CD) shows a significant signal indicating α-helix, which can be attributed to the SAA portion of the molecule; these are the first CD spectral data available for SAA. pH titration shows persistence of helix domains for the fusion protein at pH 3.0, in contrast to the denaturation of SN under the same conditions. (The entire fusion protein shows a random coil pattern below pH 3.0.) By exploiting the structural and solubility properties of SN, this fusion protein has provided the first structural data about SAA - the precursor of the amyloid deposits in secondary amyloidosis. This fusion protein should be useful for further physical and physiologic studies of SAA. Proteins 30:381-387, 1998. © 1998 Wiley-Liss, Inc.
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    The PDP: Past, present, and future (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 1-1 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Direct observation of an altered quaternary-structure transition in a mutant aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 383-390 
    Details
    ISSN: 0887-3585
    Keywords: time-resolved small-angle X-ray scattering ; allosterism ; domain closure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Time-resolved small-angle X-ray scattering (TR-SAXS) was used to monitor the structural changes that occur upon the binding of the natural substrates to a mutant version of the allosteric enzyme aspartate transcarbamoylase from Escherichia coli, in which the creation of a critical link stabilizing the R state of the enzyme is hindered. Previously, SAXS experiments at equilibrium showed that the structures of the unligated mutant enzyme and the mutant enzyme saturated with a bisubstrate analog are indistinguishable from the T and R state structures, respectively, of the wild-type enzyme (Tauc et al., Protein Sci. 3:1998-2004, 1994). However, as opposed to the wild-type enzyme, the combination of one substrate, carbamoyl phosphate, and succinate, an analog of aspartate, did not convert the mutant enzyme into the R state. By using TR-SAXS we have been able to study the transient steady-state during catalysis using the natural substrates rather than the nonreactive substrate analogs. The steady-state in the presence of saturating amount of substrates is a mixture of 60% T and 40% R structures, which is further converted entirely to R in the additional presence of ATP. These results provide a structural explanation for the reduced cooperativity observed with the mutant enzyme as well as for the stimulation by ATP at saturating concentrations of substrates. They also illustrate the crucial role played by domain motions and quaternary-structure changes for both the homotropic and heterotropic aspects of allostery. Proteins 31:383-390, 1998. © 1998 Wiley-Liss, Inc.
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    Structural investigation of C4b-binding protein by molecular modeling: Localization of putative binding sites (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 391-405 
    Details
    ISSN: 0887-3585
    Keywords: complement control protein ; protein modeling ; blood coagulation ; C4b-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one β-chain and seven α-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its α-chains and with protein S through its β-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP α-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the α-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions. Proteins 31:391-405, 1998. © 1998 Wiley-Liss, Inc.
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    Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 406-416 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; Brownian dynamics ; triose phosphate isomerase ; diffusion-control ; similarity index ; rate enhancement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate. Proteins 31:406-416, 1998. © 1998 Wiley-Liss, Inc.
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    Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 434-444 
    Details
    ISSN: 0887-3585
    Keywords: hinge ; structural change ; xylose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hingefind program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a ‘hinge-bending’ motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII. Proteins 31:434-444, 1998. © 1998 Wiley-Liss, Inc.
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    Interaction of human SRY protein with DNA: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 417-433 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; sex-determining region Y (SRY) protein ; high mobility group (HMG) box ; DNA-binding proteins ; DNA bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been conducted to study the interaction of human sex-determining region Y (hSRY) protein with DNA. For this purpose, simulations of the hSRY high mobility group (HMG) domain (hSRY-HMG) with and without its DNA target site, a DNA octamer, and the DNA octamer alone have been carried out, employing the NMR solution structure of hSRY-HMG-DNA complex as a starting model. Analyses of the simulation results demonstrated that the interaction between hSRY and DNA was hydrophobic, just a few hydrogen bonds and only one water molecule as hydrogen-bonding bridge were observed at the protein-DNA interface. These two hydrophobic cores in the hSRY-HMG domain were the physical basis of hSRY-HMG-DNA specific interaction. They not only maintained the stability of the complex, but also primarily caused the DNA deformation. The salt bridges formed between the positive-charged residues of hSRY and phosphate groups of DNA made the phosphate electroneutral, which was advantageous for the deformation of DNA and the formation of a stable complex. We predicted the structure of hSRY-HMG domain in the free state and found that both hSRY and DNA changed their conformations to achieve greater complementarity of geometries and properties during the binding process; that is, the protein increased the angle between its long and short arms to accommodate the DNA, and the DNA became bent severely to adapt to the protein, although the conformational change of DNA was more severe than that of the hSRY-HMG domain. The sequence specificity and the role of residue Met9 are also discussed. Proteins 31:417-433, 1998. © 1998 Wiley-Liss, Inc.
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    Density functional studies on herpes simplex virus type 1 thymidine kinase-substrate interactions: The role of Tyr-172 and Met-128 in thymine fixation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 453-459 
    Details
    ISSN: 0887-3585
    Keywords: quantum mechanical calculations ; substrate-enzyme interactions ; mutants ; functional role of amino acids ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The enzyme herpes simplex virus type 1 thymidine kinase (HSV1 TK) salvages thymidine into the DNA metabolism of the virus. In the active site, the thymine ring of the nucleoside binds in a pocket, formed by two residues, Tyr-172 and Met-128, in a sandwich-type orientation. To investigate the nature of the thymine-enzyme pocket interactions, we have carried out density functional theory calculations with gradient-corrected exchange-correlation functionals of models of the thymine-HSV1 TK adduct. Our calculations indicate that the role of Met-128 in the substrate fixation is purely steric and hydrophobic, while the substrate-Tyr-172 interaction is essentially electrostatic in nature. These findings are completely consistent with the available catalytic properties of mutants on the 128 position. Proteins 31:453-459, 1998. © 1998 Wiley-Liss, Inc.
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    Electrostatics, allostery, and activity of the yeast chorismate mutase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 445-452 
    Details
    ISSN: 0887-3585
    Keywords: chorismate mutase ; activity ; allosteric ; electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The predicted active site of chorismate mutase of baker's yeast Saccharomyces cerevisiae has been studied by continuum electrostatics, molecular surface/volume calculations, and molecular modeling. Our study shows that despite being subject to an allosteric transition, the enzyme's active-site pocket neither decreased in volume nor deformed significantly in shape between the active R state and the inactive T state. We find that the polar atmosphere in the pocket is responsible for the enzyme's affinity. A single amino acid, Glu23, can adequately account for the atmospheric variation. This residue swings into the active-site pocket from the R state to the T state. In the R state, Glu23 on helix H2 doubly pairs with Arg204 and Lys208 of H11, which is packed against H2. In the T state, a slide occurs between H11 and H2 such that Glu23 can no longer interact with Lys208 and competes with Asp24 for interacting with Arg204. Consequently, Glu23 is found in the T state to couple with Arg157, an active-site residue critical to substrate binding. The tandem sliding of H11 in both monomers profoundly changes the interactions in the dimer interface. The loop between H11 and H12 demonstrates the largest conformational change. Hence, we establish a connection between the allosteric transition and the activity of the enzyme. The conformational change in the transition is suggested to propagate into the active-site pocket via a series of polar interactions that result in polarity reversal in the active-site pocket, which regulates the enzyme's activity. Proteins 31:445-452, 1998. © 1998 Wiley-Liss, Inc.
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    Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 477-485 
    Details
    ISSN: 0887-3585
    Keywords: X-ray structure ; L-chain apoferritin ; metal binding sites ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 Å and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f′′ = 3.6 e-) of cadmium at 1.375 Å, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f′′ = 0.44 e-). Proteins 31:477-485, 1998. © 1998 Wiley-Liss, Inc.
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    The biology workbench - A seamless database and analysis environment for the biologist (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 1-2 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 39-48 
    Details
    ISSN: 0887-3585
    Keywords: antibody ; antigen ; electrostatics ; binding ; finite difference ; Poisson-Boltzmann ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The change in free energy of binding of hen egg white lysozyme (HEL) to the antibody HyHel-10 arising from ten point mutations in HEL (D101K, D101G, K96M, K97D, K97G, K97G, R21E, R21K, W62Y, and W63Y) was calculated using a combination of the finite difference Poisson-Boltzmann method for the electrostatic contribution, a solvent accessible surface area term for the non-polar contribution, and rotamer counting for the sidechain entropy contribution. Comparison of experimental and calculated results indicate that because of pKa shifts in some of the mutated residues, primarily those involving Aspartate or Glutamate, proton uptake or release occurs in binding. When this effect was incorporated into the binding free energy calculations, the agreement with experiment improved significantly, and resulted in a mean error of about 1.9 kcal/mole. Thus these calculations predict that there should be a significant pH dependence to the change in binding caused by these mutations. The other major contributions to binding energy changes comes from solvation and charge charge interactions, which tend to oppose each other. Smaller contributions come from nonpolar interactions and sidechain entropy changes. The structures of the HyHel-10-HEL complexes with mutant HEL were obtained by modeling, and the effect of the modeled structure on the calculations was also examined. “Knowledge based” modeling and automatic generation of models using molecular mechanics produced comparable results. Proteins 33:39-48, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase KAtomic coordinates have been deposited with the Protein Data Bank, Brookhaven National Laboratory. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 30-38 
    Details
    ISSN: 0887-3585
    Keywords: lactoferrin ; proteinase K ; complex, hydrolysis ; structure ; inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lactoferrin is an iron binding glycoprotein with a molecular weight of 80 kDa. The molecule is divided into two lobes representing the N-terminal and C-terminal halves of the polypeptide chain, each containing an iron binding site. The serine proteinases such as trypsin, chymotrypsin, and pepsin hydrolyze lactoferrin into two unequal halves while proteinase K divides this protein into two equal halves. In the first step of hydrolysis by proteinase K, the C- and N-lobes, each having a molecular weight of approximately 40 kDa, are generated. In the next step, the lobes are further hydrolyzed into small molecular weight peptides. The proteinase K isolated from the hydrolyzed product does not show enzymatic activity suggesting that the enzyme is inhibited. Furthermore, the hydrolysis experiments on N-lobe and C-lobe showed that the inhibitory fragment came from the C-lobe. The purified lactoferrin fragment was found to be a decapeptide with an amino acid sequence of H2N-Val-Ala-Gln-Gly-Ala-Ala-Gly-Leu-Ala-COOH. The complex formed between proteinase K and lactoferrin fragment was crystallized by microdialysis. The crystals belonged to the monoclinic space group P21with cell dimensions a = 44.4 Å, b = 38.6 Å, c = 79.2 Å, β = 105.8o and Z = 2. The crystal structure has been determined at 2.4 Å resolution. It has been refined to an R factor of 0.163 for 9044 reflections. The Lf-fragment forms several intermolecular interactions with proteinase K. The Ser-224 Oγ and His-57 Nε2 move away to a distance of 3.68 Å in the complex. In the crystal structure, Gln-3I (I indicates inhibitor i.e., lactoferrin fragment) is involved in a direct intermolecular interaction with a symmetry related proteinase K molecule through a strong hydrogen bond with Asp-254. The mode of intermolecular interactions in the complex conformational features of the enzyme and placement of the fragment with respect to the enzyme resemble with the molecular complex of proteinase K with its natural inhibitor PKI3 from wheat. Proteins 33:30-38, 1998. © 1998 Wiley-Liss, Inc.
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    Dictionary of recurrent domains in protein structures (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 88-96 
    Details
    ISSN: 0887-3585
    Keywords: fold classification ; substructures ; Dali ; protein families ; structural similarity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures. Proteins 33:88-96, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 97-106 
    Details
    ISSN: 0887-3585
    Keywords: antigenic peptides ; class I MHC molecules ; HLA-A2 complexes ; hydrogen bonds ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structures of class I major histocompatibility complex (MHC) molecules complexed with antigenic peptides revealed a network of hydrogen bonds between the charged amino- and carboxyl-termini of the peptides and conserved MHC residues at both ends of the peptide binding site. These interactions were shown to contribute substantially to the stability of class I MHC/peptide complexes by thermal denaturation studies using synthetic peptides in which either the amino- or carboxyl-terminal group is substituted by a methyl group. Here we report crystal structures of HLA-A*0201 complexed with these terminally modified synthetic peptides showing that they adopt the same bound conformation as antigenic peptides. A number of variations in peptide conformation were observed for the terminally modified peptides, including in one case, a large conformational difference in four central peptide residues that is apparently caused by the lattice contact. This is reminiscent of the way binding a T-cell receptor changed the conformation of central residues of an MHC-bound peptide. The structures determined identify which conserved hydrogen bonds are eliminated in terminally substituted peptides and suggest an increased energetic importance of the interactions at the peptide termini for MHC-peptide stability. Proteins 33:97-106, 1998. © 1998 Wiley-Liss, Inc.
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    AmbiPack: A systematic algorithm for packing of macromolecular structures with ambiguous distance constraints (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 26-42 
    Details
    ISSN: 0887-3585
    Keywords: intermolecular restraints ; solid-state NMR ; symmetric multimer ; branch and bound ; amyloid ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of β-amyloid (an ordered aggregate). Proteins 32:26-42, 1998. © 1998 Wiley-Liss, Inc.
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    Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 204-217 
    Details
    ISSN: 0887-3585
    Keywords: rotamer libraries ; energy minimization ; self consistent mean-field theory ; torsion space ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The ab initio folding problem can be divided into two sequential tasks of approximately equal computational complexity: the generation of native-like backbone folds and the positioning of side chains upon these backbones. The prediction of side-chain conformation in this context is challenging, because at best only the near-native global fold of the protein is known. To test the effect of displacements in the protein backbones on side-chain prediction for folds generated ab initio, sets of near-native backbones (≤ 4 Å Cα RMS error) for four small proteins were generated by two methods. The steric environment surrounding each residue was probed by placing the side chains in the native conformation on each of these decoys, followed by torsion-space optimization to remove steric clashes on a rigid backbone. We observe that on average 40% of the χ1 angles were displaced by 40° or more, effectively setting the limits in accuracy for side-chain modeling under these conditions. Three different algorithms were subsequently used for prediction of side-chain conformation. The average prediction accuracy for the three methods was remarkably similar: 49% to 51% of the χ1 angles were predicted correctly overall (33% to 36% of the χ1+2 angles). Interestingly, when the inter-side-chain interactions were disregarded, the mean accuracy increased. A consensus approach is described, in which side-chain conformations are defined based on the most frequently predicted χ angles for a given method upon each set of near-native backbones. We find that consensus modeling, which de facto includes backbone flexibility, improves side-chain prediction: χ1 accuracy improved to 51-54% (36-42% of χ1+2). Implications of a consensus method for ab initio protein structure prediction are discussed. Proteins 33:204-217, 1998. © 1998 Wiley-Liss, Inc.
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    Molecular dynamics simulations of human carbonic anhydrase II: Insight into experimental results and the role of solvation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 119-134 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; proton transfer ; enzyme catalysis ; mutations ; molecular mechanics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism. Proteins 33:119-134, 1998. © 1998 Wiley-Liss, Inc.
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    Sequence and structure conservation in a protein core (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 358-366 
    Details
    ISSN: 0887-3585
    Keywords: homologous proteins ; superfamilies ; sequence conservation ; protein structure ; protein evolution ; sequence-structure relationships ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In order to study structural aspects of sequence conservation in families of homologous proteins, we have analyzed structurally aligned sequences of 585 proteins grouped into 128 homologous families. The conservation of a residue in a family is defined as the average residue similarity in a given position of aligned sequences. The residue similarities were expressed in the form of log-odd substitution tables that take into account the environments of amino acids in three-dimensional structures. The protein core is defined as those residues that have less then 7% solvent accessibility. The density of a protein core is described in terms of atom packing, which is investigated as a criterion for residue substitution and conservation. Although there is no significant correlation between sequence conservation and average atom packing around nonpolar residues such as leucine, valine and isoleucine, a significant correlation is observed for polar residues in the protein core. This may be explained by the hydrogen bonds in which polar residues are involved; the better their protection from water access the more stable should be the structure in that position. Proteins 33:358-366, 1998. © 1998 Wiley-Liss, Inc.
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    Extraction of geometrically similar substructures: Least-squares and Chebyshev fitting and the difference distance matrix (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 320-328 
    Details
    ISSN: 0887-3585
    Keywords: structural similarity ; optimal superposition ; common substructure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In analysis, comparison and classification of conformations of proteins, a common computational task involves extractions of similar substructures. Structural comparisons are usually based on either of two measures of similarity: the root-mean-square (r.m.s.) deviation upon optimal superposition, or the maximal element of the difference distance matrix. The analysis presented here clarifies the relationships between different measures of structural similarity, and can provide a basis for developing algorithms and software to extract all maximal common well-fitting substructures from proteins.Given atomic coordinates of two proteins, many methods have been described for extracting some substantial (if not provably maximal) common substructure with low r.m.s. deviation. This is a relatively easy task compared with the problem addressed here, i.e., that of finding all common substructures with r.m.s. deviation less than a prespecified threshold. The combinatorial problems associated with similar subset extraction are more tractable if expressed in terms of the maximal element of the difference distance matrix than in terms of the r.m.s. deviation. However, it has been difficult to correlate these alternative measures of structural similarity. The purpose of this article is to make this connection.We first introduce a third measure of structural similarity: the maximum distance between corresponding pairs of points after superposition to minimize this value. This corresponds to fitting in the Chebyshev norm. Properties of Chebyshev superposition are derived.We describe relationships between the r.m.s. and minimax (Chebyshev) deviations upon optimal superposition, and between the Chebyshev deviation and the maximal element of the difference distance matrix. Combining these produces a relationship between the r.m.s. deviation upon optimal superposition and the maximal element of the difference distance matrix. Based on these results, we can apply algorithms and software for finding subsets of the difference distance matrix for which all elements are less than a specified bound, either to select only subsets for which the r.m.s.deviation is less than or equal to a specified threshold, or to select subsets that include all subsets for which the r.m.s. deviation is less than or equal to a threshold. Proteins 33:320-328, 1998. © 1998 Wiley-Liss, Inc.
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    Flexible docking using tabu search and an empirical estimate of binding affinity (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 367-382 
    Details
    ISSN: 0887-3585
    Keywords: ligand-protein docking ; molecular recognition ; tabu search ; empirical scoring function ; binding affinity prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This article describes the implementation of a new docking approach. The method uses a Tabu search methodology to dock flexibly ligand molecules into rigid receptor structures. It uses an empirical objective function with a small number of physically based terms derived from fitting experimental binding affinities for crystallographic complexes. This means that docking energies produced by the searching algorithm provide direct estimates of the binding affinities of the ligands. The method has been tested on 50 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. All water molecules are removed from the structures and ligand molecules are minimized in vacuo before docking. The lowest energy geometry produced by the docking protocol is within 1.5 Å root-mean square of the experimental binding mode for 86% of the complexes. The lowest energies produced by the docking are in fair agreement with the known free energies of binding for the ligands. Proteins 33:367-382, 1998. © 1998 Wiley-Liss, Inc.
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    Folding-unfolding energy change of a simple sphere model protein and an energy landscape of the folding process (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 408-416 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; potential energy curve ; two state model ; semi-empirical calculation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have calculated the free energy of a spherical model of a protein or part of a protein generated in the way of protein folding. Two spherical models are examined; one is a homogeneous model consisting of only one residue type - hydrophobic. The other is a heterogeneous model consisting of two residue types - strong hydrophobic and weak hydrophobic. Both models show a folding transition state, and the latter model reproduces the trend of the experimental folded-unfolded energy change. The heterogeneous model suggests that in the folding process of a protein of more than 70 residues, a specific region of the protein folds first to form a stable region, then the other residues follow the folding process. The energy landscape of folding of a small protein is approximately a funnel model, whereas a flatter energy landscape is suggested for larger proteins of more than 55-70 residues. Proteins 33:408-416, 1998. © 1998 Wiley-Liss, Inc.
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    Structural model for family 32 of glycosyl-hydrolase enzymes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 383-395 
    Details
    ISSN: 0887-3585
    Keywords: glycosidases ; protein structure prediction ; correlated mutations ; sequence space ; phylogenic relationships ; threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structural model is presented for family 32 of the glycosyl-hydrolase enzymes based on the beta-propeller fold. The model is derived from the common prediction of two different threading methods, TOPITS and THREADER. In addition, we used a correlated mutation analysis and prediction of active-site residues to corroborate the proposed model. Physical techniques (circular dichroism and differential scanning calorimetry) confirmed two aspects of the prediction, the proposed all-beta fold and the multi-domain structure. The most reliable three-dimensional model was obtained using the structure of neuraminidase (1nscA) as template. The analysis of the position of the active site residues in this model is compatible with the catalytic mechanism proposed by Reddy and Maley (J. Biol. Chem. 271:13953-13958, 1996), which includes three conserved residues, Asp, Glu, and Cys. Based on this analysis, we propose the participation of one more conserved residue (Asp 162) in the catalytic mechanism. The model will facilitate further studies of the physical and biochemical characteristics of family 32 of the glycosyl-hydrolases. Proteins 33:383-395, 1998. © 1998 Wiley-Liss, Inc.
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    Molecular dynamics simulations of epidermal growth factor and transforming growth factor-α structures in water (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 396-407 
    Details
    ISSN: 0887-3585
    Keywords: AMBER ; epidermal growth factor ; transforming growth factor-alpha ; conformation ; receptor binding ; domain movement ; weakly polar interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: AMBER v. 4.1 force field in 1.5 ns NPT molecular dynamics simulations of murine epidermal growth factor (mEGF), human epidermal growth factor (hEGF), and human transforming growth factor-α (hTGF-α) structures with explicit TIP3P solvation were used to investigate differences in backbone stability, changes in secondary structure, interdomain flexibility, and weakly polar interactions. Backbone root mean square deviations of sections of each peptide show that the most stable regions in mEGF and hEGF are the A-, B-, and C-loops, whereas the most stable regions in hTGF-α are the A- and B-loops. The secondary structure in the B-loops of mEGF and hEGF differ significantly from the nuclear magnetic resonance (NMR) structures of mEGF and hEGF. The position and type of turns in the B-loop of mEGF and hEGF increase the interstrand distance of the antiparallel β-sheets thereby disrupting their structure. The interdomain flexibility of simulated hTGF-α structure is greater than in either mEGF or hEGF. The φ, ψ dihedrals of hTGF-α occupy two distinct populations of phase space corresponding to either a C7eq or an α-helical conformation. This change in dihedral angle is stabilized by Phe15 with Arg42 and Phe17 with Arg42 N-π weakly polar interactions that are present only in hTGF-α but not in mEGF or hEGF. Proteins 33:396-407, 1998. © 1998 Wiley-Liss, Inc.
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    Analysis of domain motions by approximate normal mode calculations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 417-429 
    Details
    ISSN: 0887-3585
    Keywords: protein energy surface ; crambin ; lysozyme ; ATCase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The identification of dynamical domains in proteins and the description of the low-frequency domain motions are one of the important applications of numerical simulation techniques. The application of these techniques to large proteins requires a substantial computational effort and therefore cannot be performed routinely, if at all. This article shows how physically motivated approximations permit the calculation of low-frequency normal modes in a few minutes on standard desktop computers. The technique is based on the observation that the low-frequency modes, which describe domain motions, are independent of force field details and can be obtained with simplified mechanical models. These models also provide a useful measure for rigidity in proteins, allowing the identification of quasi-rigid domains. The methods are validated by application to three well-studied proteins, crambin, lysozyme, and ATCase. In addition to being useful techniques for studying domain motions, the success of the approximations provides new insight into the relevance of normal mode calculations and the nature of the potential energy surface of proteins. Proteins 33:417-429, 1998. © 1998 Wiley-Liss, Inc.
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    Helix-helix packing angle preferences for finite helix axes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 457-459 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger. Proteins 33:457-459, 1998. © 1998 Wiley-Liss, Inc.
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    A homology model for the human theta-class glutathione transferase T1-1 (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 444-454 
    Details
    ISSN: 0887-3585
    Keywords: hGSTT1-1 ; homology modeling ; menaphthyl sulfate ; dichloromethane ; dehalogenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A manual threading approach is used to model the human glutathione transferase T1-1 based on the coordinates of the related Theta class enzyme T2-2. The low level of sequence identity (about 20%), found in the C-terminal extension in conjunction with a relative deletion of about five residues makes this a challenging modeling problem. The C-terminal extension contributes to the active site of the molecule and is thus of particular interest for understanding the molecular mechanism of the enzyme. Manual docking of known substrates and non-substrates has implicated potential candidates for the T1-1 catalytic residues involved in the dehalogenation and epoxide-ring opening activities. These include the conserved Theta class residues Arg 107, Trp 115, and the conserved GSTT1 subclass residue His 176. Also, the residue at position 234 is implicated in the modulation of T1-1 activity with different substrates between species. Proteins 33:444-454, 1998. © 1998 Wiley-Liss, Inc.
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    Intersubunit hydrogen bond acts as a global molecular switch in Escherichia coli aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 430-443 
    Details
    ISSN: 0887-3585
    Keywords: pyrimidine biosynthesis ; protein crystallography ; allostery ; long-range interactions ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Tyr 165 in the catalytic subunit of Escherichia coli aspartate transcarbamoylase (ATCase, EC 2.1.3.2) forms an intersubunit hydrogen bond in the T state with Glu 239 in the 240s loop of a second catalytic subunit, which is broken in the T to R transition. Substitution of Tyr 165 by Phe lowers substrate affinity by approximately an order of magnitude and alters the pH profile for enzyme function. We have determined the crystal structure of Y165F at 2.4 Å resolution by molecular replacement, using a wild-type T state structure as the probe, and refined it to an R value of 25.2%. The Y165F mutation induces a global conformational change that is in the opposite direction to the T to R transition and therefore results in an extreme T state. The two catalytic trimers move closer by ∼0.14 Å and rotate by ∼0.2°, in the opposite direction to the T→R rotation; the two domains of each catalytic chain rotate by ∼2.1°, also in the opposite direction to the T→R transition; and the 240s loop adopts a new conformation. Residues 229 to 236 shift by ∼2.4 Å so that the active site is more open. Residues 237 to 244 rotate by ∼24.1°, altering interactions within the 240s loop and at the C1-C4 and C1-R4 interfaces. Arg 167, a key residue in domain closure and interactions with L-Asp, swings out from the active site to interact with Tyr 197. This crystal structure is consistent with the functional properties of Y165F, expands our knowledge of the conformational repertoire of ATCase, and indicates that the canonical T state does not represent an extreme. Proteins 33:430-443, 1998. © 1998 Wiley-Liss, Inc.
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    A hierarchical method for generating low-energy conformers of a protein-ligand complex (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 475-495 
    Details
    ISSN: 0887-3585
    Keywords: docking ; landscape ; dynamics ; dielectric ; affinity ; binding ; methotrexate ; thermolysin ; dihydrofolate reductase ; HIV protease ; generalized Born ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of the method to three complexes of known crystal structure provides insights into the energy functions used for selecting low-energy docked conformations and into the structure of the binding-energy surface. Evidence is presented that the local energy minima of a ligand in a binding site are arranged in a hierarchical fashion. This observation motivates the construction of a hierarchical docking algorithm that substantially enriches the population of ligand conformations close to the crystal conformation. The algorithm is also adapted to permit docking into a flexible binding site and preliminary tests of this method are presented. Proteins 33:475-495, 1998. © 1998 Wiley-Liss, Inc.
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    Energy landscape of a native protein: Jumping-among-minima model (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 496-517 
    Details
    ISSN: 0887-3585
    Keywords: energy landscape ; hierarchical conformational substates ; molecular dynamics ; normal mode analysis ; principal component analysis ; jumping-among-minima model ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation. Proteins 33:496-517, 1998. © 1998 Wiley-Liss, Inc.
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    Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 518-534 
    Details
    ISSN: 0887-3585
    Keywords: structure databank ; superfold ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage - whether a given fold occurs in a particular organism. Of the ∼340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in all-helical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture - eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a “Zipf-like” law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes. Further information pertinent to this analysis is available at http://bioinfo.mbb.yale.edu/genome. Proteins 33:518-534, 1998. © 1998 Wiley-Liss, Inc.
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    The slow step of folding of Staphylococcus aureus PC1 β-lactamase involves the collapse of a surface loop rate limited by the Trans to Cis isomerization of a non-proline peptide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 550-557 
    Details
    ISSN: 0887-3585
    Keywords: mutagenesis ; c.d. spectroscopy ; unfolding ; Ω-loop ; molten-globule ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We wished to test the hypothesis that the non proline cis to trans isomerization of the peptide bond at position 167 in the S. aureus β-lactamase PC1 exerts a significant controlling effect on the folding pathway of this enzyme. The previous data presented in support of this hypothesis could not rule out the effect of factors unrelated to non-proline cis/trans isomerization. We have used the plasmid pET9d to direct soluble overproduction of the S. aureus β-lactamase PC1 and a site-directed mutant (Ile 167 to Pro) in Escherichia coli. Following purification the proteins were subjected to a comparative analysis of the kinetics of unfolding and refolding using the techniques of near- and far-UV circular dichroism spectroscopy and fluorescence spectroscopy in conjunction with “double-jump” experiments. Results show that the fully-unfolded I167P mutant enzyme retains 20% of molecules in a fast-refolding form and that slower-refolding molecules fold faster than the recombinant wild-type enzyme. The final stage of folding involves folding of the Ω-loop into a conformation essential for enzymatic activity. In support of the original hypothesis, the folding of this Ω-loop is rate limited by the isomerization of the Glu 166-Ile 167 peptide bond. Proteins 33:550-557, 1998. © 1998 Wiley-Liss, Inc.
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    Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 116-127 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; X-ray crystallography ; essential dynamics ; lysozyme ; hinge bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations describe domain motions. The protein consists of an N- and C-terminal domain connected by a long helix. The analysis of the distribution of crystallographic conformations reveals that the N-terminal helix rotates together with either of these two domains. The main domain fluctuation describes a closure mode of the two domains in which the N-terminal helix rotates concertedly with the C-terminal domain, while the domain fluctuation with second largest amplitude corresponds to a twisting mode of the two domains, with the N-terminal helix rotating concertedly with the N-terminal domain. For the closure mode, the difference in hinge-bending angle between the most open and most closed X-ray structure along this mode is 49 degrees. In the MD simulation that shows the largest fluctuation along this mode, a rotation of 45 degrees was observed. Although the twisting mode has much less freedom than the closure mode in the distribution of crystallographic conformations, experimental results suggest that it might be functionally important. Interestingly, the twisting mode is sampled more extensively in all MD simulations than it is in the distribution of X-ray conformations. Proteins 31:116-127, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 96
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    Electronic Resource
    Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 558-566 
    Details
    ISSN: 0887-3585
    Keywords: Drosophila melanogaster couch potato protein ; Werner's syndrome ; restrained molecular dynamics ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by “homology distance constraints,” while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good conformational energies and are physically reasonable. The effects of misalignment of the unknown and the template sequences were also explored in order to determine the feasibility of this homology modeling method for distinguishing possible sequence alignments based on considerations of the resulting conformational energies of modeled structures. Differences in the alignments of the unknown and the template sequences result in significant differences in the conformational energies of the calculated homology models. These results suggest that conformational energies and residual constraint violations in these homology-constrained simulated annealing calculations can be used as criteria to distinguish between correct and incorrect sequence alignments and chain folds. Proteins 33:558-566, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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  • 97
    Electronic Resource
    Electronic Resource
    Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of β-glucosidase A from Bacillus polymyxa (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 567-576 
    Details
    ISSN: 0887-3585
    Keywords: bacterial cellobiase ; mutated β-glucosidase ; family 1 ; thermoresistance ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The increasing development of the biotechnology industry demands the design of enzymes suitable to be used in conditions that often require broad resistance against adverse conditions. β-glucosidase A from Bacillus polymyxa is an interesting model for studies of protein engineering. This is a well-characterized enzyme, belonging to glycosyl hydrolase family 1. Its natural substrate is cellobiose, but is also active against various artificial substrates. In its native state has an octameric structure. Its subunit conserves the general (α/β)8 barrel topology of its family, with the active site being in a cavity defined along the axis of the barrel. Using random-mutagenesis, we have identified several mutations enhancing its stability and it was found that one them, the E96K substitution, involved structural changes. The crystal structure of this mutant has been determined by X-ray diffraction and compared with the native structure. The only difference founded between both structures is a new ion pair linking Lys96 introduced at the N-terminus of helix α2, to Asp28, located in one of the loops surrounding the active-site cavity. The new ion pair binds two segments of the chain that are distant in sequence and, therefore, this favorable interaction must exert a determinant influence in stabilizing the tertiary structure. Furthermore, analysis of the crystallographic isotropic temperature factors reveals that, as a direct consequence of the introduced ion pair, an unexpected decreased mobility of secondary structure units of the barrel which are proximal to the site of mutation is observed. However, this effect is observed only in the surrounding of one of the partners forming the salt bridge and not around the other. These results show that far-reaching effects can be achieved by a single amino acid replacement within the protein structure. Consequently, the identification and combination of a few single substitutions affecting stability may be sufficient to obtain a highly resistant enzyme, suitable to be used under extreme conditions. Proteins 33:567-576, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    Mass spectrometry (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 1-2 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
    Type of Medium: Electronic Resource
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  • 99
    Electronic Resource
    Electronic Resource
    Kinetics and interaction studies between cytochrome c3 and Fe-only hydrogenase from Desulfovibrio vulgaris hildenborough (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 590-600 
    Details
    ISSN: 0887-3585
    Keywords: [Fe] hydrogenase ; protein-protein interaction ; BIAcore analysis ; crystallization ; cooperativity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrogenases from Desulfovibrio are found to catalyze hydrogen uptake with low potential multiheme cytochromes, such as cytochrome c3, acting as acceptors. The production of Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough was improved with respect to the growth phase and media to determine the best large-scale bacteria growth conditions. The interaction and electron transfer from Fe-only hydrogenase to multiheme cytochrome has been studied in detail by both BIAcore and steady-state measurements. The electron transfer between [Fe] hydrogenase and cytochrome c3 appears to be a cooperative phenomenon (h = 1.37). This behavior could be related to the conductivity properties of multihemic cytochromes. An apparent dissociation constant was determined (2 × 10-7 M). The importance of the cooperativity for contrasting models proposed to describe the functional role of the hydrogenase/cytochrome c3 complex is discussed. Presently, the only determined structure is from [NiFe] hydrogenase and there are no obvious similarities between [NiFe] and [Fe] hydrogenase. Furthermore, no crystallographic data are available concerning [Fe] hydrogenase. The first results on crystallization and X-ray crystallography are reported. Proteins 33:590-600, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    Surface properties of adipocyte lipid-binding protein: Response to lipid binding, and comparison with homologous proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 577-589 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; accessible surface area ; fatty acid binding proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Adipocyte lipid-binding protein (ALBP) is one of a family of intracellular lipid-binding proteins (iLBPs) that bind fatty acids, retinoids, and other hydrophobic ligands. The different members of this family exhibit a highly conserved three-dimensional structure; and where structures have been determined both with (holo) and without (apo) bound lipid, observed conformational changes are extremely small (Banaszak, et al., 1994, Adv. Prot. Chem. 45, 89; Bernlohr, et al., 1997, Annu. Rev. Nutr. 17, 277). We have examined the electrostatic, hydrophobic, and water accessible surfaces of ALBP in the apo form and of holo forms with a variety of bound ligands. These calculations reveal a number of previously unrecognized changes between apo and holo ALBP, including: 1) an increase in the overall protein surface area when ligand binds, 2) expansion of the binding cavity when ligand is bound, 3) clustering of individual residue exposure increases in the area surrounding the proposed ligand entry portal, and 4) ligand-binding dependent variation in the topology of the electrostatic potential in the area surrounding the ligand entry portal. These focused analyses of the crystallographic structures thus reveal a number of subtle but consistent conformational and surface changes that might serve as markers for differential targeting of protein-lipid complexes within the cell. Most changes are consistent from ligand to ligand, however there are some ligand-specific changes. Comparable calculations with intestinal fatty-acid-binding protein and other vertebrate iLBPs show differences in the electrostatic topology, hydrophobic topology, and in localized changes in solvent exposure near the ligand entry portal. These results provide a basis toward understanding the functional and mechanistic differences among these highly structurally homologous proteins. Further, they suggest that iLBPs from different tissues exhibit one of two predominant end-state structural distributions of the ligand entry portal. Proteins 33:577-589, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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