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  • 1985-1989  (3,384)
  • 1980-1984  (2,123)
  • Biochemistry and Biotechnology  (4,807)
  • Gas chromatography
  • Nuclear reactions
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Years
Year
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Archives of toxicology 63 (1989), S. 107-111 
    ISSN: 1432-0738
    Keywords: Analysis ; Biological monitoring ; Butoxyacetic acid ; Ethoxyacetic acid ; Gas chromatography ; Glycol ethers ; Metabolism ; Methoxyacetic acid ; Pentoxyacetic acid ; Urine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Alkoxyacetic acids are metabolically formed and excreted in urine after exposure to ethylene glycol monoalkyl ethers (alkoxyethanols) or their acetate esters. This paper presents a sensitive method based on extractive alkylation for determination of alkoxyacetic acids in urine. Alkoxyacetate ions were extracted from 200 μl urine into methylene chloride, with tetrabutylammonium acting as counter ion, and derivatized with pentafluorobenzyl bromide in a single step. After separation of the methylene chloride phase, evaporation, and dissolution of the residues in hexane the esters were analyzed by fused silica capillary column gas chromatography and electron capture detection. The esters formed were stable for at least 2 weeks at room temperature. The limit of quantification was estimated to 2 μM (corresponding to an injected amount of 2 pg) for methoxyacetic (MAA) and ethoxyacetic acid (EAA) in urine. The corresponding values for butoxyacetic acid (BAA) were 4 μM and 5 pg, respectively. The detector response was linear up to 80 μM and the formation of derivative at least up to 1 mM. The method error may be reduced by using a second alkoxyacetic acid derivative, EAA, BAA or 2-pentoxyacetic acid (PAA), as an internal standard. The sensitivity, stability, reduced number of extractions, and small volumes of reagents and sample needed make the present method useful in biomonitoring of occupational exposure to ethylene glycol ethers.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    International archives of occupational and environmental health 61 (1989), S. 249-254 
    ISSN: 1432-1246
    Keywords: Ethylene glycol ethers ; Alkoxyacetic acids ; Pentafluorobenzylbromide ; Gas chromatography ; Urine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary A sensitive and specific method for the determination in urine of alkoxyacetic acids, the metabolites of ethylene glycol monoalkyl ethers, was developed by combining the advantages of two previously described methods. The acids were determined gas chromatographically as their pentafluorobenzylesters. The alkylation with pentafluorobenzylbromide was performed after dissolving the dry residue of lyophilized urine in methanol. Quantitative derivatization was obtained when the urinary pH was adjusted to pH 7.0, when the reagent concentration was 5% v/v, and when the reaction mixture was heated at 90°C for 3 h. Sample clean-up was performed by adding bidistilled water and the esters were extracted with methylene chloride with high yields (95%). Alkoxyacetic acid concentrations in the range of 0.1 to 200 mg/l could be determined with an average imprecision of ± 3.5%.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1612-1112
    Keywords: Gas chromatography ; FAME fingerprinting ; Animal fats ; Transesterification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The triglycerides of animal fats from milk, meat or cheese can also be characterized by the gaschromatographic pattern of the fatty acid methylesters (FAME) after conversion by an unsophisticated transesterification procedure. Even from the FAME pattern falsifications of commercial animal fats can be revealed by the fast separation of the FAME using a standard CW 20 M (polyethyleneglycol) capillary column. Characteristic patterns of FAME originating from different animals are shown. The patterns of the FAME from different races of the same animal are very similar, so that the characterisation according to the type of animal is not disturbed.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 596-600 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Mass spectrometry ; Azines
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary We have studied the gas chromatographic behaviour of several 3-methyl-2-benzothiazolone-azines. In HPLC analysis all the unsymmetrical azines show double peaks, whereas in HRGC analysis only some of these compounds show the two peaks corresponding to the Z (syn) and E (anti) isomers. By means GC/MS analysis the mass spectrum of each azine was recorded. We have assigned the E and Z configurations to the first and second gas chromtographic peaks on the basis of the ratio between the relative abundances of the two most significant framment ions at m/z 163 and 164.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 221-224 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Large volume sample injection ; Closed on-column injector
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A new simplified version of a “closed” on-column injector is introduced. Because of its design isobaric injection conditions do not have to be followed and a wide range of injection temperatures above the boiling point of the sample solvent can be chosen for on-column injections in capillary gas chromatography. Also, when following certain basic injection rules, injections of large sample volumes (≥20 μl or more) give accurate and reproducible results without further problems.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 28 (1989), S. 139-142 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Silica surface ; Silanols ; Strongly interacting sites
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The paper describes how the method of gas-phase titration of the strongest adsorption sites can be utilized to calculate a relative strength of interaction of the sites with chromatographic solutes. An excellent correlation with earlier, theoretical predictions of Giddings is noted. Significant influence of the sites on the width of a chromatographic band is observed when the interactions are an order of magnitude stronger than those of normal sites.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 28 (1989), S. 167-169 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Determination of monomer in polymers ; Sealed glass capillary sampling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Residual styrene in polystyrene and free phenol in phenolic plywood adhesive have been determined by sealing samples in glass capillary tubes. To prevent loss of sample the ends of the capillary tubes were sealed with a kind of putty made of anhydrous calcium sulfare, calcium carbonate and a small quantity of phenylmethylsilicone fluid. No volatile compounds were released from this sealing material when the capillary tubes were placed in a quartz vaporising furnace at temperatures up to 300°C.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 28 (1989), S. 237-240 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Slope of log plot ; Homologous series ; Retention index ; Retention time ; Uncertainty ; Free energy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The free energy of partition of a methylene group $$\Delta G_{CH_2 }^ \circ $$ is constant within a homologous series down to C5 and nearly constant to C3, contrary to the finding of Golovnya and Grigoryeva [5]. Retention indices are linear with carbon number: values may be extrapolated from higher carbon numbers to C5 within experimental uncertainty, to C4 with error no greater than 5 units and to C3 with error no greater than 10 units. Error in extrapolating the logarithm of the adjusted retention time, log t′R, to C5 is thus negligible, to C4 has possible error up to 5b/100 and to C3 up to 10b/100, whereb is the slope of the plot of log t′R against carbon number.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Optimization of gas-solid separations ; Plate height equation ; Computer mapping procedure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary This paper proposes an optimization model for gas-solid chromatographic separations in a non-linear programming form and an approximate equation of the plate height for the model. A computer-modified mapping procedure is also described for searching the optimum separation conditions. Just five experiments and about 20 minutes of the computer time are needed to establish the optima of column temperature and of the carrier gas linear velocity. The relative deviation between the predicted and the experimental values was found to be within 20% for the plate heights, and within 1.5% for the retention times.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 37-43 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Methylbromide ; Charcoal tubes ; Pollution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Air sampling of methylbromide using 900 mg HBr-treated activated charcoal tubes, followed by solvent desorption and FID or ECD chromatographic analysis, makes it possible to evaluate concentrations ranging from 0.2 ppm (1 mg×m−3) to 250 ppm (1g×m−3) at ambient temperature even with a high hygrometric level. Thermal desorption does not lead to satisfactory results.
    Type of Medium: Electronic Resource
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  • 11
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 60-66 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Mass loadability ; Stationary phase capacity ; Capillary columns
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary In GLC the mass load can be normalized with respect to the amount of stationary phase in one plate. This quantity can be used for a specified solute-liquid phase combination in any capillary or packed column, irrespective of the column dimensions or the number of plates. For each individual solute in a given stationary phase a unique factor β″ can be found, which accounts for the specific shape of the isotherm of this particular combination. this factor β″ corresponds well with the activity coefficients of the solutes in the stationary phase, by which a fairly good approximation of the mass loadability of the column at hand can be made without need for experiment.
    Type of Medium: Electronic Resource
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 552-558 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Radio gas chromatography ; 3H- and14C-labelled compounds ; Isotope effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Radio gas chromatography (RGC) is a valuable tool for the analysis of radioactively labelled compounds. Recent advances in capillary GC, especially in column technology and instrumentation have also induced new possibilities in this field. With regard to the preservation of the achieved separation efficiency, radioactivity detection is the main problem in capillary RGC. Based on published data and on our extensive experience in conventional RGC, a simple, reliable and versatile method has been developed for the radioactive detection: purge gas is added to the effluent of the capillary column and the RGC detection unit with conversion tube and flow-through proportional counter is used maintaining small dead volumes and dimensions. The influence of the extra-column volumes and of the total gas flow rate (of the carrier, purge and quenching gases) on the peak shape was investigated. It was also found that the isotopic effect commonly known in GC of2H- and3H-labelled compounds is hardly measurable for larger [G-14C] labelled species such as [G-14C] labelled higher fatty acids with high isotopic abundance of14C, even on the highly efficient capillary columns. The quantitative aspects of the detection method used are discussed and some applications to the analysis of labelled biochemicals (amino and fatty acids) are demonstrated.
    Type of Medium: Electronic Resource
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  • 13
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Coke oven gas evolution ; On-line gas analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A gas chromatograph will thermal conductivity detector (TCD) connected on line via a cleaning train to the semi-industrial scale Coke Oven Text Plant of the Spanish National Coal Institute (INCAR), has been used to control the evolution of the permanent gases during the coking process. The undesirable presence of oxygen in the coke oven gas can be detected with this system that will be applied to determine the end of the coking process by quantitative analysis of the gas evolved.
    Type of Medium: Electronic Resource
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  • 14
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Microwave plasma detector ; Thiophenes ; Shale oil distillates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A series of alkylthiophenes and dimethyl disulfide were tentatively identified in an oil shale retort gas condensate from a 6-kg bench-scale retort using gas chromatography with a microwave-induced helium plasma detector (GC-MIP). The sulfur species were present in concentrations ranging from 1.5 to 10.7 mol ppm in the undiluted offgas. The GC-MIP technique was successful in selectively detecting the sulfur components in the complex mixture. Quantitation was simplified relative to GC with flame-photometric detection because of the absence of quenching or other interference problems at the concentrations studied. Attempts to determine stoichiometry of the sulfur components by comparison of carbon, hydrogen, and sulfur ratios with those of standards were unsuccessful because of the complexity of the carbon and hydrogen chromatograms.
    Type of Medium: Electronic Resource
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  • 15
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Air pollutants ; Adsorbent enrichment ; Thermal desorption
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A new automatic method is described for quantitative determination of some light C2–C4 hydrocarbons in urban air: ethene, ethyne, propane, propene, butane and iso-butane. This method is based on an enrichment step at room temperature using a solid sorbent and subsequent thermal desorption for gas chromatographic separation and FID detection. The instrument is built up of a small commercial gas chromatograph and a laboratory-made trap and desorption unit. The sampling parameters, sample volume, concentration and humidity of air have been investigated.
    Type of Medium: Electronic Resource
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 159-163 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Flame photometric detector ; Sulfur compounds ; Response quenching
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The long time retardation of the main hydrocarbon peak in the chimney of the flame photometric detector greatly reduces the responses of later-eluting sulfur compounds. In the absence of hydrocarbons in the flame, the slope (s) of the log I vs. log [S] plot (where I is the sulfur response and [S] is the sulfur concentration in the sample) is of the highest value and is constant for all experimental conditions tested. Flame hydrocarbons cause the s value to decrease, and this is dependent on the oxygen to hydrogen ratio in the flame (O/H) and, under certain conditions, also on the sulfur to carbon ratio (S/C) of the sample. The abnormalities observed in the determination of methyl thiol in natural gas are explained on the basis of the present study.
    Type of Medium: Electronic Resource
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 631-632 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Wide-bore glass capillary columns ; End-sealing ; Static coating
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary An end-sealing method to be used for static coating of wide-bore glass capillaries is described. After the capillary was completely filled with the coating solution, one end is connected to a gas-tight syringe (10-ml volume) via silicone tubing and the other end is fixed with shortcutted silicone tubing for sealing with a plug. The method is highly successful.
    Type of Medium: Electronic Resource
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  • 18
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 233-237 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; FTIR ; Hemoglobin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The use of N, O (S)-tert.-Butyldimethylsilyl derivatives of amino acids for capillary gas chromatography and FTIR identification of amino acids is described. Rapid identification is achieved by computerised comparison of FTIR spectra. Derivatives that are characterised by identical sets of ions in gas chromatography-mass spectrometry experiments are clearly distinguished and identified by means of their infrared spectra. This, for example, is the case with alanine, β-alanine and sarcosine, which norvaline and valine, and with norleucine, leucine and isoleucine. Unknows are also promptly detected. This is especially useful in screening biological samples for less common amino acids. Screening of hemoglogin hydrolysates for amino acid adducts is exemplified.
    Type of Medium: Electronic Resource
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  • 19
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Ethyl carbamate ; Direct injection quantification ; Cold injection system ; Optimised SIM
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary An integrated procedure is described which allows direct injection quantitative screening to single figure parts per billion (μg/L) levels of ethyl carbamate in the natural matrix of distilled alcoholic beverage. Injection and detection performance was studied and optimized to allow this routine, reproducible, trace analysis without any sample pre-treatment. All aspects of the analysis including autosampler run sequences and automated internal standard report generation are initiated and controlled from a single GC/MS workstation.
    Type of Medium: Electronic Resource
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  • 20
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Trichloroethyl ester ; Dicarboxylic acid ; Urine samples ; Electron capture ; Biological monitoring
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Dicarboxylic acids were esterified by 2,2,2-trichloroethanol by using trifluoroacetic anhydride and phosphoric acid as catalysts. The method was developed to facilitate the evaluation of workers' exposure to sensitising acid anhydrides and other compounds metabolised to acids in the body. The sensitivity of the acid determination in urine was in the order of 2–4 ng ml−1 for aliphatic and alicyclic acids and 15ng ml−1 for phthalic acid.
    Type of Medium: Electronic Resource
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  • 21
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 499-508 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Electron capture detector ; Space-charge model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Mathematical analysis, allowing the determination of the distribution of the electron and positive ion concentration in an electron-capture detector with a cylindrical electrode arrangement and with constant and pulsed voltage supplies, has been carried out. The measurements obtained confirm the assumptions concerning the “space change” model of the ECD introduced by Gobby et al. and cast doubt upon the general assumption of the complete removal of the electrons from the detector by the voltage pulse. The physical factors influencing the current characteristics of the detector and the possible distortions connected with the electrode geometry have been explained on the basis of the measurements carried out.
    Type of Medium: Electronic Resource
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  • 22
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 455-460 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Surface free energy ; Silane-covered materials ; Film pressure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The surface free energy, or film pressure, π0, is measured for mica (Mica HK), silane-covered mica (Mica NP), Chromosorb W DMCS and glass beads. The film pressure is obtained from gas chromatography. The materials are used as adsorbents and benzyl alcohol and n-dodecane are used as molecular probes. Adsorption isotherms at 353 K are obtained from gas chromatography data and the surface free energy is computed with the help of the Gibbs equation. Values of π0 for a given surface are found to vary with the molecular probe. With benzyl alcohol π0 varies from 44 erg/cm2 for Mica 60 HK to 76 erg/cm2 for glass. In the case of n-dodecane π0 is found to vary in the same manner but the values range from 25 to 45 erg/cm2. The results are in good agreement with the values obtained with the contact angle method.
    Type of Medium: Electronic Resource
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  • 23
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 27 (1989), S. 469-471 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Headspace analysis ; Ethylene oxide ; Capillary column
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A headspace gas chromatographic method for determination of traces of ethylene oxide (EO) in sterilized materials has been developed. The method allows the determination of the amount of EO by putting the samples directly into acetonitrile and analysing by means of headspace GC. The procedure described is simple, sensitive, reproducible and linear. The lower limit of detection is 0.015 μg/g of sterilized material.
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  • 24
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Colloidal stationary phases ; Liquid crystals as stationary phases
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Colloid systems consisting of the nematic liquid crystals p,p′-azoxyphenetol and p,p′-methoxyethoxyazoxybenzene and high-disperse mineral particles (aerosil, carbon black) are proposed to be used as stationary phases in gas chromatography. The dependence of the retention of normal paraffins, Rohrschneider and McReynolds test solutes (benzene, ethanol, methyl ethyl ketone, nitromethane, pyridine, butanol-1, 2-pentanone, and nitropropane) on the composition of the colloid systems was investigated. The investigated colloid sorbents including liquid crystals retain their selectivity for meta/para isomers up to 50% of the aerosil content and practically at all studied carbon black concentrations.
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  • 25
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 28 (1989), S. 24-26 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Anesthetics ; Pharmacokinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A sensitive capillary gas chromatographic method is described for the simultaneous determination of lidocaine, tetracaine, procaine and dibucaine. The method was applied to the determination of anesthetics in tissue homogenates incubated at 38°C at doses between 10 and 400 mg/kg. In the liver tissue thein vitro metabolization of the studied anesthetics is most rapid for tetracaine, also fast for procaine, while for lidocaine and dibucaine the metabolization is very slow. In brain tissue thein vitro metabolization of anesthetics is very slow. The method shows good analytical parameters: linearity between 5 and 40 μg/ml; day-to-day reproducibility ca. 8% for a concentration of 20 μg/ml, precision ca. 7% for a concentration of 20μg/ml. Accuracy is also very good.
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  • 26
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Chlorinated methanes ; Activated charcoal sampling ; Pollution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A sampling method using activated charcoal, followed by percolation with ethanol and FID or ECD chromatographic analysis, depending on the concentrations to be monitored, makes it possible to evaluate concentrations of methylene chloride between 5 and 1000mg m−3, chloroform between 0.1 and 2000mg m−3, and carbon tetrachloride between 0.015 and 1000mg m−3.
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  • 27
    ISSN: 1612-1112
    Keywords: Gas chromatography ; GC/MS and headspace GC ; Elastomeric stoppers for injectables ; Trace hydrocarbons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Elastomeric stoppers for injectables have been surveyed by means of GC/MS screening. Residual contamination by hexanes (2-methylpentane, 3-methylpentane, n-hexane, methylcyclopentane, cyclohexane) toluene and xylenes occurred in all the samples tested. A headspace GC purity test is suggested, by using these residual chemicals as purity indexes.
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  • 28
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 28 (1989), S. 313-314 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Fused-silica columns ; Static coating ; Sealing method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary In this paper a new sealing method for the static coating of capillary columns is described. When one end of the fully filled capillary was immersed into liquid nitrogen in a Dewar flask, the coating solution at this end would be frozen and became a temporary seal, and an air-free solvent/seal interface was obtained. No bumping has ever been found at the interface, even when butane was used as solvent. By applying this sealing method, several capillary columns, including some narrow bore capillary, had been successfully coated.
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  • 29
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Renewal theory ; Monte-Carlo simulation ; Prediction of retention and peak widths
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A new method for prediction of gas chromatographic retention times and peak half widths is based on the renewal theory. The only requirements are the heats of vaporization of the compounds to be separated and one calibration measurement. With this data, retention times and peak half widths can be predicted for isothermal as well as temperature-programmed gas chromatography. For the separation of non-polar substances on non-polar stationary phases the prediction error for retention times is approx. 1–2%. First simulations of polar molecules and polar stationary phases indicate that this method is also applicable in these cases but some extension will be required.
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  • 30
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 125-131 
    ISSN: 0887-3585
    Keywords: protein conformation ; dynamics ; Monte Carlo simulation ; conformational energy ; minimization ; plastic deformation ; conformational heterogeneity ; hierarchy in dynamics ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Differences in atom packing are studied in the minimum energy conformations derived from the record of the Monte Carlo simulation of conformational fluctuation in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations observed among the minima which are found in the previous paper are accompanied by rearrangement of atom packing. Spatial locations of the local deformations in the three-dimensional folded structure are also studied. It is foundthat the local deformations are distributed in space in several clusters inthe folded structure. The size and location of the clusters characterize the respective fluctuations of the first and the second levels observed in the simulation. In the fluctuations of the first level local deformations, each of which usually involves a few side chains and one main chain local segment, are thermally exited independently of each other near thesurface of the molecule. The observed fluctuation of the second level involves a cooperative deformation involving many side chains and local main chain segments all in one cluster, which goes though the core of the molecule. The collective local deformations observed both in the first and second levels are plastic in the sense that they are accompanied with rearrangement of atom packing.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 31
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    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 139-148 
    ISSN: 0887-3585
    Keywords: protein architecture ; packing ; evolutionary relationships ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: α/β barrel structures very similar to that first observed in triose phosphate isomerase are now known to occur in 14 enzymes. To understand the origin of this fold, we analyzed in three of these proteins the geometry of the eight-stranded β-sheets and the packing of the residues at the center of the barrel. The Packingin thisregion is seen in its simplest form in glycolate oxidase. It consists of 12 residues arranged in three layers. Each layer contains four side chains. The packing of RubisCO and TIM can be understood in terms of distortions of this simple pattern, caused by residues with small side chains at someof the positions inside the barrel. Two classes of packing are found. In one class, to which RubisCO and TIM belong, the central layer is formed by a residue from the first, third, fifth, and seventh strands; the upper and lower layers are formed by residues fromthe second, fourth, sixth, and eighth strands. In the second class, to which GAO belongs, this is reversed: it is side chains from the even-numbered strands that form the central layer, and side chains from the oddnumbered strands that form the outer layers. Our results suggest that not all proteins with this fold are related by evolution, but that they represent a common favorable solution to the structural problems involved in the creation of a closed β barrel.
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  • 32
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 170-182 
    ISSN: 0887-3585
    Keywords: modeling ; flavodoxin ; structure prediction ; side chains ; database ; structure analysis ; protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The tertiary structure of flavodoxin has been model build from only the X-ray crystallographic α-carbon coordinates. Main-Chain atoms were generated from a dictionary of backbone structures. Side-chain conformations were initially set according to observed statistical distributions, clashes were resolved with reference to other knowledge-based parameters, and finally, energy minimization was applied. The RMSD of the model was 1.7 Å across all atoms to the native structure. Regular secondary structural elements were modeledmore accurately than other regions. About 40%of the ξ1 torsional angles were modeled correctly. Packing of side chains in the core was energetically stable but diverged significantly from the native structure in some regions.The modeling of protein structures is increasing in popularity but relatively few checks have been applied to determine the accuracy of the approach. In this work a variety of parameters have been examined. It was found that close contact, and hydrogen-bonding patterns could identifypoorly packed residues. These tests, however, did not indicate which residues had a conformation different from the native structure or how to move such residues to bring them into agreement. To assist in the modeling of interacting side chains a database of known interactions has been prepared.
    Additional Material: 8 Ill.
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  • 33
    ISSN: 0887-3585
    Keywords: yeast hexokinase II ; dimerization ; in vivo functions ; glucose repression ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The function of the N-terminal amino acids of Saccharomyces cerevisiae hexokinase II was studied in vivo using strains producing a form of hexokinase II lacking its first 15 amino acids (short form).This short form of hexokinase II was produced from a fusion between the promoter region of the PGK1 gene and the HXK2 coding sequence except the first 15 codons. As expected, the in vitro analysis of the short from protein by gel filtration chromatography indicates that the short protein does not form dimers under conditions where the wild-type protein dimerizes. Kinetic studies show that the enzymatic activities are very similarto wild-type behavior. The physiological experiments performed on the strains containing the fusion allele demonstrate that the short form ofthe enzyme is similar to the wild-type both in terms of phosphorylation of hexoses and glucose repression. We conclude that the N-terminalamino acids of hexokinase II are not required in vivo either for phosporylation of hexoses or for glucose repression.
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  • 34
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 289-312 
    ISSN: 0887-3585
    Keywords: aconitase ; iron-sulfur enzyme ; crystal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of the 80,000 Da Fe—S enzyme aconitase has been solved and refined at 2.1 Å resolution. The protein contains four domains; the first three from the N-terminus are closely associated around the [3Fe-4S] cluster with all three cysteine ligands to the cluster being provided by the third domain. Associationof the larger C-terminal domain with the first three domains createsan extensive cleft leading to the Fe—S cluster. Residues from all four domains contribute to the active site region, which is defined by the Fe—S cluster and a bound SO42-ion. This region of the structure contains 4 Arg, 3 His, 3 Ser, 2 Asp, 1 Glu, 3 Asn, and 1 Gln residues, as well asseveral bound water molecules. Three of these side chains reside on a threeturn 310 helix in the first domain. The SO42-ion is bound 9.3 Å from the center of the [3Fe-4S] cluster by the side chains of 2 Arg and 1 Gln rsidues. Each of 3 His side chains in the putative active site is paired with Asp or Glu side chains.
    Additional Material: 13 Ill.
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  • 35
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 271-280 
    ISSN: 0887-3585
    Keywords: antifluorescyl monoclonal antibody ; high-affinity binding site ; effects of MPD on hapten binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of a fluorescein-Fab (4-4-20) complex was determined at 2.7 Å resolution by molecularreplacement methods. The starting model was the refined 2.7 Å structure of unliganded Fab from an autoantibody (BV04-01) with specificity for single-stranded DNA. In the 4-4-20 complex fluorescein fits tightly into a relatively deep slot formed by a network of tryptophan and tyrosine side chains. The planar xanthonyl ring of the hapten is accommodated at the bottom of the slot while the phenylcarboxyl group interfaces with solvent. Tyrosine 37 (light chain) and tryptophan 33 (heavy chain) flank the xanthonyl group and tryptophan 101 (light chain) provides the floor of the combining site. Tyrosine 103 (heavy chain) is situated near the phenyl ring of the hapten and tyrosine 102 (heavy chain) forms part of the boundary of the slot. Histidine 31 and arginine 39 of the light chain are located in positions adjacent to the two enolic groups at opposite ends of the xanthonyl ring, and thus account for neutralization of one of two negative charges in the haptenic dianion. Formation of an enol-arginine ion pair in a region of low dielectric constant may account for an incremental increase in affinity of 2-3 orders of magnitude in the 4-4-20 molecules relative to other members of an idiotypic family of monoclonalantifluorescyl antibodies. The phenyl carboxyl group of fluorescein appearsto be hydrogen bonded to the phenolic hydroxyl group of tyrosine 37 of the light chain. A molecule of 2-methyl-2,4-pentanediol (MPD), trapped in the interface of the variable domainsjust below the fluorescein binding site, may be partly responsible for the decrease in affinity for the hapten in MPD.
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  • 36
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 355-373 
    ISSN: 0887-3585
    Keywords: protein ; structure ; prediction ; primary ; secondary ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of Cα coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set ofstandard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can “replace” about 76% ofall hexamers in well-refined known proteins with an error of less than 1 Å, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.
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  • 37
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 20-31 
    ISSN: 0887-3585
    Keywords: ribonuclease ; active site ; conformational change ; protein-nucleic ; acid interactions ; fluorescence depolarization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations were performed on free RNase T1 and the 2′GMP-RNase T1 complex in vacuum and with water in the active site along with crystallographically identified waters, allowing analysis of both active site and overall structural and dynamics changes due to the presence of 2′GMP. Difference in the active site include a closing in the presence of 2′GMP, which is accompanied by a decrease in mobility of active site residues. The functional relevance of the active site fluctuations is discussed. 2′GMP alters the motion of Tyr-45, suggesting a role for that residue in providing a hydrophobic environment for the protein-nucleic acid interactions responsible for the specificity of RNase T1. The presence of 2′GMP causes a structural change of the C-terminus of the α-helix, indicating the transmission of structural changes from the active site through the protein matrix. Overall fluctuations of both the free and 2′GMP enzyme forms are in good agreement with X-ray temperature factors. The motion of Trp-59 is influenced by 2′GMP, indicating difference in enzyme dynamics away from the active site, with the calculated changes following those previously seen in time-resolved fluorescence experiments.
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  • 38
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 324-337 
    ISSN: 0887-3585
    Keywords: aspartyl protease ; HIV/AIDS ; yeast expression ; polyprotein processing ; α-factor ; secretion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The protease of the human immunodeficiency virus type I (HIV1) was expressed both intracellularly and extracellularly in Saccharomyces cerevisiae. Intracellular expression of the protease was achieved by fusing a 179 amino acid precursor form of the protease to human superoxide dismutase (hSOD). Self-processing of the viral enzyme from the hybrid precursor was demonstrated to ocur within the yeast host. Secretion of the protease was achieved by fusing the leader sequence of yeast α-factor to the precursor form of the protrease or to the 99 amino acid mature form of the protease. Authentic and active forms of the retroviral enzyme were detected in yeast supernatants of cells expressing the precursor or the mature form of the protease. A D25E active site variant of the retroviral enzyme exhibited diminished autocatalytic activity when expressed intracellularly or secreted from yeast. The wild-type protease was active in an in vitro assay on the natural substrate, myristylated gag precursor, Pr53gag. Correct processing of Pr53gag at the Tyr 138-Pro 139 junction was confirmed by amino terminal sequence analysis of the resulting capsid protein (CA, p24). The secreted protease was purified to homogeneity from yeast media using preparative isoelectric focusing and reverse-phase HPLC. Amino terminal sequence analysis showed a sequence beginning at amino acid 1 of the mature enzyme (Pro) and another sequence beginning at amino acid 6 (Trp). This shorter sequence may represent a natural autolytic product of the proteaseaspartyl protease.
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  • 39
    ISSN: 0887-3585
    Keywords: protein tertiary structure ; incorrect and correct folding ; molecular surfaces ; solvation free energy ; solution and crystal structure ; disulfide connectivity determination ; squash inhibitor family ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Refinement of distance geometry (DG) structures of EETI-II (Heitz et al.:Biochemistry 28:2392-2398, 1989), a member of the squash family trypsin inhibitor, have been carried out by restrained molecular dynamics (RMD) in water. The resulting models show better side chain apolar/polar surface ratio and estimated solvation free energy than structures refined “in cacuo.” The consistent lower values of residual NMR constraint violations, apolar/polar surface ration and solvation free energy of one of these refined structures allowed prediction of the 3D folding and disulfide connectivity of EETI-II. Except for the few first residues for which no NMR constraints were available, this computer model fully agree with X-ray structures of CMTI-I (Boe et al.: FEBS Lett. 242:285-292, 1989) and EETI-II complexed with trypsin that appeared after the RMD simulation was completed. Restrained molecular dynamics n water is thus proved to highly valuable for refinement of DG structures Also, the successful use of apolar/polar surface ratio and solvation free energy reinforce the analysis of Novotny et al. (Proteins 4: 19-30, 1988) and shows that these criteria are useful indicators of correct versus misfolded models.
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  • 40
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 41
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 155-167 
    ISSN: 0887-3585
    Keywords: protein structure comparison ; dihedral angles ; protein conformation ; hemoglobin structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An efficient algorithm was characterized that determines the similarity in main chain conformation between short protein substructures. The algorithm computes Δt, the root mean square difference in φ and ψ torsion angles over a small number of amino acids (typically 3-5). Using this algorithm, large number of protein substrates comparisons were feasible. The parameter Δt was sensitive to variations in local protein conformation, and it correlates with Δr, the root mean square deviation in atomic coordinates. Values for Δt were obtained that define similarity thresholds, which determine whether two substructure are considered structurally similar. To set a lower bound on the similarity threshold, we estimated the component of Δt due to measurement noise fromcomparisons of independently refined coordinates of the same protein. A sample distribution of Δt from nonhomologous protein comparisons identified an upper bound on the similarity threshold, one that refrains from incorporating large numbers of nonmatching comparisons large numbers of nonmatching comparisons. Unlike methods based on Cα atoms alone, Δt was sensitive to rotations in the peptide plane, shown to occur in several proteins. Comparisons of homologus proteins by Δt showed that the active site torsion angles are highly conserved. The Δt method was applied to the α-chain of human hemoglobin, where it readily demonstrated the local differences in the structures of different ligation states.
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  • 42
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 193-209 
    ISSN: 0887-3585
    Keywords: protein folding ; simulated annealing ; empirical potentials ; Monte Carlo dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximately the effect of each side chains. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealinghas been used to dynamically sample the conformations available to this sample model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence-dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide, suggestion the model may accurately simulate the folding process.
    Additional Material: 8 Ill.
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  • 43
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 249-258 
    ISSN: 0887-3585
    Keywords: DNA binding domain ; etheno-M13 DNA ; single-stranded DNA affinity chromatography ; proteolytic fragments ; truncated topoisomerase ; protein-DNA interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Limited digestion of E. coli DNA topoisomerase I with trypsin or papain generated a DNA-binding domain of MW 14,000 corresponding to the carboxyl terminal of the enzyme. This fragment binds to single-stranded DNA agarose as tightly as the intact enzyme. It required around 400 mM NaCl for elution. A truncated topoisomerase that lacks this C-terminal domain was purified. It was eluted from the single-stranded DNA agarose column at around 150 mM NaCl. Although the truncated enzyme could relax negatively supercoiled DNA as efficiently as the intact enzyme at low ionic strength, its processivity was more sensitive to increasing salt concentration. Measurement of binding to fluorescent etheno-M13 DNA also demonstrated that the presence of the C-terminal domain confers higher affinity to DNA for the enzyme.
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  • 44
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 275-283 
    ISSN: 0887-3585
    Keywords: mutagenesis ; structure-function relationships ; enzymatic catalysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Site saturation mutagenesis has been carried out at Ala-237 in RTEM-1 β-lactamase to assess the role of this site in modulating differences in specificity of β-lactamases for penams vs. cephams as substrates. (An Ala-237 Thr mutation had previously been shown to increase activity on cephems by about 30-80%.1,2) Screening of all 19 possibles mutants on penams and cephems revealed the even more active Ala-237 Asn mutant. Detailed kinnetic analysis showns that this mutant has about four times the activity toward cephalothin and cephalosporin C as the wild-type enzyme. Both mutations reduce the activity toward penams to about 10% that of RETM-1 β-lactamase and lower by about 5°C the tempreature at which the enzyme denatures. Functional properties of the other mutants have also been surveyed. The most intresting aspect of these results is that two quite disparate amino acids, theronine and asparagine, when intorduced for Ala-237, cause such similar changes in enzyme specificity while more similar residues do not alter the catalytic properties of the enzyme to such a significant degree.
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  • 45
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 338-340 
    ISSN: 0887-3585
    Keywords: cytochrome c ; axial ligand ; semisynthesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Semisynthesis has been employed to replace the axial methionine in horse heart cytochrome c with histidine. The reduction potential of the His-80 protein (cyt c-His-80) is 41 mV vs NHE (0.1 M phosphate; pH 7.0; 25°C). The absorption spectra of oxidized and reduced cyt c-His-80 are very similar to those of the native protein in the porphyrin region, but the 695 nm band is absent in the oxidized His-80 protein.
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  • 46
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 47
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 372-381 
    ISSN: 0887-3585
    Keywords: cytochromec ; Saccharomyces cerevisiae ; protein secondary structures ; protein design ; protein engineering ; protein folding ; protein evolution ; modular exchange ; loop swap ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ω(Omega)-loops are protein secondary structural elements having small distance between segment termini. It should be possible to delete or replace certain of these Ω-loops without greatly distorting the overall structure of the remaining portion of the molecule. Functional requirements of regions of iso-1-cytochrome c from the yeast Saccharomyces cerevisiae were in investigated by determining the biosynthesis and activity in vivo of mutant forms in which four different Ω-loops were individually deleted, or in which one Ω-loop was replaced with five different segments. Deletion encompassing amino acid positions 27-33 and79-83 either prevented synthesis of the holoprotein, or produced highly labile iso-1-cytochromes c, whereas deletions encompassing position 42-45 and 48-55 allowed partial synthesis and activity. These two latter regions, therefore, are not absolutely required for any biosynthetic process such as heme attachment, mitochondrial import, or for enzymatic interactions. All replacements in Loop A (residue position 24-33) with the same size (10 amino acid residues), longer (13 and 15 amino acid residues), or shorter segments (6 amino acid residues), resulted in strains having at least partial levels of iso-1-cytochrome c; however, the relative activities ranged from zero to almost the normal level. Thus, Loop A does not appear to be essential for such biosynthetic steps as heme attachment and mitochondrial import. In contrast, the full range of relative activities suggest that this region interacts with physiological partners to carry out efficient electron transport.
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  • 48
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 418-423 
    ISSN: 0887-3585
    Keywords: accessible area ; power law fit ; bootstrap analyses ; fractal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The coefficients in a power low fit of accessible area versus molecular weight for high-reslution monomeric protein structures are assessed with respect to statistical accuracy using bootstrap analyses, and with respect to physical significance using model systems and the concept of roughness or fractal structure of the protein surface.
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  • 49
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 38-46 
    ISSN: 0887-3585
    Keywords: reconstitution ; membrane protein folding/unfolding ; pH effects ; differential scanning calorimetry ; circular dichroism ; electron microscopy ; HPLC ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Thermal unfolding experiments on bacteriorhodopsin in mixed Phospholipid/detergent micelles were performed. Bacteriorhodopsin was extracted from the purple membrane in a denatured state and then renatured in the micellar system. The purpose of this study was to compare the changes, if any, in the structure and stability of a membrane protein that has folded in a nonnative environment with results obtained on the native system, i.e., the purple membrane. The purple membrane crystalline lattice is an added factor that may influence the structural stability of bacteriorhodopsin. Micelles containing bacteriorhodopsin are uniformly sized disks 105 ± 13 Å in diameter (by electron microscopy) and have an estimated molecular mass of 210 kDa (by gel filtration HPLC). The near-UV CD spectra (which is indicative of tertiary structure) for micellar bacteriorhodopsin and the purple membrane are very similar. In the visible CD region of retinal absorption, the double band seen in the spectrum of the purple membrane is replaced with a broad positive band for micellar bacteriorhodopsin, indicating that in micelles, bacteriorhodopsin is monomeric. The plot of denaturational temperature vs. pH for micellar bacteriorhodopsin is displaced downward on the temperature axis, illustrating the lower thermal stability of micellar bacteriorhodopsin when compared to the purple membrane at the same pH. Even though micellar bacteriorhodopsin is less stable, similar changes in response to pH and temperature are seen in the visible absorption spectra of micellar bacteriorhodopsin and the purple membrane. This demonstrates that changes in the protonation state or temperature have a similar affect on the local environment of the chromophore and the protein conformation. We conclude that the tertiary structure of the bacteriorhodopsin monomer is essentially the same in micelles and the purple membrane. On the other hand, in the synthetic mixed micelle system, the packing between the nonnative amphiphiles and bacteriorhodopsin is probably not optimal, protein-protein interactions have been lost, and thehelical packing may be looser because the crystalline lattice is absent. Itis likely that a combination of these effects leads to the decreased stability of micellar bacteriorhodopsin.
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  • 50
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 22-37 
    ISSN: 0887-3585
    Keywords: sequence homology ; tertiary structure prediction ; molecular dynamics ; energy minimization ; hydrophobic interactions ; aromatic ring-ring interactions ; salt bridges ; calcium binding ; thermoactinomyces vulgaris ; extracellular protease ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Subtilisin family of proteases has four members of known sequence and structure: subtilisin Carlsberg, Subtilisin novo, proteinase K, and thermitase. Using thermitase as a test case, we ask two questions. How good are methods for model building a three-dimensional structure of a protein based on sequence homology to a known structure? And what are the molecular causes of thermostability? First, we compare predicted models of thermitase, refined by energy minimization and varied by molecular dynamics, with the preliminary crystal structure. The predictions work best in the conserve structural core and less well in seven loop regions involving insertions and deletions relative to Subtilisin. Here, variation of loop regions by molecular dynamics simulation in vacuo followed by energy minimization does not improve the prediction since we find no correlation between in vacuo energy and correctness of structure when comparing local energy minima. Second, in order to identify the molecular case of thermostability we confront hypotheses erived by calculation of the details of interatomic interactions with inactivation experiments. As a result, we can exclude salt bridges and hydrophobic interactions as main cause of thermostability. Based on a combination of theoretical and experimental evidence, the unusually tight binding of calcium by thermitase emerges as the most likely single influence responsible for its increased thermostability.
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  • 51
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 166-169 
    ISSN: 0887-3585
    Keywords: α-crystallin ; enthalpy ; entropy of solution ; light scattering ; second virial coefficient ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Light scattering studies were performed on bovine α-crystallin measuring the scattering intensities as a function of scattering angle, concentration, and temperature. The data yielded the molecular weight, radius of gyration, and second virial coefficient of α-crystallin at different temperatures. The second virial coefficient increased with increasing temperature. Both the enthalpy and entropy of solution of α-crystallin are positive. The Flory thetatemperature was found to be 271 K.
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  • 52
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 202-210 
    ISSN: 0887-3585
    Keywords: enhanced stability ; λCro ; genetic suppression ; intracellular proteolysis ; antibody screen ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A mutant Cro protein, which bears the Ile-30→ Leu substitution, is thermally unstable and degraded more rapidly than wildtype Cro in vivo. Using an antibody screen, we have isolated five different second site suppressor substitutions that reduce the proteolytic hypersensitivity of this mutant Cro protein. Two of the suppressor substitutions increase the thermal stability of Cro by 12°C to 14°C. These amino acid substitutions affect residues 16 and 26, which are substitutions affect residues 16 and 26, which are substantially exposed to solvent in the crystal structure of wild-type Cro.
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  • 53
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 211-217 
    ISSN: 0887-3585
    Keywords: tyrosin ; mutant protein ; amino acid substitution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: CD spectra in the aromatic region of a series of the mutant α-subunits of tryptophan synthase from Escherichia coli, substituted at position 49 buried in the interior of the molecule, were measured at pH 7.0 and 25°C. The measurements were taken to gain information on conformational change produced by single amino acid substitutions. The CD spectra of the mutant proteins, substituted by Tyr or Trp residue in place of Glu residue at position 49, showed more intense positive bands due to one additional Tyr or Trp residue at position 49. The CD spectra of other mutant proteins also differed from that of the wild-type protein, despite the fact that the substituted residues at position 49 were not aromatic. Using the spectrum of the wild-type protein (Glu49) as a standard, the spectra of the other mutants were classified into three major groups. For 10 mutant proteins substituted by Ile, Ala, Leu, Met, Val, Cys, Pro, Ser, His, or Gly, their CD values of bands (due to Tyr residues) decreased in comparison with those of thewild-type protein. The mutant protein substituted by Phe also belonged to this group. These substituted amino acid residues are more hydrophobic than the original residue, Glu. In the second group, three mutant proteins were substituted by Lys, Gln, or Asn, and the CD values of tyrosyl bands increased compared to those of the wild-type proteins. These residues are polar. In the third group, the CDvalues of tyrosyl bands of two mutant proteins substituted by Asp or Thr were similar to those of the wild-type protein, except for oneband at 276.5 nm. these results suggested that the changes in the CD spectra for the mutant proteins were affected by the hydrophobicity of the residuesat position 49.
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  • 54
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 55
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 266-270 
    ISSN: 0887-3585
    Keywords: crystallization ; purification ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single crystals of T7 RNA polymerase have been grown to a maximum size of 1.8 × 0.3 × 0.3 mm. The crystals are composed of fully intact T7 RNA polymerase which in enzymatically active upon dissolution. These crystals belong to the monoclinic space group P21 and have unit cell parameters a =114.5 Å, b=139.6 Å, c=125.7 Å, β=98.1° Self-rotation function studies indicate that there are three molecules per asymmetricunit. The crystals diffract to at least 3.0 Å resolution. These are the first crystals of a DNA-dependent RNA polymerase suitable for high-resolution X-ray structure determination.
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  • 56
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 233-247 
    ISSN: 0887-3585
    Keywords: protein folding ; crystallographic data base ; structural analysis ; computer program system ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: PKB is a computer program system that combines a data base of three-dimensional protein structures with a series of algorithms for pattern recognition, data analysis, and graphics. By typing relatively simple commands the user may search the data base for instances of a structural motif and analyze in detail the set of individual structures that are found. The application of PKB to the study of protein folding is illustrated in three examples. The first analysis compares the conformations observed for a short sequential motif, sequences similar to the cell-attachment signal Arg-Gly-Asp. The second compares sequences observed for a conformational motif, a 16-residue βαβ unit. The third analysis considers a population of substructures containing ion-pair interaction, examining the relationship offrequency of occurrence to calculated electrostatic energy.
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  • 57
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 58
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 46-60 
    ISSN: 0887-3585
    Keywords: macromolecular conformation ; protein folding ; helical axis ; secondary structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present a general and mathematically rigorous algorithm which allows the helicoidal structure of a protein to be calculated starting from the atomic coordinated of its peptide backbone. This algorithm yields a unique curved axis which quantifies the folding of the backbone and a full set of helicoidal parameters describing the location of each peptide unit. The parameters obtained form a complete and independent set and can therefore be used for analyzing, comparing, or reconstructing protein backbone geometry. This algorithm has been implemented in a computer program named P-Curve. Several examples of its possible applications are discussed.
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  • 59
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 61-69 
    ISSN: 0887-3585
    Keywords: peptides ; hormones ; amphipathic helix ; hydrophobic moment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eisenberg's helical hydrophobic moment (〈μH〉) algorithm was applied to the analysis of the primary structure of amphipathic α-helical peptide hormones and an optimal method for identifying other peptides of this class determined. We quantitate and compare known amphipathic helical peptide hormones with a second group of peptides with proven nonamphipathic properties and determine the best method of distinguishing between them. The respective means of the maximum 11 residue 〈μH〉 for the amphipathic helical and control peptides were 0.46 (±/-0.07) and 0.33 (0.07) (P+0.004). To better reflect the amphipathic potential of the entire peptide, the percent of 11 residue segments in each peptide above a particular 〈μH〉 was plotted vs 〈μH〉. The resulting curves are referred to as HM-C. The mean HM-C (of the two groups) was highly significantly different such that the HM-C method was superior to others in its ability to distinguish amphipathic from nonamphipathic peptides. Several potential new members of this structural class were identified using this approach. Molecular modeling of a portion of one of these, prolactin inhibitory factor, reveals a strongly amphipathic α helix at residues 4-21. This computer-based method may enable rapid identification of peptide of the amphipathic α-helix class.
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  • 60
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 128-138 
    ISSN: 0887-3585
    Keywords: DNA repair ; ultravioletlight ; pyrimidine dimers ; glycosylase ; apurinic/apyrimidinic endonuclease ; DNA repair enzymology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous structure/function analyses of the DNA repairenzyme, T4 endonuclease V, have suggested that the extreme carboxyl portion of the enzyme is associated with pyrimidine dimer-specific binding (Recinos and Lloyd, and Stump and Lloyd, Biochemistry 27:1832-1838 and 1839-1843, 1988, respectively). Within the final 11 amino acids there are 5 aromatic, 2 basic, and no acidic residues and it has been proposed that these residues stack with and electrostatically interact with the kinked DNA at the site of a pyrimidine dimer. The role of the tyrosine residue at position 129 has beeninvestigated by oligonucleotide site-directed mutagenesis in which the codon for Tyr-129 has been altered to reflect conservative changesof Trp and Phe and more dramatic changes of Ser- a stop, codon, deletion of the codon or introduction of a frameshift. Both changesto the aromatic amino acids resulted in proteins which accumulated will in E. coli and not only significantly enhanced the UV survival of repair, deficient cells but also complemented a defective denV gene within UV-irradiated T4 phage. Partially purified preparations of the Tyr-129 → Trp and Tyr-129 → Phe mutants were assayed for their ability to processively incise UV-irradiated plasmid DNA (a nicking reaction carried out at low 25 mM salt concentrations). The mutant enzymes Tyr-129 → Phe and Tyr-129 → Trp displayed a 1000% and 500% enhanced specific nicking activity, respectively. These reactions were also shown to be completely processive. Assays performed at higher (100 mM) salt concentrations reduced the specific activities of the mutant enzymes approximately to that of wild type for the Tyr-129 → Phe mutant and to 20% that of wild type for the Tyr1-29 → Trp mutant.
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  • 61
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 168-192 
    ISSN: 0887-3585
    Keywords: salt bridge ; ab initio ; calcium ; magnesium ; carboxylate ; phosphate ; ammonium ; guanidinium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Equilibrium geometries and binding energies of model “salt” or “ion” bridge systems have been computed by ab initio quantum chemistry techniques (GAUSSIAN82) and by empirical techniques (AMBER2.0). Formate and dimethyl phosphate served as anions in the model compounds while interacting with several organic cations, including methyl ammonium, methyl guanidinium, and divalent metal ion (either Mg2+ or Ca2+) without and with an additional chloride; and a divalent metal ion (either Mg2+ or Ca2+), chloride, and four water molecules of hydration about the metal ion. The majority of the quantum chemical computations were performed using a split-valence basis set. For the model compounds studied we find that the ab initio geometries are in remarkably goodagreement with the molecular mechanics geometries.Several Calculations werealso performed using diffuse fractions. The formate anion binds these modelcations more strongly than does dimethyl phosphate, while the organiccation methyl ammonium binds model anions more strongly than does methyl guanidinium. Finally, in model compounds including organic anions, Mg2+ or Ca2+ and four molecules of water, and a chloride anion, we find that the equilibrium structure of the magnesium complex involves a solvent separated ion pair (the magnesium ion is six coordinate), whereas the calcium ion complex remains seven coordinate. Molecular mechanics overestimates binding energies, but the estimates may be close enough to actual binding energies togive useful insight into the details energies to give useful insight into the details of salt bridges in biological systems.
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  • 62
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 306-315 
    ISSN: 0887-3585
    Keywords: oncogene ; GTP-binding protein ; cancer ; S. cerevisiae adenylyl cyclase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Biologically active forms of Ras complexed to GTP can bind to the GTP ase-activating protein (GAP), which has been implicated as a possible target of Ras in mammalian cells. In order to study the structural features of Ras required for this interaction, we have evaluated a series of mutant ras proteins for the ability to bind GAP and a series of Ras peptides for the ability to interfere with this interaction. Point mutations in the putative effector region of Ras (residues 32-40) that inhibit biological activity also impair Ras binding to GAP. An apparent exception is the Thr to Ser substitution at residue 35; [Ser-35]Ras binds to GAP as effectively as wild-type Ras even though this mutant is biologically weak in both mammalian and S. cerevisiae cells. In vitro, [Ser-35]Ras can also efficiently stimulate the S. cerevisiae target of Ras adenylyl cyclase, indicating that other factors may influence Ras/protein interactions in vivo. Peptides having Ras residues 17-44 and 17-32 competed with the binding of RAS to E. coli-expressed GAP with IC50 values of 2.4 and 0.9 μM, respectively, whereas Ras peptide 17-26 was without effect up to 400 μM. A related peptide from the yeast GTP-binding protein YPT1 analogous to Ras peptide 17-32 competed with an IC50 value of 19 μM even though the YPT1 protein itself is unable to bind to GAP. These results suggest that determinants within Ras peptide 17-32 may be important for Ras binding to GAP.
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  • 63
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 357-371 
    ISSN: 0887-3585
    Keywords: sea anemone toxin ; NMR ; distance geometry ; restrained energy minimization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: With the aid of 1H nuclear magnetic resonance (NMR) spectroscopy, the three-dimensional structure in aqueous solution was determined for ATX Ia, which is a 46 residue polypeptide neurotoxin of the sea anemone Anemonia sulcata. The input for the structure calculations consisted of 263 distance constraints from nuclear Overhauser effects (NOE) and 76 vicinal coupling constants. For the structure calculation several new or ammended programs were used in a revised strategy consisting of five successive computational steps. First, the program HABAS was used for a complete search of all backbone and χ1 conformations that are compatible with the intraresidual and sequential NMR constraints. Second, using the program DISMAN, we extended this approach to pentapeptides by extensive sapling of al conformations that are consistent with the local and medium-range NMR constraints. Both steps resulted in the definition of additional dihedral angle constraints and in stereospecific assignments for a number of β-methylene groups. In the next two steps DISMAN was used to obtain a group of eight conformers that contain no significant residual violations of the NMR constraints or van der Waals contacts. Finally, these structures were subjected to restrained energy refinement with a modified version of the molecular mechanics module of AMBER, which in addition to the energy force field includes potentials for the NOCE distance constraints and the dihedral angle constraints. The average of the pairwise minimal RMS distances between the resulting refined conformers calculated for the well defined molecular core, which contains the backbone atoms of 35 residues and 20 interior side chains, is 1.5 ± 0.3 Å. This core is formed by a four-stranded β-sheet connected by two well-defined loops, and there is an additional flexible loop consisting of the eleven residues 8-18. The core of the protein is stabilized by three disulfide bridges, which are surrounded by hydrophobic residues and shielded on one side by hydrophilic residues.
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  • 64
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 424-430 
    ISSN: 0887-3585
    Keywords: ultracentrifugation ; calcium-binding proteins ; fluorescence resonance energy transfer ; pH effect ; hydrophobic interactions ; troponin C dimer ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated pH-dependent changes of the properties of troponin C from rabbit skeletal muscle. At pH 7.5 this protein is a monomer and at pH 5.2 it is a dimer. In contrast, bovine cardiac troponin C remains essentially monomeric at pH 5.2. Bovine brain calmodulin is not a dimer, but significantly aggregated at the same acidic pH. The dimerization of skeletal troponin C was demonstrated by low-speed (16,000 rpm) sedimentation equilibrium measurements carried out at 20°C and by polyacrylamide gel electrophoresis under nondenaturing conditions. Dimer formation was significantly inhibited in the ultracentrifuge at rotor speeds of 30,000 and 40,000 rpm at 20°C, and was completely prevented at a rotor speed of 40,000 rpm and 4°C. This temperature and pressure dependence of dimerization strongly suggests that hydrophobic bonding is a major factor in promoting skeletal troponin C association at pH 5.2. The intramolecular distance between Met-25 and Cys-98 of rabbit skeletal troponin C deduced from fluorescence resonance energy transfer measurements increased by a factor of two upon lowering the pH from 7.5 to 5.2, indicating a pH-dependent transition in which the protein changed from a relatively compact conformation to an elongated conformation. The protein-induced increase in the energy transfer distance is related to the acid-induced dimerization of the protein. The extended conformation observed at pH 5.2 is compatible with the dumbbell-shaped structure of skeletal troponin C crystals obtained from turkey at pH 5.0 [Herzberg, O., James, M. N. G. Nature (London) 313:653-659, 1985] and chicken at pH 5.1 (Sundaralingam, M., Bergstrome, R., Strasburg, G., Rao, S. T., Roychowdhury, P., Greaser, M., Wang, B. C. Science 227:945-948, 1985). However, the conformation in neural solution deviates form that predicted by crystallography. Intermolecular interactions leading to dimer formation likely play an important role in promoting the extended conformation that exists at acidic pH.
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  • 65
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 8-12 
    ISSN: 0887-3585
    Keywords: ribonuclease A ; protein deamidation ; protein conformation ; disulfide bonds ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The effect of the folded conformation of a protein on the rate of deamidation of a specific asparaginyl residue has been determine. Native and unfolded ribonuclease A (RNase A) could be compared under identical conditions, because stable unfolded protein was generated by breaking irreversibly the protein disulfide bonds.Deamidation of the labile Asn-67 residue of RNase A was followedelectrophoretically and chromatographically. At 80°C, similar rates of deamidation were observed for the disulfidebonded form, which is thermally unfolded, and the reduced form. At 37°C and pH 8, however, the rate of deamidation of native RNase A was negligible, and was more than 30-fold slower than that of reduced, unfolded RNase A. This demonstrates that the Asn-67 residue is located in a local conformation in the native protein that greatly inhibits deamidation. This conformation is the β-turn of residues 66-68.
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  • 66
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 1-7 
    ISSN: 0887-3585
    Keywords: helix stabilization ; helix dipole ; charged group ; pH titration ; electrostatic interaction ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Interactions between the α-helix peptide dipoles and charged groups close to the ends of the helix were found to be an important determinant of α-helix stability in a previous study.1 The charge on the N-terminal residue of the C-peptide from ribonuclease A was varied chiefly by changing the α-NH2 blocking group, and the correlation of helix stability with N-terminal charge was demonstrated. An alternative explanation for some of those results is that the succinyl and acetyl blocking groups stabilize the helix by hydrogen bonding to an unsatisfied main-chain NH group. The helix dipole model is tested here with peptides that contain either a free α-NH3+ α-COO- groups, and no other charged groups that would titrate with similar pKa's. This model predicts that α-NH3α-COO- groups are helix-destabilizingand that the destabilizing interactions are electrostatic in origin. The hydrogen bonding model predicts that α-NH3 and α-COO- groups are not themselves helix-destabilizing, but that an acetyl or amide blocking group at the N- or C- terminus, respectively, stabilizes the helix by hydrogen bonding to an unsatisfied main-chain NH or CO group.The results are as follows: (1) Removal of the charge from α-NH3 and α-COO- groups by pH titration stabilizes an α-helix. (2) The increase in helix stability on pH titration of these groups is close to the increase produced by adding an acetyl or amide blocking group. (3) The helix-stabilizing effect of removing the charge from α-NH3 and α-COO- groups by pH titration is screened by increasing the NaCl concentration, and therefore the effect is electrostatic in origin. (4) Replacing the C-terminal amide blocking group with a methylester blocking group, which cannot donate a hydrogen bond, causes little change in helix stability.
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  • 67
    ISSN: 0887-3585
    Keywords: template-assembled synthetic protein (TASP) ; 4-helix bundle ; β-barrel structure ; protein de novo design ; peptide synthesis ; peptide conformation ; orthogonal protection ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The construction of a template-assembled synthetic protein (TASP) designed to contain both a 4-helix bundle and a β-barrel as two folding “domains” is described. For the de novo design of proteins, amphiphilic helices (α) and β-sheets (β) are covalently attached to a template peptide (T) carrying functional side chains suitably oriented to promote intarmolecular folding of the secondary structure blocks into a characteristic packing arrangement, i.e., T8-(4α)(4β). The design of this new macromolecule was assisted by computer modeling, which suggested a low-energy conformation with tight hydrophobic packing of the secondary structure subunits. Solid-phase synthesis of the “two-domain” TASP molecule was achieved using orthogonal protection techniques. The solution properties as well as circular dichroism (CD) and infrared spectroscopy (IR) data under various experimental conditions are consistent with the folded conformation suggested by modeling.
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  • 68
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 313-321 
    ISSN: 0887-3585
    Keywords: protein ; electron transfer ; molecular dynamic simulations ; dielectric ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic calculations have been carried out on a number of structural conformers of tuna cytochrome c Conformers were generated using molecular dynamics simulations with a range of solvent simulating, macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. Structures generated using the lowest dielectric models were relatively tight, with-side chains collapsed on the surface, while those from the higher dielectric modelshad more internal and external fluidity, with surface side chains exploring a fuller range of conformational space. The average structure generated with the explicitly solvated model corresponded most closely with the crystal structure. Individual pK values, overall titration curves, and electrostatic potential surfaces were calculated for average structures and along each simulation. Differences between structural conformers within each simulation give rise to substantial changes in calculated local electrostatic interactions, resulting in pK value fluctuations for individual sites in the protein that very by 0.3-2.0 pK units from the calculated time average. These variations are due to the thermal side chain reorientations that produce fluctuations in charge site separations. Properties like overall titration curves and pH dependent stability are not as sensitive to side chain fluctuations within a simulation, but there are substantial effects between simulation due to markeddifferences in average side chain behavior. These findings underscore the importance of proper dielectric formalism in molecular dynamics simulations when used to generate alternate solution structures from a crystal structure, and suggest that conformers significantly removed from the averagestructure have altered electrostatic properties that may prove important inepisodic protein properties such as catalysis.
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  • 69
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 78-92 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 70
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 97-103 
    ISSN: 0887-3585
    Keywords: protein conformation ; dynamics ; Monte Carlo simulation ; conformational energy ; minimization ; spin glass ; conformational substates ; conformational heterogeneity ; hierarchy in dynamics ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A computer experiment of protein dynamics is carried out, which consists of two steps: (1) A Monte Carlo simulation of thermal fluctuations in the native state of a globular protein, bovinepancreatic trypsin inhibitor; and (2) a simulation of the quick freezingof fluctuating conformations into energy minima by minimization of the energy of a number of conformations sampled in the Monte Carlo simulations sampled in the Monte Carlo simulation. From the analysis of results of the computer experiment is obtained the following picture of protein dynamics:multiple energy minima exist in the native state, and they are distributedin clusters in the conformational space. The dynamics has a hierarchical structure which has at least two levels. In the first level, dynamics is restricted within one of the clusters of minima. In the second, transitions occur among the clusters. Local parts of a protein molecule, side chains and local main chain segments, can take multiple locally stable conformations in the native state. Many minima result from combinations of these multiple local conformations. The hierarchical structure in the dynamics comes from interactions among the local parts. Protein moleculeshave two types of flexibility, each associated with elastic and plastic deformations, respectively.
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  • 71
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 149-155 
    ISSN: 0887-3585
    Keywords: solution scattering ; low-angle scattering ; spherical averaging ; spherical harmonics ; spherical Fourier transform ; bound water ; solvent structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: If one expands the structure factor equation in spherical coordinates, rotational averaging of the molecular Fourier transform, which leads directly to the solution scattering profile, is greatly simplified. It becomes a projection in the polar and azimuthal angular variables. The profile is given by The index j runs over all atoms; r, θ, φ are atomic coordinates and ε and N are constants; the Ym,n are complex spherical harmonics, and Jn are spherical Bessel functions; R = 2 sin θ/λ. The effects of solvent have been modeled by subtracting from each protein atom a properly weighted water. Hydrogens have been included by using scattering curves fj derived from the spherical averaging ofprotein atoms with their attached hydrogens. This approach may also be satisfactory for neutron scattering. Published scattering profiles2 for lysozyme and BPTI have been accurately matched in less than one-tenth the time required by other methods. Separate, adjustable temperature factors for the protein, solvent waters, and bound watersare used, and appear to be needed. In the case of BPTI, as suggested by NMR observations, the observed diffraction pattern was much better accounted for by including only 4 tightly bound waters rather than the roughly 60 seen by crystallography.
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  • 72
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 156-165 
    ISSN: 0887-3585
    Keywords: retrovirus integrase ; circular dichroism ; homologous proteins ; secondary structural predictions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The retrovirus integrase (IN) protein is essentialfor integration of viral DNA into host DNA. The secondary structure of thepurified IN protein from avian myeloblastosis virus was investigated by bothcircular dichroism (CD) spectroscopy and five empirical prediction methods. The secondary structures determined from the resolving of CD spectra through a least-squares curve fitting procedure were compared with those predicted from four statistical methods, e.g., the Chou-Fasman, arnier-Osguthorpe-Robson, Nishikawa-Ooi, and a JOINT scheme which combined all three of these methods, plus a pure a priori one, the Ptitsyn-Finkelstein method. Among all of the methods used, the Nishikawa-Ooiprediction gave the closest match in the composition of secondary structureto the CD result, although the other methods each correctly predictedoneor more secondary structural group. Most of the α-helix and β-sheet states predicted by the Ptitsyn-Finkelstein methodwere in accord with the Nishikawa-Ooi method. Secondary structural predictions by the Nishikawa-Ooi method were extended further toinclude IN proteins from four phylogenetic distinct retroviruses. The structuralrelationships between the four most conserved amino acid blocks of these IN proteins were compared using sequence homology and secondary structure predictions.
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  • 73
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 183-201 
    ISSN: 0887-3585
    Keywords: crystallographic refinement ; restrained least-squares refinement ; Konnert-Hendrickson refinement ; phosphodiesterase ; protein structure ; enzyme mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3′,5′-biophosphate (pdTp) has been refined by stereochemically restrained leastsquares minimization to a crystallographic R value of 0.161 at Å resolution. The estimated root-mean-square (rms) error in the coordinates in 0.16 Å. The final model comprises 1082 protein atoms, onecalcium ion, the pdTp molecule, and 82 protein atoms, onecalcium ion, the pdTp molecule, and 82 solvent water molecules;it displays an rms deviation from ideality of 0.017 Å for bond distances and 1.8° for bond angles.The mean distance between corresponding α carbons in the refined and unrefined structures is 0.6 Å we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket.The details of the calcium liganding and solvent structure in the activesite are clearly shown in the final electron density map. The structure ofthe catalytic site is consistent with mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that enzyme and substrate.
    Additional Material: 13 Ill.
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  • 74
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 75
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 224-232 
    ISSN: 0887-3585
    Keywords: effective pore's radius ; α-ketoglutarate dehydrogenase complex ; branched chain α-keto acid dehydrogenase complex ; electron microscopy ; multienzyme complex ; two-dimensional ; electrophoresis ; multienzyme complex ; aggregation of Pyruvate dehydrogenase complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In the studies of the size and structure of multienzyme complexes, a procedure complementary to electron microscopy for determining the molecular dimensions of hydrated multisubunit complexes is needed. For some applications this procedure must be capable of detecting aggregation of complexes and must be applicable to impure preparations. In the present study, a procedure of two-dimensional agarose gel electrophoresis (2d-AGE) (Serwer, P. et al. Anal. Biochem. 152: 339-345, 1986) was modified and employed to provide accurate sizemeasurements of several classical multienzyme complexes. To improve band clarity and to achieve required gel pore sizes, a hydroxyethylated agarose was used. The effective pore's radius (PE) as a function of gel concentration was determined for this agarose inthe range of PE value needed for multienzyme complexes (effective radius, R = 10-30 nm). Appropriate conditions wereestablished to measure R value ± 1% of the pyruvate (PDC), α-ketoglutarate (α-KGDC), and the branched chain α-keto acid (BCDC) dehydrogenase multienzyme complexes; the accuracy of R was limited by the accuracy of the determinations of the R value for the sizestandards. The PDC from bovine heart was found to have an R = 22.4 ± 0.2 nm following cross-linking with glutaraldehyde that was necessary for stabilization of the complex. Dimers and trimers of PDC, present in the preparations used, were separated from monomeric PDCduring 2d-AGE. All R values for the enzyme complexes studied were agreement with, though more accurate than, R valuesobtained by use of electron microscopy. In contrast to this statement, the internal dihydrolipoyl transacetylase core of PDC (E2) had an R of 18.8 ± 0.2 nm using 2d-AGE, but 10.5 nm by electron microscopy. This observation confirms the proposal that the core of the PDC has externally projecting fibrous domains invisibleto electron microscopy.
    Additional Material: 7 Ill.
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  • 76
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 259-265 
    ISSN: 0887-3585
    Keywords: cDNA expression ; deletion mutagenesis ; zymogen activation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cultured mouse myeloma cells were transfected with expression vectors encoding the aspartyl proteinase, human renin. The full construct, encoding the renin precursor prorenin, allows transfected cellsto secrete the enzymically inactive pro-protein. Activity is detectable only following trypsin treatment which mimics the physiological activation step. Accordingly, it appears that myeloma cells do not contain detectable levels of an appropriate activating proteinase. However, when these cells are transfected with a construct from which the pro-peptide coding sequence has been deleted, they secrete an apparently fully active enzyme which is indistinguishable from mature renin. We conclude that expression of the pro-peptide is not necessary to allow correct folding of the molecule and its passage through the secretory pathway.
    Additional Material: 3 Ill.
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  • 77
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 281-288 
    ISSN: 0887-3585
    Keywords: Hu protein ; integration host factor ; transcription factor 1 ; DNA bending protein ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The prokaryotic protein HU, integration host factor (IHF) from Escherichia coli and transcription factor 1 (TF1) from bacteriophage SPO1 are closely related molecules. Biochemical results suggest that the role of these proteins is to bind and bend DNA. From the high-resolution structure of HU, we propose a model for thisinteraction with DNA. Crucial amino acid differences between the proteins can be rationalized in terms of their different specific functions.
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  • 78
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 322-336 
    ISSN: 0887-3585
    Keywords: sequence conservation ; exon ; gene duplication ; protein folding ; structure-function ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Detailed analysis of the CuZn superoxide dismutase (SOD) structure provides new results concerning the significance and molecular basis for sequence conservation, intron-exon boundary locations, gene duplication, and Greek key β-barrel evolution. Using 15 aligned sequences, including a new mouse sequence, specific roles have been assigned to all 23 invariant residues and additional residues exhibiting functional equivalence. Sequence invariance is dominated by 15 residues that form the active site stereochemistry, supporting a primary biological function of uperoxide dismutation. The β-strands have no sequence insertions and deletions, whereas insertions occur within the loops connecting the β-strands and at both termini. Thus, the β-barrel with only four invariant residues is apparently over determined, but dependent on multiple cooperative side chain interactions. The regions encoded by exon I, a proposed nucleation site for protein folding, and exon III, the Zn loop involved in stability and catalysis, are the major structural subdomains not included in the internal twofold axis of symmetry passing near the catalytic Cu ion. This provides strong confirmatory evidence for gene evolution by duplication and fusion followed by the addition of these two exons. The proposed evolutionary pathway explains the structural versatility ofthe Greek key β-barrel through functional specialization and subdomain insertions in new loop connections, and provides a rationale for the size of the present day enzyme.
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  • 79
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 1-19 
    ISSN: 0887-3585
    Keywords: virus crystallography ; molecular dynamics ; hydrophobic pockets ; antiviral agents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-Ray diffraction data have been obtained for nine related antiviral agents (“WIN compounds”) while bound to human rhinovirus 14 (HRV14).These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (∼60percnt;) occupancies of these compounds in the crystal, (2) the large (up to 7.9 Å) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps.The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the β-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the β-barrel.
    Additional Material: 10 Ill.
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  • 80
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 81
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 104-127 
    ISSN: 0887-3585
    Keywords: lac repressor; lac operator ; lac headpiece-operator complex ; protein-DNA specificity ; molecular dynamics ; computer simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The results of a 125 psec molecular dynamics simulation of a lac headpiece-operator complex in aqueous solution are reported. The complexsatisfies essentially all experimental distance information derived from two-dimensional nuclear magnetic resonance (2-D-NMR) studies. The interaction between lac repressor headpiece and its operator based on many direct- and water-mediated hydrogenbonds and nonpolar contacts which allow the formation of a tight complex. Nostable hydrogen bonds between side chains and bases and found, while specific contacts occur between both nonpolar groups and, to a lesserextent, through water-mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, andchemically induced dynamic nuclear polarization (CIDNP) data.
    Additional Material: 9 Ill.
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  • 82
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 83
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 217-221 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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  • 84
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 240-248 
    ISSN: 0887-3585
    Keywords: substrate-assisted catalysis ; serine protease ; fusion proteins ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A combination of protein engineering and substrate optimization was used to create variants of the serine protease, subtilisin BPN′, which efficiently and specifically cleave a designed target sequence in a fusion protein. The broad substrate specificity of wildtype subtilisin BPN′ is greatly restricted by substitution of the catalytic histidine 64 with alanine (H64A) so that certain histidine-containing substrates are preferentially hydrolysed (Carter, P., Wells, J. A. Science 237:394-399, 1987). The catalytic efficiency, (kcat/Km), of this H64A variant was increased almost 20-fold by judicious choice of substrate and by installing three additional mutations which increase the activity of wild-type subtilisin. The most favorable substrate sequence identified was introduced as a linker in a fusion protein between a synthetic IgG binding domain of Staphylococcus aureus protein A and Escherichia coli alkaline phosphatase. The fusion protein (affinity purified on an IgG column) was cleaved by the prototype H64A enzyme and its improved variant, efficiently and exclusively at the target site, to liberate an alkaline phosphatase product of the expected size and N-terminal sequence. Several features of H64A variants of subtilisin make them attractive for site-specific proteolysis of fusion proteins: they have exquisite substrate specificity on the N-terminal side of the cleavage site and yet are broadly specific on the C-terminal side; they can be produced in large quantities and remain highly active even in the presence of detergents, reductants (modest concentrations), protease inhibitors, at high temperatures, or when specifically immobilized on a solid support.
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  • 85
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 284-293 
    ISSN: 0887-3585
    Keywords: calmodulin ; peptides ; fluorescence spectroscopy ; photoaffinity labeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Calmodulin is known to bind target enzymes and basic, amphiphilic peptides in a Ca2+-dependent manner. Recently, we introduced a photoaffinity label, p-benzoylphenylalanine (Bpa), into the sequence of a model, α-helical, calmodulin-binding peptide. When the Bpa residue was introduced at the third position of the peptide, Met-144 on the C-terminal domain of calmodulin was labeled, whereas when the photolabel was placed at the thirteenth position, Met-71 on the N-terminal do main was labeled. Assuming that both peptides bind in similar orientations, these results are not consistent with the crystal structure of calmodulin, in which the domains are held at a significant distance from one another by a long α-helical segment. To test the assumption that both peptides bind in similar orientations, we have synthesized a calmodulin-binding peptide with the photolabel in both the third and the thirteenth positions. Upon photolysis, this peptide forms a cross-link between Met-71 and Met 124 on the N- and C-terminal domains, respectively. Furthermore, a peptide with a Bpa in the thirteenth position and a Trp residue in the third position was also synthsized. After photocross-linking the Bpa redidue of this peptide to Met-71 of calmodulin, it could be shown that the fluorescence properties of the Trp residue were consistent with its side chain being buried in a hydrophobic pocket on the C-terminal domain of calmodulin. These data indicate that, when complexed with basic, amphiphi peptides, calmodulin can adopt a conformation in which its two domains are significantly closer than in the crystal sturcture of the uncommplexed protein.
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  • 86
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 231-239 
    ISSN: 0887-3585
    Keywords: phosphotyrosine linkage ; protein-DNA transesterification ; enzyme mechanism ; DNA-protein covalent complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Tyrosine 319 of E. coli topoisomerase I is shown to be the activesite tyrosine that becomes covalently attached to a DNA 5′ phosphoryl group during the transient breakage of a DNA internucleotide bond by the enzyme. The tyrosine was mapped by trapping the covalent complex between the DNA and DNA topoisomerase I, digesting the complex exhaustively with trypsin, and sequencing the DNA-linked tryptic peptide. Site-directed mutagenesis converting Tyr-319 to a serine or phenylalanine completely inactivates the enzyme. The structure of the enzyme andits catalysis of DNA strand breakage, passage, and rejoining are discussed in terms of the available information.
    Additional Material: 4 Ill.
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  • 87
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 259-266 
    ISSN: 0887-3585
    Keywords: protein folding ; folding intermediate ; hydrophobic effect ; tryptophan fluorescence ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The rapid kinetic phase that leads from unfolded species to transient folding intermediates in dihydrofolate reductase from Escherichia coli was examined by site-directed mutagenesis and by physicochemical means. The absence of this fluorescence-detected phase in the refolding of the Trp-74Phe mutant protein strongly implies that this early phase in refolding can be assigned to just one of the five Trp residues in the protein, Trp-74. In addition, water-soluble fluorescence quenching agents, iodide and cesium, have a much less significant effect on this early step in refolding than on the slower phases that lead to native and nativelike conformers. These and other data imply that an important early event in the folding of dihydrofolate reductase is the formation of a hydrophobic cluster which protects Trp-74 fromsolvent.
    Additional Material: 3 Ill.
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  • 88
    ISSN: 0887-3585
    Keywords: α-helix ; EPR ; trypsinolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Colicin E1 is an E. coli plasmid-lencoded water-soluble protein that spontaneously inserts into lipid membranes to form a voltage-gated ion channel. We have employed a novel approach is which site-directed mutagenesis is used to provide highly specific attachment points for nitroxide spin labels. A series of colicin mutants, differing only by the position of a single cysteine residue, were prepared and selectively labeled at that cysteine. A hydrophilic sequence (398-406) within the C-terminal domain of the water-soluble form of the protein was investigated and exhibited an electron paramagnetic resonancc (EPR) spectral periodicity strongly suggesting an amphiphilic α-helix. After removal of the N—terminus of the protein with trypsin, the spectra for this sequence indicate increased label mobility and a more flexible structure.
    Additional Material: 7 Ill.
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  • 89
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 382-394 
    ISSN: 0887-3585
    Keywords: immunoglobulins ; hydrogen bonding ; hairpin loops ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Loops are integral components of protein structures, providing links between elements of secondary structure, and in many cases contributing to catalytic and binding sites.The conformations of short loops are now understood to depend primarily on their amino acid sequences. In contrast, the structural determinants of longer loops involve hydrogen-bonding and packing interactions within the loop and with other parts of the protein. By searching solved protein structures for regions similar in main chain conformation to the antigen-binding loops in immunoglobulins, we identified medium-sized loops of similar structure in unrelated proteins, and compared the determinants of their conformations.For loops that form compact substructures the major determinant of the conformation is the formation of hydrogen bonds to inward-pointing main chain atoms. For oops that have more extended conformations, the major determinant of their structure is the packing of a particular residue or residues against the rest of the protein.The following picture emerges: Medium-sized lops of similar conformation are stabilized by similar interaction. The groups that interact with the loop have very similar spatial dispositions with respect to the loop. However, the residues that provide these interactions may arise from dissimilar parts of the protein: The conformation of the loop requires certain interactions that the protein may provide in a variety of ways.
    Additional Material: 11 Ill.
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  • 90
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 341-356 
    ISSN: 0887-3585
    Keywords: neuraminidase (sialidase) of influenza virus ; structure ; enzyme active site ; escape mutants ; structure of epitopes ; structures of neuraminidase ; Fab complexes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: It is the enzyme neuraminidase, projecting form the surface of influenza virus particles, which allows the virus to leave infected cells and spread in the body. Antibodies which inhibit the enzyme limit the infection, but antigenic variation of the neuraminidase renders it ineffective in a vaccine. This article describes the crystal structure of influenza virus neuraminidase, information about the active site which may lead to development of specific and effective inhibitors of the enzyme, and the structure of epitopes (antigenic determinants) on the neuraminidase. The 3-dimensional structure of the epitopes was obtained by X-ray diffraction methods using crystals of neuraminidase complexed with monoclonal antibody Fab fragments. Escape mutants, selected by growing virus in the presence of monoclonal antibodies to the neuraminidase, possess single amino acid sequence changes. The crystal structure of two mutants showed that the change in structure was restricted to that particular sidechain, but the change in the epitope was sufficient to abolish antibody binding even though it is known in one case that 21 other amino acids on the neuraminidase are in contact with the antibody.
    Additional Material: 15 Ill.
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  • 91
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 395-404 
    ISSN: 0887-3585
    Keywords: folding pathway ; tryptophan synthase ; acid denaturation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The β2 subunit of Escherichia coli tryptophan synthase can be either unfolded in 6 M guanidine, or extensively denatured at acidic pH. These two denatured form of β2 have different circular dichroism spectra and thus correspond to distinct physical states. Here we compare the folding pathways of these two different denatured forms of β chains. We describe the kinetics of regain of a variety of physical, functional, ad immunochemical signals characteristic of six successive steps previously identified on the folding pathway of guanidine unfolded β2. It is shown that whereas identical molecular events over with the same kinetics, the two folding pathways are different, and involve different structural intermediates.
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  • 92
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 47-65 
    ISSN: 0887-3585
    Keywords: crystal growth ; helical conformation ; repetitive octapeptide ; icelike molecular surface ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The active conformation of an icenucleation protein, whose major portion consists of a long polypeptide segment of nearly repetitive octapeptides, is predicted by the analyses of conformational energy and the mechanism of crystal growth. The protein ideally has an exact octapeptide repetition and is assumed to have a helical conformation. The present study searched for low-energy helical conformations and each of the obtained low-energy conformations examined as to whether it has a surface structure that can promote crystal formation. Two conformations obtained were good candidates for an ice nucleus. Both were found to have on their surfaces an arrangement of hydrogen-bonding sites, which fits well with those of hydrogen bonds in hexagonal ice crystal. Further, one of the two conformations had a hexagonal conformational symmetry consistent with the hexagonal ice crystal structure. The other conformation had apentagonal conformational symmetry that could enable the growth of an ice crystal-dendritic polycrystalline snow crystal-which grows on metastable cubic ice.
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  • 93
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 66-77 
    ISSN: 0887-3585
    Keywords: subunit interactions ; allosteric regulation ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Although ionizable groups are known to play important roles in the assembly, catalytic, and regulatory mechanisms of Escherichia coli aspartate transcarbamylase, these groups have not been characterized in detail. We report the application of static accessibility modified Tanford-Kirkwood theory to model electrostatic effects associated with the assembly of pair of chains, subunits, and the holoenzyme. All of the interchain interfaces except R1-R6 are stabilized by electrostatic interactions by -2 to -4 kcal-m-1 at pH 8. The pH dependence of the electrostatic component of the free energy of stabilization of intrasubunit contacts (C1-C2 and R1-R6) is qualitatively different from that of intersubunit contacts (C1-C4, C1-R1, and C1-R4). This difference may allow the transmission of information across subunit interfaces to be selectively regulated. Groups whose calculated pK or charge changes as a result of protein-protein interactions have been identified and the results correlated with available information about their function. Both the 240s loop of the c chain and the region near the Zn(II) ion of the r chain contain clusters of ionizable groups whose calculated pK values change by relatively large amounts upon assembly. These pK changes in turn extend to regions of the protein remote from the interface. The possibility that networks of ionizable groups are involved in transmitting information between binding sites is suggested.
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  • 94
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 95
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 93-95 
    ISSN: 0887-3585
    Keywords: folding intermediate ; molten globule state ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous results from equilibrium and kinetic studies of the folding of bovine growth hormone (bGH) have demonstrated that bGH does not follow a simple two-step folding mechanism. These results are summarized and interpreted according to the “molten globule” model. The molten globule state of bGH is characterized as a folding intermediate which largely a-helical, retains a compact hydrodynamic radius, has packing of the aromatic side chains that is similar to the unfolded state, and possesses a solvent-exposed hydrophobic surface along helix 106127 that readily leads association.
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  • 96
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    Proteins: Structure, Function, and Genetics 5 (1989), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 97
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 104-112 
    ISSN: 0887-3585
    Keywords: conformational fluctuations ; conformational heterogeneity ; conformational energy ; hierarchical structure ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Conformational fluctuations in a globular protein, bovine pancreatic trypsin inhibitor, in the time range between picoseconds and nanoseconds are studied by a Monte Carlo simulation method. Multipleenergy minima are derived from sampled conformations by minimizing their energy. They are distributed in clusters in the conformational space. A hierarchical structure is observed in the simulated dynamics. In the time range between 10-14 and 10-10 seconds dynamics is well represented by a superposition of vibrational motions within an energy well with transitions among minima within each cluster. Transitions among clusters take place in the time range of nanoseconds or longer.
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  • 98
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 113-124 
    ISSN: 0887-3585
    Keywords: conformational fluctuations ; Monte Carlo simulation ; conformational energy ; conformational heterogeneity ; side chain conformation ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis is carried out of differences in the minimum energy conformations obtained in the previous paper by energy minimization starting from conformations sampled by a Monte Carlo simulation of conformational fluctuations in the native state of a globular protein, bovine pancreatictrypsin inhibitor. Main conformational differences in each pair of energy minima are found usually localized in several side chains and in a few localmain chain segments. Such side chains and local main chain segments are found to take a few distinct local conformations in the minimum energy conformations. Energy minimum conformations can thus be described in terms of combinations of these multiple local conformations.
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  • 99
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    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 132-138 
    ISSN: 0887-3585
    Keywords: protein conformation ; dynamics ; Monte Carlo simulation ; conformational energy ; minimization ; hierarchy in dynamics ; conformational heterogeneity ; flexibility ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Distances between centers of gravity of individual residues are compared among the minimum energy conformations derived from the recordof the Monte Carlo simulation of conformational fluctuations in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations originating from the multiplicity of localconformations cause deformations of the whole structure of the molecule in various ways, which can be classified into two types. Type 1:When a local deformation occurs in a region consisting of a few residues near the surfaceof the molecule, the whole shape of the molecule responds by deforming elastically. The magnitude of this deformation is in the range of thermalfluctuations calculated by the harmonic approximation around a singleminimum. Type 2: We have observed one case belonging to the second type in which local deformations occur cooperatively in an extended region. This regiongoes across the whole molecule and divide the remaining parts into two. Atom packing changes in and around the extended region of local deformations. For this reason deformation in this region is plastic. Relative locationand orientation between the divided two parts change very much. Deformationof the whole shape in this case, associated with the plastic deformationin an extended region, demonstrates that protein molecules have a flexibility beyond the harmonic limit.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 248-257 
    ISSN: 0887-3585
    Keywords: subunit interactions ; icosahedral capsid ; electrostatic potential ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The role of the electrostatic interactions in the stability of the icosahedral β60 capsid of heavy riboflavin synthase from Bacillus Subtilis has been investigated using an approach based on the theory of Kirkwood and Tanford. The pH dependence of the electrostatic subunit interaction agrees well with experimental data. The electrostatic subunit interaction energy has a pronounced minimum at pH 8.2 for both the ligated and ligand-free capsid. The latter is characterized by a reduction of the magnitude and the pH range of the electrostatic attraction. It is found that only 8 charged groups, which form one cluster and two ion pairs, provide a significant contribution to the capsid stability. The analysis has shown that the aggregation/disaggregation equilibrium seems to be regulated by electrostatic interactions between β-subunits forming dimers, which connect the relatively stable pentamers in the β-60 capsid. The release of the ligand causesareduction of the electrostatic attraction of the dimers, which may induce disaggregation of the capsid. The electrostatic potential field due tothe titratable groups and α-helix macrodipoles has been calculated on the basic of the Coulomb relation. Two different values of the dielectric constant have been used for the protein and the surrounding solvent, respectively. The electrostatic potential shows a radially polardistribution with a positive pole at the inner capsid wall and a negative pole outside the capsid. An interesting feature of the electrostatic field is the formation of the positive potential “channels” that coincide with the channels constituted by the pentameric and trimeric β-subunit aggregates. It is supposed that the electrostatic potential field plays a role in enzyme-substrate recognition.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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