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  • Chemistry  (9,908)
  • Atomic, Molecular and Optical Physics  (441)
  • 1990-1994  (10,349)
  • 1965-1969
  • 1992  (10,349)
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  • 1990-1994  (10,349)
  • 1965-1969
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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 6 (1992), S. 229-229 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 6 (1992), S. i 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 0886-9383
    Keywords: Predictive ability ; Regression ; PLS ; SDEP ; Cross-validation ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The standard deviation of prediction errors (SDEP) is used to evaluate and compare the predictive ability of some regression models, namely MLR, ACE and linear and non-linear PLS, the last being the best one. The parameter is determined by a cross-validation approach as an average of several runs obtained on forming groups in a random way. The variation in SDEP with the number of latent variables in PLS is also discussed.
    Additional Material: 3 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 6 (1992), S. 177-188 
    ISSN: 0886-9383
    Keywords: PLS ; Prediction error ; Background constituents ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A modification of a technique proposed by Lorber and Kowalski for the estimation of prediction errors is presented. The method is applied to five data sets. The results show that for some data sets the estimated prediction errors are close to the actual prediction errors for samples within the calibration range, while samples outside the calibration range must be background corrected before quantification of the prediction error.
    Additional Material: 10 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 6 (1992), S. 189-198 
    ISSN: 0886-9383
    Keywords: Robust regression ; Partial least squares ; QSAR ; Perturbation study ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A robust partial least squares (PLS) regression algorithm is developed. This is achieved by substitution of the univariate regression steps in the iterative PLS2 algorithm by a robust alternative. The angle between loading vectors from both perturbed and unperturbed solutions is used as a measure of robustness. By means of a perturbation study on a structure-activity data set, it is demonstrated that the stability of the robust method is superior to standard PLS.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 10
    ISSN: 0886-9383
    Keywords: Principal factor analysis ; Factor analysis ; Eigenvalue analysis ; Multivariate analysis ; Weighted factor analysis ; Procrustean analysis ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two approximate methods for weighted principal components analysis (WPCA) were devised and tested in numerical experiments using either empirical variances (obtained from replicated data) or assumed variances (derived from unreplicated data). In the first (‘spherical’) approximation each data vector was assigned a weight proportional to the geometrical mean of its variances in all dimensions. The arithmetical mean of variances was used instead in the other approximation. Both the numerical experiments with artificial data containing random errors of various kinds (constant, proportional, constant plus proportional, Poisson) and the analysis of two sets of Raman spectra clearly indicated the necessity of introducing statistical weights. The spherical approximation was found to be slightly better than the arithmetical one. The application of statistical weighting was found to improve the performance of PCA in estimation problems.
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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 6 (1992), S. 357-357 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 13
    ISSN: 0886-9383
    Keywords: Derivatization reaction ; Factorial design ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A number of nucleophiles have been successfully identified and quantified using the Kröhnke reaction with 2,3-diphenyl derivatives of quinolizinium salts. Optimization of the reaction conditions by means of a mathematical model involving analysis of the response surface has led to a better understanding of the factors exerting an influence on the above reaction.The parameters chosen were temperature, reaction time, base concentration, water concentration and nucleophile concentration. The reaction was developed in polar aprotic solvents (acetone, acetonitrile). To facilitate the nucleophilic attack, the presence of an organic base (triethylamine) was necessary, although concentrations in excess of 0·15M did not alter the development of the reaction. Since pharmaceutical solutions are often aqueous, the influence of water on the reaction was studied. Low water volumes have no significant influence on the opening of the quinolizinium ring by the nucleophilic reagent. However, when the water proportion exceeded that of the organic solvent, the fluorescence intensity was lower than expected. Development of the fluorescent reaction product was first detected 5 min after the reaction started. The fluorescence intensity reached its optimum value after 138 min.
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: hematopoiesis ; colony-stimulating factors ; structure-function relationships ; GM-CSF ; IL-3 ; helical proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The hematopoietic growth factors are a family of glycoproteins involved in the production of blood cells from their bone marrow precursors and in the activation of mature blood cells. Much has been learned about the structural features of these molecules responsible for their characteristic biological activities. Most studies have been based upon mutagenesis strategies of intact polypeptides and on epitope mapping of informative monoclonal antibodies to the growth factors. A more limited amount of physical data is available. This review will summarize these findings, highlight the growing body of evidence suggesting that many of these proteins share common evolutionary origins and structural elements, and hopefully point to the directions being taken for further investigations of these scientifically informative and clinically useful group of proteins.
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  • 15
    ISSN: 0887-3585
    Keywords: computer-aided drug design ; database search ; molecular docking ; protein structure ; protein-ligand interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A computer algorithm, CLIX, capable of searching a crystallographic database of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenzavirus hemagglutinin and of proposing a number of potential new ligands to this protein.
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  • 16
    ISSN: 0887-3585
    Keywords: crystallization ; X-ray diffraction ; immunoaffinity chromatography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The class I major histocompatibility (MHC) antigen HLA-B27 was purified by immunoaffinity chromatography from the homozygous human B lymphoblastoid cell line LG-2. Detergent-soluble HLA-B27 was cleaved with the protease papain to remove the hydrophobic transmembrane region and the cytoplasmic tail. Crystals of the resulting water-soluble extracellular fragments were obtained in hanging drops by the vapor-diffusion method. The crystals are triclinic, space group P1, with unit cell dimensions a = 45.9 Å, b = 71.0 Å, c = 83.7 Å, α = 79.4°, β = 88.5°, γ = 89.9°, and diffract beyond 2.5 Å resolution.
    Additional Material: 3 Ill.
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  • 17
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 18
    ISSN: 0887-3585
    Keywords: protein folding ; multiple minima problem ; peptide conformation ; energy calculation ; helices ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated the conformational properties of a truncated analogue of mastoparan and of mastoparan X, both peptides from wasp venom. The electrostatically driven Monte Carlo method was used to explore the conformational space of these short peptides. The initial conformations used in this study, mainly random ones, led to α-helical conformations. The α-helical conformations thus found exhibit an amphipathic character. These results are in accord with experimental data from NMR and CD spectroscopy.
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  • 19
    ISSN: 0887-3585
    Keywords: neutron D2O—H2O solvent difference maps ; neutron diffraction ; trypsin water structure ; density modification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method of determining the water structure in protein crystals is described using neutron solvent difference maps. These maps are obtained by comparing the changes in diffracted intensities between two data sets, one in which H2O is the major solvent constituent, and a second in which D2O is the solvent medium. To a good first approximation, the protein atom contributions to the scattering intensities in both data sets are equal and cancel, but since H2O and D2O have very different neutron-scattering properties, their differences are accentuated to reveal an accurate representation of the solvent structure. The method also employs a series of density modification steps that impose known physical constraints on the density distribution function in the unit cell by making real space modifications directly to the density maps. Important attributes of the method are that (1) it is less subjective in the assignment of water positions than X-ray analysis; (2) there is threefold improvement in the signal-to-noise ratio for the solvent density; and (3) the iterative density modification produces a low-biased representation of the solvent density. Tests showed that water molecules with as low as 10% occupancy could be confidently assigned.About 300 water sites were assigned for trypsin from the refined solvent density; 140 of these sites were defined in the maps as discrete peaks, while the remaining were found within less-ordered channels of density. There is a very good correspondence between the sites in the primary hydration layer and waters found in the X-ray structure. Most water sites are clustered into H-bonding networks, many of which are found along intermolecular contact zones. The bound water is equally distributed between contacting apolar and polar atoms at the protein interface. A common occurence at hydrophobic surfaces is that apolar atoms are circumvented by one or more waters that are part of a larger water network. When the effects on surface accessibility by neighboring molecules in the crystal lattice are taken into consideration, only about 29% of the surface does not interface ordered water. About 25% of the ordered water is found in the second hydration sphere. In many instances these waters bridge larger clusters of primary layer waters. It is apparent that, in certain regions of the crystal, the organization of ordered water reflects the characteristics of the crystal environment more than those of trypsin's surface alone.
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  • 20
    ISSN: 0887-3585
    Keywords: α/β-barrels ; protein structure ; loops ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A systematic survey of seven parallel α/β barrel protein domains, based on exhaustive structural comparisons, reveals that a sizable proportion of the αβ loops in these proteins - 20 out of a total of 49 - belong to either one of two loop types previously described by Thornton and co-workers. Six loops are of the αβ1 type, with one residue between the α-helix and β-strand, and 13 are of the αβ3 type, with three residues between the helix and the strand. Protein fragments embedding the identified loops, and termed αβ connections since they contain parts of the flanking helix and strand, have been analyzed in detail revealing that each type of connection has a distinct set of conserved structural features. The orientation of the β-strand relative to the helix and loop portions is different owing to a very localized difference in backbone conformation. In αβ1 connections, the chain enters the β-strand via a residue adopting an extended conformation, while in αβ3 it does so via a residue in a near α-helical conformation. Other conserved structural features include distinct patterns of side chain orientation relative to the β-sheet surface and of main chain H-bonds in the loop and the β-strand moieties. Significant differences also occur in packing interactions of conserved hydrophobic residues situated in the last turn of the helix. Yet the α-helix surface of both types of connections adopts similar orientations relative to the barrel sheet surface. Our results suggest furthermore that conserved hydrophobic residues along the sequence of the connections, may be correlated more with specific patterns of interactions made with neighboring helices and sheet strands than with helix/strand packing within the connection itself. A number of intriguing observations are also made on the distribution of the identified αβ1 and αβ3 loops within the α/β-barrel motifs. They often occur adjacent to each other; αβ3 loops invariably involve even numbered β-strands, while αβ1 loops involve preferentially odd β-strands; all the analyzed proteins contain at least one αβ3 loop in the first half of the eightfold α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel motifs are discussed.
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  • 21
    ISSN: 0887-3585
    Keywords: serine protease ; MNDO Hamiltonian ; SCF charges ; energy minimization ; dissociation constant ; inhibitor design ; catalytic mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A step leading to the formation of the covalent complexes between porcine pancreatic elastase (PPE) and 7-[(alkylcarbamoyl)amino]-4-chloro-3-ethoxyisocoumarins (alkylHNCO-EICs) is the formation of the non-covalent Michaelis complex. No average structures are available for the Michaelis complexes of PPE with alkylHNCO-EICs. We present the results of an initial step in obtaining these structures and have determined kinetic constants as well. The kinetic results indicate that formation of the Michaelis complex is what differentiates the effectiveness of these inhibitors in inactivating PPE. The structural and kinetic results together suggest that the structure of the Michaelis complex is necessary for the design of potent alkylHNCO-EIC inhibitors of PPE. Two novel alkylHNCO-EICs are predicted to be the best inhibitors of this series. An alternate mechanism for serine protease inhibition is also proposed. Evidence for, and studies that may add support to, the hypothesized mechanism are discussed. © 1992 Wiley-Liss, Inc.
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  • 22
    ISSN: 0887-3585
    Keywords: bacterial lactate dehydrogenase ; X-ray crystallography ; site-directed mutation ; stereospecificity ; image plates ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bacillus stearothermophilus lactate dehydrogenase, one of the most thermostable bacterial enzymes known, has had its three-dimensional structure solved, the gene coding for it has been cloned, and the proteincan be readily overexpressed. Two mutants of the enzyme have been prepared. In one, Arg171 was changed to Trp (R171W) and Gln102 was changed to Arg (Q102R). In the other, the mutation Q102R was maintained, but Arg171 was changed to Tyr (R171Y). In addition, an inadvertent C97G mutant was present. Both mutants have been crystallized by the hanging drop vapor diffusion method at room temperature. Bipyrimidal crystals have been obtained against (NH4)2SO4in 50 mM piperazine HCI buffer. The crystals belong to space group P6622 (P6622) (whereas the native enzyme, the structure of which has been solved by Piontek et al., Proteins 7:74-92, 1990) crystallized in the space group (P61) with a = 102.3 Å, c = 168.6 Å for the R171W, Q102R, C97G triple mutant, and a = 98.2 Å; c = 162.1 Å for the R171Y, Q102R, C97G mutant. These crystal forms appear to contain one-quarter of a tetramer (Mr 135,000)in the asymmetric unit and have (VM values of 3.8 and 3.3 Å3/dalton, respectively). The R171W mutant diffracts to 2.5 Å and the R171Y mutant to approximately 3.5 Å © 1992 Wiley-Liss, Inc.
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  • 23
    ISSN: 0887-3585
    Keywords: crystallography ; protein structure ; refinement ; dinucleotide binding domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional crystal structure of the NAD+-linked glutamate dehydrogenase from Clostridium symbiosum has been solved to 1.96 Å resolution by a combination of isomorphous replacement and molecular averaging and refined to a conventional crystallographic R factor of 0.227. Each subunit in this multimeric enzyme is organised into two domains separated by a deep cleft. One domain directs the self-assembly of the molecule into a hexameric oligomer with 32 symmetry. The other domain is structurally similar to the classical dinucleotide binding fold but with the direction of one of the strands reversed. Difference Fourier analysis on the binary complex of the enzyme with NAD+ shows that the dinucleotide is bound in an extended conformation with the nicotinamide moiety deep in the cleft between the two domains. Hydrogen bonds between the carboxyamide group of the nicotinamide ring and the side chains of T209 and N240, residues conserved in all hexameric GDH sequences, provide a positive selection for the syn conformer of this ring. This results in a molecular arrangement in which the A face of the nicotinamide ring is buried against the enzyme surface and the B face is exposed, adjacent to a striking cluster of conserved residues including K89, K113, and K125. Modeling studies, correlated with chemical modification data, have implicated this region as the glutamate/2-oxoglutarate binding site and provide an explanation at the molecular level for the B type stereospecificity of the hydride transfer of GDH during the catalytic cycle.
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  • 24
    ISSN: 0887-3585
    Keywords: enzyme catalysis ; Laue diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hexagonal crystals of turkey egg white lysozyme have been examined for activity in order to evaluate their potential for use in time-resolved X-ray crystallographic experiments. Substrates used in this study were hexa-N-acetylglucosamine (hexa-GlcNAc) and a modified analogue of hexa-GlcNAc where the terminal sugar ring was opened by reduction with tritiated sodium borohydride. This gave a labeled β-N-acetylglucosaminitol unit at the sixth position of the sugar chain and allowed easy quantitation of enzymatic cleavage on TLC plates. Using these substrates, it has been shown that turkey egg white lysozyme is enzymatically active in the crystal. Enzyme dispersed in the buffer surrounding the crystal does not show detectable activity under conditions relevant to an X-ray experiment. Unmodified hexa-GlcNAc is hydrolyzed into di-, tri-, and tetrasaccharides in the crystal. This cleavage pattern is different from that obtained with hen egg white lysozyme in solution and likely causes of the differences are discussed. The reduced radiolabeled oligosaccharide has a unique cleavage pattern with trisaccharides as the products. The specific activity of the enzyme with the radiolabelled analogue was 9.8 (± 1.0) × 10-7 mmol/min/mg protein at 22°C in the crystal.
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  • 25
    ISSN: 0887-3585
    Keywords: carboxylate groups ; difference maps ; fiber diffraction ; lead ; virus assembly ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lead has been used as a substitute for calcium binding to tobacco mosaic virus (TMV). The high atomic number of lead has allowed us to use difference maps from X-ray fiber diffraction data to characterize a calcium-binding site in the virus. The metal ligands are slightly different from those previously believed to bind calcium to TMV, although the binding site is very close to one previously described. Two acetate groups are also bound to the lead atom. There is no significant backbone conformational change in the protein as a result of metal binding; the binding is accomplished by means of relatively small movements in amino acid side chains.
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  • 26
    ISSN: 0887-3585
    Keywords: X-ray structure ; TLS analysis ; aspartic proteinases ; inhibitor complexes ; catalysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparison of the three-dimensional structures of native endothiapepsin (EC 3.4.23.6) and 15 endothiapepsin oligopeptide inhibitor complexes defined at high resolution by X-ray crystallography shows that endothiapepsin exists in two forms differing in the relative orientation of a domain comprising residues 190-302. There are relatively few interactions between the two parts of the enzyme; consequently, they can move as separate rigid bodies. A translational, librational, and screw analysis of the thermal parameters of endothiapepsin also supports and model in which the two parts can move relative to each other. In the comparison of different aspartic proteinases, the rms values are reduced by up to 47% when the two parts of the structure are superposed independently. This justifies description of the differences, including those between pepsinogen and pepsin (EC 3.4.34.1), as a rigid movement of one part relative to another although considerable distortions within the domains also occur. The consequence of the rigid body movement is a change in the shape of the active site cleft that is largest around the S3 pocket. This is associated with a different position and conformation of the inhibitors that are bound to the two endothiapepsin forms. The relevance of these observations to a model of the hydrolysis by aspartic proteinases is briefly discussed.
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  • 27
    ISSN: 0887-3585
    Keywords: apolipoprotein[a] ; lipoprotein[a] ; plasminogen ; kringle ; prothrombin ; lysine-binding site ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Apolipoprotein[a], the highly glycosylated, hydrophilic apoprotein of lipoprotein[a] (Lp[a]), is generally considered to be a multimeric homologue of plasminogen, and to exhibit atherogenic/thrombogenic properties. The cDNA-inferred amino acid sequence of apo[a] indicates that apo[a], like plasminogen and some zymogens, is composed of a kringle domain and a serine protease domain. To gain insight into possible positive functions of Lp[a], we have examined the apo[a] primary structure by comparing its sequence with those of other proteins involved in coagulation and fibrinolysis, and its secondary structure by using a combination of structure prediction algorithms. The kringle domain encompasses 11 distinct types of repeating units, 9 of which contain 114 residues. These units, called kringles, are similar but not identical to each other or to PGK4. Each apo[a] kringle type was compared with kringles which have been shown to bind lysine and fibrin, and with bovine prothrombin kringle 1. Apo[a] kringles are linked by serine/threonine- and proline-rich stretches similar to regions in immunoglobulins, adhesion molecules, glycoprotein Ib-α subunit, and kininogen. In comparing the protease domains of apo[a] and plasmin, apo[a] contains a region between positions 4470 and 4492 where 8 substitutions, 9 deletions, and 1 insertion are apparent. Our analysis suggests that apo[a] kringle-type 10 has a high probability of binding to lysine in the same way as PGK4. In the only human apo[a] polymorph sequenced to date, position 4308 is occupied by serine, whereas the homologous position in plasmin is occupied by arginine and is an important site for proteolytic cleavage and activation. An alternative site for the proteolytic activation of human apo[a] is proposed.
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  • 28
    ISSN: 0887-3585
    Keywords: protein folding ; protein structure ; hydrogen bond ; serine protease ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 Å resolution and by neutron diffraction to 2.1 Å resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X-ray diffraction, which were verified by comparison to D2O—H2O difference neutron scattering density. Six of 184 water molecules in the X-ray structure, all with B-factors greater than 50 Å2, were found to be spurious after comparison with neutron results. Roughly two-thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one-half of the water of hydration was located by X-ray diffraction. Polar regions of the protein are well hydrated, and significant D2O—H2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures.Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X-ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two β-strands, which may resemble an intermediate in the formation of β sheets during the folding of a protein.
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  • 29
    ISSN: 0887-3585
    Keywords: folding nucleation ; hydrophobic cluster ; conserved loop length ; structure-sequence relationship ; sequence patterns ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Greek key β-barrel topology is a folding motif observed in many proteins of widespread evolutionary origin. The arthropodan hemocyanins also have such a Greek key β-barrel, which forms the core of the third domain of this protein. The hemocyanin β-barrel was found to be structurally very similar to the β-barrels of the immunoglobulin domains, Cu,Zn-superoxide dismutase and the chromophore carrying antitumor proteins. The structural similarity within this group of protein families is not accompanied by an evolutionary or functional relationship. It is therefore possible to study structure-sequence relations without bias from nonstructural constraints. The present study reports a conserved pattern of features in these Greek key β-barrels that is strongly suggestive of a folding nucleation site. This proposed nucleation site, which we call a “β-zipper,” shows a pattern of well-conserved, large hydrophobic residues on two sequential β-strands joined by a short loop. Each β-zipper strand is near the center of one of the β-sheets, so that the two strands face each other from opposite sides of the barrel and interact through their hydrophobic side chains, rather than forming a hydrogen-bonded β-hairpin. Other protein families with Greek key β-barrels that do not as strongly resemble the immunoglobulin fold - such as the azurins, plastocyanins, crystallins, and prealbumins - also contain the β-zipper pattern, which might therefore be a universal feature of Greek key β-barrel proteins.
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  • 30
    ISSN: 0887-3585
    Keywords: conformational search ; directed searches ; α-carbon coordinates ; modeling ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A directed conformational search algorithm using the program CONGEN (ref. 3), which samples backbone conformers, is described. The search technique uses information from the partially built structures to direct the search process and is tested on the problem of generating a full set of backbone Cartesian coordinates given only α-carbon coordinates. The method has been tested on six proteins of known structure, varying in size and classification, and was able to generate the original backbone coordinates with RMSs ranging from 0.30-0.87Å for the α-carbons and 0.5-0.99Å RMSs for the backbone atoms. Cis peptide linkages were also correctly identified. The procedure was also applied to two proteins available with only α-carbon coordinates in the Brookhaven Protein Data Bank; thioredoxin (SRX) and triacyiglycerol acylhydrolase (TGL). All-atom models are proposed for the backbone of both these proteins. In addition, the technique was applied to randomized coordinates of flavodoxin to assess the effects of irregularities in the data on the final RMS. This study represents the first time a deterministic conformational search was used on such a large scale. © 1992 Wiley-Liss, Inc.
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  • 31
    ISSN: 0887-3585
    Keywords: phage peptide libraries ; conformationally constrained peptides ; IIb/IIIa peotide antagonists ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Methods have recently been developed to present vast libraries of random peptides on the surface of filamentous phage. To introduce a degree of conformational constraint into random peptides, a library of hexapeptides flanked by cysteine residues (capable of forming cyclic disulfides) was constructed. This library was screened using the platelet glycoprotein, IIb/IIIa, which mediates the aggregation of platelets through binding of fibrinogen. A variety of peptides containing the sequence Arg-Gly-Asp or Lys-Gly-Asp were discovered and synthesized. The cyclic, disulfide bonded forms of the peptides bound IIb/IIIa with dissociation constants in the nanomolar range, while reduced forms or an analogue in which Ser replaced the Cys residues bound considerably less tightly. These results demonstrate the feasibility for introducing conformational constraints into random peptide libraries and also demonstrates the potential for using phage peptide libraries to discover pharmacologically active lead compounds. © 1992 Wiley-Liss, Inc.
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  • 32
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: secondary structure prediction ; input space ; parallel processing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using a backpropagation neural network model we have found a limit for secondary structure prediction from local sequence. By including only sequences from whole α-helix and non-α-helixstructures in our training and test sets - sequences spanning boundaries between these two structures were excluded - it was possible to investigate directly the relationship between sequence and structure for α-helix. A group of non-α-helix sequences, that was disrupting overall prediction success, was indistinguishable to the network from α-helix sequences. These sequences were found to occur at regions adjacent to the termini of α-helices with statistical significance, suggesting that potentially longer α-helices are disrupted by global constraints. Some of these regions spanned more than 20 residues. On these whole structure sequences, 10 residues in length, a comparatively high prediction success of 78% with a correlation coefficient of 0.52 was achieved. In addition, the structure of the input space, the distribution of β-sheet in this space, and the effect of segment length were also investigated. © 1992 Wiley-Liss, Inc.
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  • 33
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; HIV-1 ; principal neutralizing determinant ; protein crystallization ; antipeptide antibody ; Fab sequence ; PEG crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-ray quality crystals of an Fab fragment from an antipeptide monoclonal antibody (R/V3-50.1) that recognizes the principal neutralizing determinant (PND) of the gpl20 glycoprotein of human immunodeficiency virus type 1 (HIV-1) (MN isolate) were grown as uncomplexed and peptide complexed forms. Crystals of the free Fab grew from high salt in orthorhombic space groups P212121 and I222 and from polyethylene glycol in space groups P1 and P21. Seeds from either the P1 and P21 native (uncomplexed) Fab crystals induced nucleation of crystals of the Fab complexed to a 16-residue synthetic peptide corresponding to the PND when streak seeded into preequilibrated solutions of this complex. Data were collected from these complex crystals and from each of the four native Fab forms to at least 2.8Å resolution. The genes for the variable domain of the Fab were cloned and sequenced and the primary amino acid sequence was deduced from this information. Knowledge of the three-dimensional structure of this Fab-pep-tide complex will be important in the understanding of the PND of HIV-1 and its recognition by neutralizing monoclonal antibodies. © 1992 Wiley-Liss, Inc.
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  • 34
    ISSN: 0887-3585
    Keywords: structural scaffolding ; sequence similarity ; sequence identity ; flavoprotein ; homology modeling ; lipoic acid ; mitochondrial enzyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The hypothesis that dihydrolipoamide dehydrogenases (E3s) have tertiary structures very similar to that of human glutathione reductase (GR) was tested in detail by three separate criteria: (1) by analyzing each putative secondary structural element for conservation of appropriate polar/nonpolar regions, (2) by detailed comparison of putative active site residues in E3s with their authentic counterparts in human GR, and (3) by comparison of residues at the putative dimeric interface of the E3s with the authentic residues in GR. All three criteria are satisfied in a convincing way for the 7 E3s that were considered, supporting the conclusion that the structural scaffolding and the overall tertiary structure (which determines the location of functional sites and residues) are remarkably similar for the E3s and for GR. These analyses together with the crystal structures of human erythrocyte GR formed the basis for construction of a molecular model for human E3. The cofactor FAD and the substrakes NAD and lipoic acid were also included in the model. Unexpectedly, the surface residues in the cleft that holds the lipoamide were found to be highly charged and predominantly acidic, allowing us to predict that the region around the lipoamide in the sub-unit should be basic in nature. The molecular model can be tested by site-directed mutagenesis of residues predicted to be in the dihydrolipoamide acetyltransferase subunit binding cleft. © 1992 Wiley-Liss, Inc.
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  • 35
    ISSN: 0887-3585
    Keywords: solvation ; Monte Carlo ; minimization ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Continuum solvation models that estimate free energies of solvation as a function of solvent accessible surface area are computationally simple enough to be useful for predicting protein conformation. The behaviour of three such solvation models has been examined by applying them to the minimization of the conformational energy of bovine pancreatic trypsin inhibitor.The model differ only with regard to how the constants of proportionality between free energy and surface area were derived. Each model was derived by fitting to experimentally measured equilibrium solution properties. For two models, the solution property was free energy of hydration. For the thrid, the property was NMR coupling constants. The purpose of this study is to determine the effect of applying these solvation models to the nonequilibrium conformations of a protein arising in the course of global searches for conformational energy minima. Two approaches were used: (1) local energy minimization of an ensemble of conformations similar to the equilibrium conformation and (2) global search trajectories using Monte Carlo plus minimization starting from a single conformation similar to the equilibrium conformation.For the two models derived from free energy measurements, it was found that both the global searches and local minimizations yielded conformations more similar to the X-ray crystallographic structures than did searches or local minimizations carried out in the absence of a solvation component of the conformational energy. The model derived from NMR coupling constants behaved similarly to the other models in the context of a global search trajectory. For one of the models derived from measured free energies of hydration, it was found that minimization of an ensemble of near-equilibrium conformations yielded a new ensemble in which the conformation most similar to the X-ray determined structure PTI4 had the lowest total free energy.Despite the simplicity of the continuum slvation models, the final conformation generated in the trajectories for each of the models exhibited some of the characteristics that have been reported for conformations obtained from molecular dynamics simulations in the presence of a bath of explicit water molecules. They have smaller root mean square (rms) deviations from the experimentally determined conformation, fewer incorrect hydrogen bonds, and slightly larger radii of gyration than do conformations derived from search trajectories carried out in the absence of sovlent. © 1992 Wiley-Liss, Inc.
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  • 36
    ISSN: 0887-3585
    Keywords: flavoenzymes ; monooxygenase ; FAD ; reduced flavin ; flavin planarity ; Pseudomonas fluorescens ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of the reduced form of the enzyme p-hydroxybenzoate hydroxylase from Pseudomonasm fluorescens, complexed with its substrate p-hydroxybenzoate, has been obtained by protein X-ray crystallography. Crystals of the reduced form were prepared by soaking crystals of the oxidized enzyme-substrate complex in deaerated mother liquor containing 300-400 mM NADPH. A rapid bleaching of the crystals indicated the reduction of the enzyme-bound FAD by NADPH. This was confirmed by single crystal spectroscopy.X-ray data to 2.3 Å were collected on oscillation films using a rotating anode generator as an X-ray source. After data processing and reduction, restrained least squares refinement using the 1.9 Å structure of the oxidized enzyme-substrate complex as a starting model, yielded a crystallographic R-factor of 14.8% for 11,394 reflections. The final model of the reduced complex contains 3,098 protein atoms, the FAD molecule, the substrate p-hydroxybenzoate and 322 solvent molecules.The structures of the oxidized and reduced forms of the enzyme-substrate complex were found to be very similar. The root-mean-square discrepancy for all atoms between both structures was 0.38 Å. The flavin ring is almost completely planar in the final model, although it was allowed to bend or twist during refinement. The observed angle between the benzene and the pyrimidine ring is 2° This value should be compared with observed values of 10° for the oxidized enzyme-substrate complex and 19° for the enzyme-product complex. The position of the substrate is virtually unaltered with respect to its position in the oxidized enzyme. No trace of a bound NADP+ or NADPH molecule was found. © 1992 Wiley-Liss, Inc.
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  • 37
    ISSN: 0887-3585
    Keywords: subdomain ; kinetics ; unfolding ; stabilization ; autolysis ; protein engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Variants of the thermolabile neutral protease (Npr) of B. subtilis (Npr-sub) and the thermostable neutral protease of B. stearothermophilus (Npr-ste) were produced by means of site-directed mutagenesis and the effects of the mutations on thermostability were determined. Mutations were designed to alter the interaction between the middle and C-terminal subdomain of these enzymes. In all Nprs a cluster of hydrophobic contacts centered around residue 315 contributes to this interaction. In thermostable Nprs (like Npr-ste) a 10 residue β-hairpin, covering the domain interface, makes an additional contribution. The hydrophobic residue at position 315 was replaced by smaller amino acids. In addition, the β-hairpin was deleted from Npr-ste and inserted into Npr-sub. The changes in thermostability observed after these mutations confirmed the importance of the hydrophobic cluster and of the β-hairpin for the structural integrity of Nprs. Combined mutants showed that the effects of individual mutations affecting the inter action between the subdomains were not additive. The effects on thermostability decreased as the strength of the subdomain interaction increased. The results show that once the subdomain interface is sufficiently stabilized, additional stabilizing mutations at the same interface do not further increase thermostability. The results are interpreted on the basis of a model for the thermal inactivation of neutral proteases, in which it is assumed that inactivation results from the occurrence of local unfolding processes that render these enzymes susceptible to autolysis. © 1992 Wiley-Liss, Inc.
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  • 38
    ISSN: 0887-3585
    Keywords: α-helix ; lysine residues ; disaccharide units ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of heparin bound to bovine platelet factor 4 (BPF4) was completed using a graphically designed heparin molecule and the crystallographic coordinates of the native bovine platelet factor 4 tetramer. The oligosaccharides had a chain length of at least eight disaccharide units with the major repeating disaccharide unit consisting of (I→4)-O-(α-L-idopyranosyluronic acid 2-sulfate)-(l→4)-(2-deoxy-2-sulfamino-2-D-glucopyra-nosyl 6-sulfate). Each disaccharide unit carried a -4.0 charge. The structure of BPF4 was solved to 2.6 Å resolution with R = 0.237. Each monomer of BPF4 contains an α-helix lying across 3 strands of antiparallel β-sheet. Each helix has four lysines, which have been implicated in heparin binding. These lysine residues are predominantly on one side of the helix and are solvent accessible. Electrostatic calculations performed on the BPF4 tetramer show a ring of strong, positive charge which runs perpendicularly across the helices. Included in this ring of density is His-38, which has been shown by NMR to have a large pKa shift when heparin binds to BPF4. Our model of heparin bound to PF4 has the anionic polysaccharide perpendicular to the α-helices, wrapped about the tetramer along the ring of positive charge, and salt linked to all four lysines on the helix of each monomer. © 1992 Wiley-Liss, Inc.
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  • 39
    ISSN: 0887-3585
    Keywords: Bacillus thuringiensis ; insecticidal ; δ-endotoxin ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: CryIIIB2, an insecticidal protein from Bacillus thuringiensis has been crystallized from 0.6 M NaBr and HEPES buffer at pH 7.0 and X-ray diffraction data collected on a native crystal to 2.4 Å. The insecticidal protein was obtained from a Bacillus thuringiensis (Bt) strain EG7231. Crystals of the endotoxin are orthorhombic, space group C2221, with unit cell dimensions of a = 122.44, b = and c = Å. A unit cell contains one molecule of the 67,000 Da endotoxin per asymmetric unit. © 1992 Wiley-Liss, Inc.
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  • 40
    ISSN: 0887-3585
    Keywords: thermodynamic mechanism ; subunit assembly ; binding free energy ; thermodynamic linkage ; mutant hemoglobin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent crystallographic studies on the mutant human hemoglobin Ypsilanti (β99 Asp→xsTyr) have revealed a previously unknownquaternary structure called “quaternary Y” and suggested that the new structure may represent an important intermediate in the cooperative oxygenationpathway of normal hemoglobin.15 Here we measure the oxygenation and subunit assembly properties of hemoglobin Ypsilanti and five additionalβ99 mutants (Asp β99→Val, Gly, Asn, Ala, His) totest for consistency between their energetics and those of the intermediatespecies of normal hemoglobin.Overall regulation of oxygen affinity in hemoglobin Ypsilanti is found to originate entirely from 2.6 kcal of quaternary enhancement, such that thetetramer oxygenation affinity is 85-fold higher than for binding to the dissociated dimers. Equal partitioning of this regulatory energy among the four tetrameric binding steps (0.65 kcal per oxygen) leads toa noncooperative isotherm with extremely high affinity (pmedian = .14 torr). Temperature and pH studies of dimer-tetramer assembly and sulfhydryl reaction kinetics suggest that oxygenation-dependent structural changes in hemoglobin Ypsilanti are small. These properties are quite different from the recently characterized allosteric intermediate, which has two ligands bound on the same side of the α1β2 interface (see ref. 1 for review). The combined results do, however, support the view that quaternary Y may represent the intermediate cooperativity state of normal hemoglobin that binds the last oxygen. © 1992 Wiley-Liss, Inc.
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  • 41
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: X-ray diffraction ; allosterism ; zinc/phenol interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hexameric insulin has been crystallized from different conditions ina variety of crystalline modifications. In the presence of ∼1%phenol and at a pH of 8.5, a new rhom-bohedral form is produced, space group R3, a = 79.92 Åand c = 40.39 Å, in whichthe asymmetric unit consists of a dimer. The structur has been solved and refined, using data between 8.0 and 2.5 Å resolution, to a residual of0.157. The two monomers in the asymmetric unit have nearly identical R conformations, that is, residues Bl through B8 are α-helical, producing a continuous α-helix from Bl through B19. A phenol molecule is hydrogen bonded to the carbonyl oxygen of A6 Cys of each monomer. Small differences in conformation and the final (2Fo-Fc) and difference electron density maps suggest that an additional phenol molecule is coordinated to one of the two zinc ions.
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  • 42
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Ill.
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  • 43
    ISSN: 0887-3585
    Keywords: protein ; conformation ; infrared ; spectroscopy ; amide I ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Fourier transform infrared spectroscopy has become well known as a sensitive and informative tool for studying secondary structure in proteins. Present analysis of the conformation-sensitive amide I region in protein infrared spectra, when combined with band narrowing techniques, provides more information concerning protein secondary structure than can be meaningfully interpreted. This is due in part to limited models for secondary structure. Using the algorithm described in the previous paper of this series, we have generated a library of substructures for several trypsin-like serine proteases. This library was used as a basis for spectra-structure correlations with infrared spectra in the amide I′ region, for five homologous proteins for which spectra were collected. Use of the substructure library has allowed correlations not previously possible with template-based methods of protein conformational analysis. © 1992 Wiley-Liss, Inc.
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  • 44
    ISSN: 0887-3585
    Keywords: cellobiohydrolase ; cellulose degradation ; substrate binding ; cellulose-binding domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The function of the cellulosebinding domain (CBD) of the cellobiohydrolase I of Trichoderma reesei was studied by site-directed mutagenesis of two amino acid residues identified by analyzing the 3D structure of this domain. The mutant enzymes were produced in yeast and tested for binding and activity on crystalline cellulose. Mutagenesis of the tyrosine residue (Y492) located at the tip of the wedge-shaped domain to alanine or aspartate reduced the binding and activity on crystalline cellulose to the level of the core protein lacking the CBD. However, there was no effect on the activity toward small oligosaccharide (4-methylumbellifery1 β-D-lactoside). The mutation tyrosine to histidine (Y492H) lowered but did not destroy the cellulose binding, suggesting that the interaction of the pyranose ring of the substrate with an aromatic side chain is important. However, the catalytic activity of this mutant on crystalline cellulose was identical to the other two mutants. The mutation P477R on the edge of the other face of the domain reduces both binding and activity of CBHI. These results support the hypothesis that both surfaces of the CBD are involved in the interaction of the binding domain with crystalline cellulose. © 1992 Wiley-Liss, Inc.
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  • 45
    ISSN: 0887-624X
    Keywords: bis-amide-imides ; poly-bismaleimides ; poly-biscitzaconimides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 5 Ill.
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  • 46
    ISSN: 0887-624X
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 47
    ISSN: 0887-624X
    Keywords: new synthetic method ; two-step synthesis ; polybenzothiazoles ; aromatic diacid chlorides ; 2,5-bisalkylthio-1,4-phenylenediamine ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A novel two-step method for the synthesis of polybenzothiazoles has been developed starting from 2,5-bis(isoprophylthio)-1,4-phenylenediamine and aromatic dicarboxylic acid chlorides. The low-temperature solution polycondensation of these monomer pairs in N-methyl-2-pyrrolidone afforded the aromatic polyamides with pendant isopropylthio groups having inherent viscosities in the range of 0.8 and 2.4 dL/g. The soluble precursor polyamides were subjected to thermal cyclization to the corresponding polybenzothiazoles along with the elimination of propylene and water. The resulting polymers were also characterized.
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  • 48
    ISSN: 0887-624X
    Keywords: polyarylate ; acidolysis ; kinetics ; mechanism ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Model reactions were carried out to simulate the acidolysis process for polyarylate synthesis by using p-tert-butylphenyl acetate (ptBuPhOAc) and benzoic acid in diphenyl ether. p-tert-Butylphenol was formed in the reaction mixture and its concentration stayed constant throughout the reaction. Acetic benzoic anhydride and benzoic anhydride were detected by NMR. Based on this experimental evidence, a mechanism for the acidolysis was proposed involving the mixed anhydride. The kinetics of the acidolysis reaction was studied for this model reaction. The overall reaction order is two and the reaction order with respect to each reactant is one. Second-order reaction rate constants were measured at different reaction conditions (200-250°C). The activation energy (Ea), activation enthalpy (ΔH≠), and activation entropy (ΔS≠) were calculated from these data. The thermodynamic parameters of the acidolysis reaction were also measured for the analogous reaction of p-tert-butylphenyl pivalate (ptBuPhOPiv) and benzoic acid. The kinetics of two other elementary reactions involved in the acidolysis reaction were also studied: p-tert-butylphenol with acetic anhydride or benzoic anhydride, and p-tert-butylphenyl pivalate with benzoic acid.
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  • 49
    ISSN: 0887-624X
    Keywords: electron beam ; solid-state polymerization ; binary mixture ; methacrylate monomer ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solid-state polymerization of a binary mixture of nonliquid-crystalline monomer and liquidcrystalline compound was carried out using electron beam. The monomers were benzoic acid containing 4-[ω-(meth)acryloyloxyalkyloxy] benzoic acids, in which the alkylene spacer was ethylene, hexamethylene, or undecamethylene. The conversion yield of monomer to polymer to a large extent increased with increasing content of a liquid-crystalline compound with a terminal carboxylic group, such as 4-n-alkyloxybenzoic acid, while the addition of a liquid-crystalline compound without terminal carboxylic group did not affect polymerization of the monomer. Phase diagrams of the mixture of monomer and liquid-crystalline compound were examined using cross-polarizing microscopy and differential scanning calorimetry (DSC). All mixtures of monomer and 4-n-alkyloxybenzoic acid or liquid-crystalline compound without terminal carboxylic group showed liquid-crystallinity in a broad composition range. It was concluded that liquid-crystalline compounds with terminal carboxylic acid may form hydrogen bondings with methacrylate or acrylate monomer having terminal carboxylic acid which enhance polymerizability of the mixture. The stereoregularity of polymers determined by NMR depended on increasing irradiation dose and temperature rather than the content of the added liquid-crystalline 4-n-decanoxybenzoic acid.
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  • 50
    Electronic Resource
    Electronic Resource
    Bognor Regis [u.a.] : Wiley-Blackwell
    ISSN: 0887-624X
    Keywords: amphiphilic polymers ; graft copolymers ; poly(ethylene glycol) ; GPC ; inverted micelles ; partition chromatography ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amphiphilic comb polymers were prepared through grafting poly(ethylene glycol) methyl ether (MPEG 2000) onto acrylic and methacrylic copolymers. The graft copolymers were purified from unreacted MPEG by partition chromatography on methanol pretreated fibrous cellulose using ethyl acetate and methanol as eluents. The separation was found to depend on the water contents of the cellulose and the eluents. It is proposed that one parameter of importance for the chromatographic separation is the formation of hydrated inverted micelles. The amphiphilic comb polymers were shown by gel chromatography on Sepharose to form high molecular weight aggregates in water. On addition of sodium lauryl sulphate or inorganic salts to the eluent at low ionic strengths these aggregates dissociated and were fractionated by the gel. It was also shown that on GPC in THF solution on Styragel columns the polymers exhibited apparent molecular weights equal or smaller than those of the corresponding backbones. This effect may be a consequence of the graft copolymers having relatively small hydrodynamic volumes, and this idea is supported by the fact that their intrinsic viscosities generally were lower than those of the backbones. However, adsorption on the Styragel columns also may be of importance.
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  • 51
    ISSN: 0887-624X
    Keywords: plasma-induced radicals ; electron spin resonance (ESR) ; crosslinked methacrylic polymer ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Plasma-induced radicals of several crosslinked methacrylic polymers such as poly(ethyleneglycol dimethacrylate) (PEDMA), poly(2-hydroxyethylmethacrylate) (PHEMA) and polymethacrylamide (PMAAm) were studied by electron spin resonance (ESR). The observed ESR spectra did not exhibit a drastic difference in the spectral feature caused by the effect of crosslinking. All the spectral features can be represented by “nine-line spectra” as a major spectral component similar to those of linear methacrylic polymers such as polymethacrylic acid (PMAA). A pronounced effect of crosslinking, however, has emerged on the specific formation in the radical structure and the stability of radicals formed, especially in PEDMA. The formation of fewer kinds of radical in PEDMA is apparently caused by the high degree of crosslinking which leads to a suppression of the occurrence of depolymerization on plasma irradiation.
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  • 52
    ISSN: 0887-624X
    Keywords: inorganic polymer ; silicic acid ; polytitanosiloxane ; SiO2-TiO2 ; oxide fibers ; tensile strength ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: From polytitanosiloxanes (PTS), SiO2-TiO2 oxide fibers with fairly good tensile strength were prepared, and their mechanical and thermal properties were investigated. The precursor fibers PTS-0.5 and PTS-1.0 were obtained by dry spinning of a highly viscous PTS solution which were formed as the reaction mixture of silicic acid (SA) with bis(2,4-pentanedionato)titanium diisopropoxide (PTP) in the molar ratios (SA/PTP) of 0.5 and 1.0. The precursor fibers PTS-0.5 were too brittle to measure their tensile strength, whereas PTS-1.0 and the heat-treated fibers were found to have tensile strength of 130 (precursor), 540 (500°C), and 450 (900°C) MPa, respectively. Heat-treatment of the fibers PTS-1.0 at above 1000°C forms anatase and rutile of titanium dioxide. The crystallization is resulted from the unreacted PTP which is not incorporated into the polymer network.
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  • 53
    Electronic Resource
    Electronic Resource
    Bognor Regis [u.a.] : Wiley-Blackwell
    ISSN: 0887-624X
    Keywords: polyethylene ; polypropylene ; oxidation ; biodegradation ; C—H bond activation ; functionalization ; XPS ; ATR-IR ; surface ; Gif ; oxidase ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modification of polyethylene and polypropylene film and powder surfaces with oxygen and hydrogen peroxide is promoted by nonporphyrinic, nonfree radical based iron reagents such as Fe3O(OCOCH3)6(C6H5N)3.5 and FeCl3 • 6H2O/picolinic acid. These oxidation systems introduced small amounts of carbonyl groups onto the surface of these hydrocarbon polymers. The most visible manifestation of this reaction was increased polyolefin wettability toward water. IR spectroscopy, XPS spectroscopy, and chemical derivatization all were used to verify that the reaction had occurred and that a chemically derivatizable surface had been prepared. The overall process produced a fraction of the density of functional groups introduced by conventional etching chemistry.
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  • 54
    ISSN: 0887-624X
    Keywords: hydrogenation ; diimide ; p-toluenesulfonylhydrazide ; polybutadiene ; polyisoprene ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hydrogenation of unsaturated polymers with diimide generated in-situ by thermolysis of p-toluenesulfonyl hydrazide (TSH) is a commonly used method for preparing laboratory scale quantities of saturated diene based polymers. The by-products from TSH, particularly p-toluenesulfinic acid, can attack at olefinic sites, adding p-tolylsulfone functionality and degrading polymer molecular weight. The addition of tri-n-propyl amine has been found to eliminate these side reactions in butadiene containing polymers and copolymers, enabling the preparation of polymers devoid of backbone unsaturation. No detectable sulfur-containing impurities were indicated by IR, NMR, or elemental analysis, and no chain degradation was observed via GPC analysis of the hydrogenated polymers. cis-Polybutadiene and butadiene containing random and block copolymers with styrene were hydrogenated cleanly using this technique. A ratio of 2 mol TSH and 2 mol amine/mol of olefin was necessary to assure 〉 99% hydrogenation, and a w/v ratio of 2 parts butadiene/100 parts o-xylene gave the most efficient hydrogenation. Polymers prepared from isoprene were only partially hydrogenated when treated with TSH in the presence of tri-n-propyl amine, and gave evidence of slight degradation of the polymer structure.
    Additional Material: 15 Ill.
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  • 55
    ISSN: 0887-624X
    Keywords: cation-radical ; transalkylation ; aromatic polyether ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis and the mechanism of oxidative polymerization of 2,2-bis[4-(1-naphthoxy)phenyl]propane (4) and 2,2-bis[4-(1-naphthyl)phenyl]propane (9) are presented. Both monomers polymerize by two different propagation steps. The first one represents a cation-radical dimerization of the naphthyl groups to dinaphthyl structure. H+[FeCl4]- generated from the first propagation step initiates a transalkylation reaction which provides structural units containing isopropylidenic groups inserted between phenyl and naphthyl, and between two naphthyl groups, respectively. Since the phenyl groups resulted from the second propagation reaction are unreactive in both the oxidative coupling and the transalkylation steps this polymerization reaction leads to polymers with low molecular weights containing phenyl chain ends.
    Additional Material: 4 Ill.
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  • 56
    ISSN: 0887-624X
    Keywords: Scholl reaction ; cation-radical polymerization ; 1,5-bis(phenoxy)pentanes ; polymerization mechanism ; polymerizability of monomers ; proton transfer reactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis and the oxidative polymerization of 1,5-bis(phenoxy)pentane, 1,5-bis(phenoxy)pentane substituted with various electron-donating groups, and 1,5-bis(phenylthio)pentane is described. The polymers derived from methyl substituted 1,5-bis(phenoxy)pentane monomers contain diphenyl methane, 1,2-diphenylethane, and benzyl chloride structural units. The mechanism for the generation of these structural units is presented. It consists of the proton transfer reactions from the cation-radical propagating species and subsequent reactions of the resulting benzyl radicals. The polymerizability of monomers with 1,5-pentanedioxy group is lower than that of the monomers with diphenyl sulfone group. This dissimilarity was attributed to the difference between both the reactivity and the concentration of the cation-radical propagating species resulted from these two classes of monomers.
    Additional Material: 3 Ill.
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  • 57
    ISSN: 0887-624X
    Keywords: multifunctional copolyamide ; β-truxinate unit ; p-phenylenebis(acrylate) unit ; p-phenylenebis (p-cyanobutadienecarboxylate) unit ; different photosensitive groups ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Copolyamides 1,9, and 10 containing both cyclobutane rings and conjugated double bonds in the main chain were synthesized by polycondensation of 1,3-di(4-piperidyl)propane (DPP) with β-truxinate (β-BNPT), with di(p-nitrophenyl) p-phenylenebis(acrylate) (p-NPDA), with di(p-nitrophenyl) p-phenylenebis (α-cyanoacrylate) (p-NPDC), and with di(p-nitrophenyl) p-phenylenebis (α-cyanobutadienecarboxylate) (p-NPDCB) in aprotic polar solvents at room temperature, respectively. Reduced viscosity of copolyamide 1 was strongly affected by the reaction process, the molar ratio of two ester monomers, and reaction time. The copolyamide 1 with the highest viscosity was prepared by the reaction of DPP with 70-50 mol % of β-BNPT for 24 h followed by the polycondensation of the resulting precursor with 30-50 mol % of p-NPDA for 24-96 h. Although copolyamide 9 with high viscosity was not obtained by the polycondensation with β-BNPT and p-NPDC, copolyamide 10 with relatively high viscosity was obtained by the reaction with β-BNPT and p-NPDCB under the same conditions applied for the synthesis of copolyamide 1. The solubility of copolyamides 1,9, and 10 decreased gradually with increasing p-NPDA, p-NPDC, and p-NPDCB units in the copolymers. Furthermore, it was found that copolyamides 1,9, and 10 crosslinked upon irradiation with 313 or 365 nm light, and these copolyamides also decomposed upon irradiation with 254 nm light. That is, the photochemical property of these copolyamides can be controlled by the selection of wavelength of the photoirradiation.
    Additional Material: 6 Ill.
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  • 58
    Electronic Resource
    Electronic Resource
    Bognor Regis [u.a.] : Wiley-Blackwell
    ISSN: 0887-624X
    Keywords: silazane ; oligosilazanes ; polysilazanes ; cyclosilazanes ; phenylendiamines ; transamination ; ring cleavage ; recyclization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Heating N,N′-diphenyltetramethylcyclodisilazane with phenylenediamines in the melt at temperatures over 200°C was found to yield oligomers composed of linear and cyclic disilazane units interlinked by phenylene groups. Increasing the temperature of the reaction of meta- and particularly para-phenylenediamine over 300°C promotes formation of crosslinked, infusible, and insoluble polymeric material. The succeeding steps of growth of the polymer molecules, which include cyclodisilazane ring cleavage, transaminations, and recyclizations, have been studied by elemental and spectroscopic analyses of the intermediate low molecular and oligomeric species in the distillable and nonvolatile products of the reactions.
    Additional Material: 3 Tab.
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  • 59
    ISSN: 0887-624X
    Keywords: photoinduced polymerization ; dimethacrylates ; benzophenone ; linear sulfides